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commit/galaxy-central: greg: Another fix for rendering the contents of a data library - the form to acti on multiple datasets should now be rendered correclty.
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5f5dae7e7ccc/ changeset: r5092:5f5dae7e7ccc user: greg date: 2011-02-18 20:53:35 summary: Another fix for rendering the contents of a data library - the form to acti on multiple datasets should now be rendered correclty. affected #: 1 file (378 bytes) --- a/templates/library/common/browse_library.mako Fri Feb 18 14:46:16 2011 -0500 +++ b/templates/library/common/browse_library.mako Fri Feb 18 14:53:35 2011 -0500 @@ -349,10 +349,6 @@ form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE info_association, inherited = folder.get_info_association( restrict=True ) - - if not self.has_accessible_datasets: - # If we already know the library contains accessible datasets, no need to check again (and we may set it to False if we do). - self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) %> %if not root_folder and ( not folder.deleted or show_deleted ): <% encoded_id = trans.security.encode_id(folder.id) %> @@ -489,7 +485,7 @@ info_association, inherited = library.get_info_association() form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE - self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) + self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles ) has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles ) tracked_datasets = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: renamed 'samples' to 'sample_widgets' in __save_samples
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6cf34552c6f5/ changeset: r5091:6cf34552c6f5 user: rc date: 2011-02-18 20:46:16 summary: renamed 'samples' to 'sample_widgets' in __save_samples affected #: 1 file (63 bytes) --- a/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 14:34:14 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 14:46:16 2011 -0500 @@ -1093,7 +1093,7 @@ request_widgets=request_widgets, displayable_sample_widgets=displayable_sample_widgets, sample_copy_select_field=sample_copy_select_field ) - def __save_samples( self, trans, cntrller, request, samples, saving_new_samples=False, **kwd ): + def __save_samples( self, trans, cntrller, request, sample_widgets, saving_new_samples=False, **kwd ): # Here we handle saving all new samples added by the user as well as saving # changes to any subset of the request's samples. A sample will not have an # associated SampleState until the request is submitted, at which time the @@ -1109,7 +1109,7 @@ else: redirect_action = 'edit_samples' # Check for duplicate sample names within the request - self.__validate_sample_names( trans, cntrller, request, samples, **kwd ) + self.__validate_sample_names( trans, cntrller, request, sample_widgets, **kwd ) if not saving_new_samples: library = None folder = None @@ -1138,8 +1138,8 @@ # TODO: make changes necessary to just send the samples... encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) # Make sure all samples have a unique bar_code if the state is changing - for sample_index in range( len( samples ) ): - current_sample = samples[ sample_index ] + for sample_index in range( len( sample_widgets ) ): + current_sample = sample_widgets[ sample_index ] if current_sample is None: # We have a None value because the user did not select this sample # on which to perform the action. @@ -1163,15 +1163,15 @@ library_id = params.get( 'sample_operation_library_id', 'none' ) folder_id = params.get( 'sample_operation_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) - for sample_index in range( len( samples ) ): - current_sample = samples[ sample_index ] + for sample_index in range( len( sample_widgets ) ): + current_sample = sample_widgets[ sample_index ] if current_sample is None: # We have a None value because the user did not select this sample # on which to perform the action. continue current_sample[ 'library' ] = library current_sample[ 'folder' ] = folder - self.__update_samples( trans, cntrller, request, samples, **kwd ) + self.__update_samples( trans, cntrller, request, sample_widgets, **kwd ) message = 'Changes made to the samples have been saved. ' else: # Saving a newly created sample. The sample will not have an associated SampleState @@ -1179,9 +1179,9 @@ # set to the first SampleState configured for the request's RequestType configured # by the admin ( i.e., the sample's SampleState would be set to request.type.states[0] ). new_samples = [] - for index in range( len( samples ) - len( request.samples ) ): + for index in range( len( sample_widgets ) - len( request.samples ) ): sample_index = len( request.samples ) - sample_widget = samples[ sample_index ] + sample_widget = sample_widgets[ sample_index ] form_values = trans.model.FormValues( request.type.sample_form, sample_widget[ 'field_values' ] ) trans.sa_session.add( form_values ) trans.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove the new/ subdirectory from the eggs repository and update the pysam egg.
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/41b368b104ff/ changeset: r5090:41b368b104ff user: natefoo date: 2011-02-18 20:34:14 summary: Remove the new/ subdirectory from the eggs repository and update the pysam egg. affected #: 2 files (5 bytes) --- a/dist-eggs.ini Fri Feb 18 13:22:31 2011 -0500 +++ b/dist-eggs.ini Fri Feb 18 14:34:14 2011 -0500 @@ -22,7 +22,7 @@ py2.4-macosx-10.3-fat-ucs2 = lonnie.bx.psu.edu /usr/local/bin/python2.4 py2.5-macosx-10.3-fat-ucs2 = lonnie.bx.psu.edu /usr/local/bin/python2.5 py2.6-macosx-10.3-fat-ucs2 = lonnie.bx.psu.edu /usr/local/bin/python2.6 -py2.6-macosx-10.6-universal-ucs2 = bach.bx.psu.edu /usr/bin/python2.6 +py2.6-macosx-10.6-universal-ucs2 = fanty.bx.psu.edu /usr/bin/python2.6 py2.4-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.4 py2.5-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.5 py2.6-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.6 --- a/eggs.ini Fri Feb 18 13:22:31 2011 -0500 +++ b/eggs.ini Fri Feb 18 14:34:14 2011 -0500 @@ -7,7 +7,7 @@ ; [general] -repository = http://eggs.g2.bx.psu.edu/new +repository = http://eggs.g2.bx.psu.edu ; these eggs must be scrambled for your local environment no_auto = pbs_python DRMAA_python @@ -69,7 +69,7 @@ bx_python = _14b6a6c95da6 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 -pysam = _kanwei_a92c29d5cdec +pysam = _kanwei_ae2bd50d9945 ; dependency source urls, necessary for scrambling. for an explanation, see ; the wiki page above Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Don't copy ez_setup.py to egg build directories anymore, and provide a more useful error message when an egg is missing a dependency with a version conflict.
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c8f8f80902d1/ changeset: r5089:c8f8f80902d1 user: natefoo date: 2011-02-18 19:22:31 summary: Don't copy ez_setup.py to egg build directories anymore, and provide a more useful error message when an egg is missing a dependency with a version conflict. affected #: 2 files (427 bytes) --- a/lib/galaxy/eggs/__init__.py Fri Feb 18 12:07:27 2011 -0500 +++ b/lib/galaxy/eggs/__init__.py Fri Feb 18 13:22:31 2011 -0500 @@ -187,6 +187,10 @@ else: raise EggNotFetchable( self ) except pkg_resources.VersionConflict, e: + if e.args[1].key != e.args[0].key: + log.error( "One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution." ) + log.error( 'Dependency "%s" requires "%s"' % ( e.args[0].project_name, str( e.args[1] ) ) ) + raise # there's a conflicting egg on the path, remove it return self.version_conflict( e.args[0], e.args[1] ) def version_conflict( self, conflict_dist, conflict_req ): --- a/lib/galaxy/eggs/scramble.py Fri Feb 18 12:07:27 2011 -0500 +++ b/lib/galaxy/eggs/scramble.py Fri Feb 18 13:22:31 2011 -0500 @@ -54,7 +54,6 @@ self.copy_build_script() if not os.path.exists( ScrambleEgg.ez_setup ): URLRetriever().retrieve( ScrambleEgg.ez_setup_url, ScrambleEgg.ez_setup ) - shutil.copyfile( ScrambleEgg.ez_setup, os.path.join( self.buildpath, 'ez_setup.py' ) ) self.run_scramble_script() new_egg = os.path.join( self.buildpath, 'dist', os.path.basename( self.distribution.location ) ) if not os.path.exists( new_egg ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Do not print summary information in FASTQ groomer when grooming an empty file.
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2af990906c8f/ changeset: r5088:2af990906c8f user: dan date: 2011-02-18 18:07:27 summary: Do not print summary information in FASTQ groomer when grooming an empty file. affected #: 2 files (168 bytes) --- a/lib/galaxy_utils/sequence/fastq.py Fri Feb 18 12:04:26 2011 -0500 +++ b/lib/galaxy_utils/sequence/fastq.py Fri Feb 18 12:07:27 2011 -0500 @@ -314,8 +314,12 @@ rval.append( fastq_format ) return rval def get_ascii_range( self ): + if not self.ascii_values_used: + return None return ( min( self.ascii_values_used ), max( self.ascii_values_used ) ) def get_decimal_range( self ): + if not self.nuc_index_quality: + return None decimal_values_used = [] for scores in self.nuc_index_quality: decimal_values_used.extend( scores.keys() ) --- a/tools/fastq/fastq_groomer.py Fri Feb 18 12:04:26 2011 -0500 +++ b/tools/fastq/fastq_groomer.py Fri Feb 18 12:07:27 2011 -0500 @@ -23,15 +23,16 @@ if read_count is not None: print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type ) + if input_type != output_type and 'solexa' in [ input_type, output_type ]: + print "Converted between Solexa and PHRED scores." + if summarize_input: + print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() ) or "None" ) + ascii_range = aggregator.get_ascii_range() + decimal_range = aggregator.get_decimal_range() + print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed + print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] ) else: print "No valid FASTQ reads were provided." - if input_type != output_type and 'solexa' in [ input_type, output_type ]: - print "Converted between Solexa and PHRED scores." - if summarize_input: - print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() ) or "None" ) - ascii_range = aggregator.get_ascii_range() - decimal_range = aggregator.get_decimal_range() - print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed - print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] ) -if __name__ == "__main__": main() \ No newline at end of file + +if __name__ == "__main__": main() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for changing the selected data library and folder for a checked list of samples ( a subset of the entire list of the request's samples ).
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c0f7d67ece33/ changeset: r5087:c0f7d67ece33 user: greg date: 2011-02-18 18:04:26 summary: Fix for changing the selected data library and folder for a checked list of samples ( a subset of the entire list of the request's samples ). affected #: 1 file (1.0 KB) --- a/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 11:18:52 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 12:04:26 2011 -0500 @@ -463,8 +463,18 @@ samples.append( sample ) else: samples.append( None ) - # The __save_samples method requires sample_widgets, not sample objects - sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd ) + # The __save_samples method requires sample_widgets, not sample objects, so we'll get what we + # need by calling __get_sample_widgets(). However, we need to take care here because __get_sample_widgets() + # is used to populate the sample widget dicts from kwd, and the method assumes that a None object in the + # received list of samples should be populated from the db. Since we're just re-using the method here to + # change our list of samples into a list of sample widgets, we'll need to make sure to keep track of our + # None objects. + sample_widgets = [ obj for obj in samples ] + sample_widgets = self.__get_sample_widgets( trans, request, sample_widgets, **kwd ) + # Replace each sample widget dict with a None object if necessary + for index, obj in enumerate( samples ): + if obj is None: + sample_widgets[ index ] = None else: sample_widgets = displayable_sample_widgets return self.__save_samples( trans, cntrller, request, sample_widgets, saving_new_samples=False, **kwd ) @@ -1155,6 +1165,10 @@ library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) for sample_index in range( len( samples ) ): current_sample = samples[ sample_index ] + if current_sample is None: + # We have a None value because the user did not select this sample + # on which to perform the action. + continue current_sample[ 'library' ] = library current_sample[ 'folder' ] = folder self.__update_samples( trans, cntrller, request, samples, **kwd ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: Backed out of changeset 5085:0ce482e2ec78
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0320a5b0d1a7/ changeset: r5086:0320a5b0d1a7 user: rc date: 2011-02-18 17:18:52 summary: Backed out of changeset 5085:0ce482e2ec78 affected #: 1 file (244 bytes) --- a/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 10:49:46 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 11:18:52 2011 -0500 @@ -445,7 +445,6 @@ kwd[ 'message' ] = message handle_error( **kwd ) if params.get( 'save_samples_button', False ): - samples = [] if encoded_selected_sample_ids: # We need the list of displayable_sample_widgets to include the same number # of objects that that request.samples has so that we can enumerate over each @@ -453,6 +452,7 @@ # used the multi-select check boxes when editing sample widgets, but didn't # select all of them. We'll first get the set of samples corresponding to the # checked sample ids. + samples = [] selected_samples = [] for encoded_sample_id in encoded_selected_sample_ids: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( encoded_sample_id ) ) @@ -467,7 +467,7 @@ sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd ) else: sample_widgets = displayable_sample_widgets - return self.__save_samples( trans, cntrller, request, samples, sample_widgets, saving_new_samples=False, **kwd ) + return self.__save_samples( trans, cntrller, request, sample_widgets, saving_new_samples=False, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, @@ -806,8 +806,7 @@ elif params.get( 'add_sample_button', False ): return self.add_sample( trans, cntrller, request_id, **kwd ) elif params.get( 'save_samples_button', False ): - samples = [] - return self.__save_samples( trans, cntrller, request, samples, displayable_sample_widgets, saving_new_samples=True, **kwd ) + return self.__save_samples( trans, cntrller, request, displayable_sample_widgets, saving_new_samples=True, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, @@ -1084,7 +1083,7 @@ request_widgets=request_widgets, displayable_sample_widgets=displayable_sample_widgets, sample_copy_select_field=sample_copy_select_field ) - def __save_samples( self, trans, cntrller, request, samples, sample_widgets, saving_new_samples=False, **kwd ): + def __save_samples( self, trans, cntrller, request, samples, saving_new_samples=False, **kwd ): # Here we handle saving all new samples added by the user as well as saving # changes to any subset of the request's samples. A sample will not have an # associated SampleState until the request is submitted, at which time the @@ -1100,7 +1099,7 @@ else: redirect_action = 'edit_samples' # Check for duplicate sample names within the request - self.__validate_sample_names( trans, cntrller, request, sample_widgets, **kwd ) + self.__validate_sample_names( trans, cntrller, request, samples, **kwd ) if not saving_new_samples: library = None folder = None @@ -1129,16 +1128,17 @@ # TODO: make changes necessary to just send the samples... encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) # Make sure all samples have a unique bar_code if the state is changing - for sample_index, sample in enumerate( samples ): - if sample is None: + for sample_index in range( len( samples ) ): + current_sample = samples[ sample_index ] + if current_sample is None: # We have a None value because the user did not select this sample # on which to perform the action. continue - current_sample = sample_widgets[ sample_index ] + request_sample = request.samples[ sample_index ] bar_code = current_sample[ 'bar_code' ] if bar_code: # If the sample has a new bar_code, make sure it is unique. - bc_message = self.__validate_bar_code( trans, sample, bar_code ) + bc_message = self.__validate_bar_code( trans, request_sample, bar_code ) if bc_message: message += bc_message kwd[ 'message' ] = message @@ -1153,15 +1153,11 @@ library_id = params.get( 'sample_operation_library_id', 'none' ) folder_id = params.get( 'sample_operation_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) - for sample_index, sample in enumerate( samples ): - if sample is None: - # We have a None value because the user did not select this sample - # on which to perform the action. - continue - current_sample = sample_widgets[ sample_index ] + for sample_index in range( len( samples ) ): + current_sample = samples[ sample_index ] current_sample[ 'library' ] = library current_sample[ 'folder' ] = folder - self.__update_samples( trans, cntrller, request, sample_widgets, **kwd ) + self.__update_samples( trans, cntrller, request, samples, **kwd ) message = 'Changes made to the samples have been saved. ' else: # Saving a newly created sample. The sample will not have an associated SampleState @@ -1169,9 +1165,9 @@ # set to the first SampleState configured for the request's RequestType configured # by the admin ( i.e., the sample's SampleState would be set to request.type.states[0] ). new_samples = [] - for index in range( len( sample_widgets ) - len( request.samples ) ): + for index in range( len( samples ) - len( request.samples ) ): sample_index = len( request.samples ) - sample_widget = sample_widgets[ sample_index ] + sample_widget = samples[ sample_index ] form_values = trans.model.FormValues( request.type.sample_form, sample_widget[ 'field_values' ] ) trans.sa_session.add( form_values ) trans.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: bug fix: bulk operations on samples for changing target data libraries was broken
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0ce482e2ec78/ changeset: r5085:0ce482e2ec78 user: rc date: 2011-02-18 16:49:46 summary: bug fix: bulk operations on samples for changing target data libraries was broken affected #: 1 file (244 bytes) --- a/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 10:42:13 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 10:49:46 2011 -0500 @@ -445,6 +445,7 @@ kwd[ 'message' ] = message handle_error( **kwd ) if params.get( 'save_samples_button', False ): + samples = [] if encoded_selected_sample_ids: # We need the list of displayable_sample_widgets to include the same number # of objects that that request.samples has so that we can enumerate over each @@ -452,7 +453,6 @@ # used the multi-select check boxes when editing sample widgets, but didn't # select all of them. We'll first get the set of samples corresponding to the # checked sample ids. - samples = [] selected_samples = [] for encoded_sample_id in encoded_selected_sample_ids: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( encoded_sample_id ) ) @@ -467,7 +467,7 @@ sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd ) else: sample_widgets = displayable_sample_widgets - return self.__save_samples( trans, cntrller, request, sample_widgets, saving_new_samples=False, **kwd ) + return self.__save_samples( trans, cntrller, request, samples, sample_widgets, saving_new_samples=False, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, @@ -806,7 +806,8 @@ elif params.get( 'add_sample_button', False ): return self.add_sample( trans, cntrller, request_id, **kwd ) elif params.get( 'save_samples_button', False ): - return self.__save_samples( trans, cntrller, request, displayable_sample_widgets, saving_new_samples=True, **kwd ) + samples = [] + return self.__save_samples( trans, cntrller, request, samples, displayable_sample_widgets, saving_new_samples=True, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, @@ -1083,7 +1084,7 @@ request_widgets=request_widgets, displayable_sample_widgets=displayable_sample_widgets, sample_copy_select_field=sample_copy_select_field ) - def __save_samples( self, trans, cntrller, request, samples, saving_new_samples=False, **kwd ): + def __save_samples( self, trans, cntrller, request, samples, sample_widgets, saving_new_samples=False, **kwd ): # Here we handle saving all new samples added by the user as well as saving # changes to any subset of the request's samples. A sample will not have an # associated SampleState until the request is submitted, at which time the @@ -1099,7 +1100,7 @@ else: redirect_action = 'edit_samples' # Check for duplicate sample names within the request - self.__validate_sample_names( trans, cntrller, request, samples, **kwd ) + self.__validate_sample_names( trans, cntrller, request, sample_widgets, **kwd ) if not saving_new_samples: library = None folder = None @@ -1128,17 +1129,16 @@ # TODO: make changes necessary to just send the samples... encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) # Make sure all samples have a unique bar_code if the state is changing - for sample_index in range( len( samples ) ): - current_sample = samples[ sample_index ] - if current_sample is None: + for sample_index, sample in enumerate( samples ): + if sample is None: # We have a None value because the user did not select this sample # on which to perform the action. continue - request_sample = request.samples[ sample_index ] + current_sample = sample_widgets[ sample_index ] bar_code = current_sample[ 'bar_code' ] if bar_code: # If the sample has a new bar_code, make sure it is unique. - bc_message = self.__validate_bar_code( trans, request_sample, bar_code ) + bc_message = self.__validate_bar_code( trans, sample, bar_code ) if bc_message: message += bc_message kwd[ 'message' ] = message @@ -1153,11 +1153,15 @@ library_id = params.get( 'sample_operation_library_id', 'none' ) folder_id = params.get( 'sample_operation_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) - for sample_index in range( len( samples ) ): - current_sample = samples[ sample_index ] + for sample_index, sample in enumerate( samples ): + if sample is None: + # We have a None value because the user did not select this sample + # on which to perform the action. + continue + current_sample = sample_widgets[ sample_index ] current_sample[ 'library' ] = library current_sample[ 'folder' ] = folder - self.__update_samples( trans, cntrller, request, samples, **kwd ) + self.__update_samples( trans, cntrller, request, sample_widgets, **kwd ) message = 'Changes made to the samples have been saved. ' else: # Saving a newly created sample. The sample will not have an associated SampleState @@ -1165,9 +1169,9 @@ # set to the first SampleState configured for the request's RequestType configured # by the admin ( i.e., the sample's SampleState would be set to request.type.states[0] ). new_samples = [] - for index in range( len( samples ) - len( request.samples ) ): + for index in range( len( sample_widgets ) - len( request.samples ) ): sample_index = len( request.samples ) - sample_widget = samples[ sample_index ] + sample_widget = sample_widgets[ sample_index ] form_values = trans.model.FormValues( request.type.sample_form, sample_widget[ 'field_values' ] ) trans.sa_session.add( form_values ) trans.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix typo in Intersect tool description.
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e7bc439ef1dd/ changeset: r5084:e7bc439ef1dd user: dan date: 2011-02-18 16:42:13 summary: Fix typo in Intersect tool description. affected #: 1 file (0 bytes) --- a/tools/new_operations/intersect.xml Thu Feb 17 17:21:54 2011 -0500 +++ b/tools/new_operations/intersect.xml Fri Feb 18 10:42:13 2011 -0500 @@ -1,5 +1,5 @@ <tool id="gops_intersect_1" name="Intersect"> - <description>the intervals of two datastes</description> + <description>the intervals of two datasets</description><command interpreter="python">gops_intersect.py $input1 $input2 $output Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Update pysam egg to 0.4.1
by Bitbucket 17 Feb '11

17 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5fa0593cd83c/ changeset: r5083:5fa0593cd83c user: kanwei date: 2011-02-17 23:21:54 summary: Update pysam egg to 0.4.1 affected #: 1 file (0 bytes) --- a/eggs.ini Thu Feb 17 15:35:07 2011 -0500 +++ b/eggs.ini Thu Feb 17 17:21:54 2011 -0500 @@ -21,7 +21,7 @@ pbs_python = 4.1.0 psycopg2 = 2.0.13 pycrypto = 2.0.1 -pysam = 0.1.1 +pysam = 0.4.1 pysqlite = 2.5.6 python_lzo = 1.08_2.03_static simplejson = 2.1.1 @@ -69,7 +69,7 @@ bx_python = _14b6a6c95da6 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 -pysam = _kanwei_90e03180969d +pysam = _kanwei_a92c29d5cdec ; dependency source urls, necessary for scrambling. for an explanation, see ; the wiki page above Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Add a "format_source" attribute to the ToolConfig output data element [JJ Johnson]. Closes #470
by Bitbucket 17 Feb '11

17 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a86e1fa82a89/ changeset: r5082:a86e1fa82a89 user: kanwei date: 2011-02-17 21:35:07 summary: Add a "format_source" attribute to the ToolConfig output data element [JJ Johnson]. Closes #470 affected #: 2 files (426 bytes) --- a/lib/galaxy/tools/__init__.py Thu Feb 17 14:48:53 2011 -0500 +++ b/lib/galaxy/tools/__init__.py Thu Feb 17 15:35:07 2011 -0500 @@ -249,10 +249,11 @@ (format, metadata_source, parent) """ - def __init__( self, name, format=None, metadata_source=None, + def __init__( self, name, format=None, format_source=None, metadata_source=None, parent=None, label=None, filters = None, actions = None ): self.name = name self.format = format + self.format_source = format_source self.metadata_source = metadata_source self.parent = parent self.label = label @@ -559,6 +560,7 @@ output = ToolOutput( data_elem.get("name") ) output.format = data_elem.get("format", "data") output.change_format = data_elem.findall("change_format") + output.format_source = data_elem.get("format_source", None) output.metadata_source = data_elem.get("metadata_source", "") output.parent = data_elem.get("parent", None) output.label = util.xml_text( data_elem, "label" ) --- a/lib/galaxy/tools/actions/__init__.py Thu Feb 17 14:48:53 2011 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Thu Feb 17 15:35:07 2011 -0500 @@ -244,6 +244,12 @@ ext = output.format if ext == "input": ext = input_ext + if output.format_source is not None and output.format_source in inp_data: + try: + ext = inp_data[output.format_source].ext + except Exception, e: + pass + #process change_format tags if output.change_format: if params is None: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 17 Feb '11

17 Feb '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/bdcc4ca64eee/ changeset: r5080:bdcc4ca64eee user: kellyv date: 2011-02-17 19:46:40 summary: Fixed BFAST functional tests (corrected problem with chromosome names in test files) affected #: 4 files (4.4 KB) --- a/test-data/bfast_out1.sam Thu Feb 17 12:05:39 2011 -0500 +++ b/test-data/bfast_out1.sam Thu Feb 17 13:46:40 2011 -0500 @@ -1,23 +1,23 @@ @HD VN:0.1.2 SO:unsorted GO:none -@SQ SN:phiX LN:5386 +@SQ SN:phiX174 LN:5386 @PG ID:bfast VN:0.6.4d -random_phiX_region_0 0 phiX 553 255 50M * 0 0 TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_1 0 phiX 3693 255 50M * 0 0 GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_2 0 phiX 375 255 50M * 0 0 AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_3 0 phiX 3168 255 50M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_4 0 phiX 5254 255 50M * 0 0 ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_5 0 phiX 5066 255 50M * 0 0 AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_6 0 phiX 1226 255 50M * 0 0 CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_7 0 phiX 1096 255 50M * 0 0 AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_8 0 phiX 535 255 50M * 0 0 CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_9 0 phiX 3669 255 50M * 0 0 CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_10 0 phiX 4887 255 50M * 0 0 TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_11 0 phiX 1849 255 50M * 0 0 TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_12 0 phiX 4145 255 50M * 0 0 AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_13 0 phiX 1853 255 50M * 0 0 TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_14 0 phiX 2800 255 50M * 0 0 CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_15 0 phiX 1910 255 50M * 0 0 AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_16 0 phiX 3366 255 50M * 0 0 GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_17 0 phiX 2165 255 50M * 0 0 CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_18 0 phiX 2051 255 50M * 0 0 TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_19 0 phiX 5099 255 50M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_0 0 phiX174 553 255 50M * 0 0 TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_1 0 phiX174 3693 255 50M * 0 0 GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_2 0 phiX174 375 255 50M * 0 0 AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_3 0 phiX174 3168 255 50M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_4 0 phiX174 5254 255 50M * 0 0 ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_5 0 phiX174 5066 255 50M * 0 0 AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_6 0 phiX174 1226 255 50M * 0 0 CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_7 0 phiX174 1096 255 50M * 0 0 AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_8 0 phiX174 535 255 50M * 0 0 CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_9 0 phiX174 3669 255 50M * 0 0 CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_10 0 phiX174 4887 255 50M * 0 0 TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_11 0 phiX174 1849 255 50M * 0 0 TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_12 0 phiX174 4145 255 50M * 0 0 AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_13 0 phiX174 1853 255 50M * 0 0 TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_14 0 phiX174 2800 255 50M * 0 0 CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2300 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:11T38 XA:i:0 +random_phiX_region_15 0 phiX174 1910 255 50M * 0 0 AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_16 0 phiX174 3366 255 50M * 0 0 GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_17 0 phiX174 2165 255 50M * 0 0 CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_18 0 phiX174 2051 255 50M * 0 0 TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_19 0 phiX174 5099 255 50M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 --- a/test-data/bfast_out2.sam Thu Feb 17 12:05:39 2011 -0500 +++ b/test-data/bfast_out2.sam Thu Feb 17 13:46:40 2011 -0500 @@ -1,23 +1,23 @@ @HD VN:0.1.2 SO:unsorted GO:none -@SQ SN:phiX LN:5386 +@SQ SN:phiX174 LN:5386 @PG ID:bfast VN:0.6.4d -random_phiX_region_0 0 phiX 553 255 50M * 0 0 TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G10122032013310033101313321021200111002331002233200 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_1 0 phiX 3693 255 50M * 0 0 GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G01032113212201012120321021321231001331220321233013 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_2 0 phiX 375 255 50M * 0 0 AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G20332013022003213122121021031212011032031313100201 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_3 0 phiX 3168 255 50M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G00130020212022012020131310131203210311202213031002 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_4 0 phiX 5254 255 50M * 0 0 ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G21331000022222231222301220321002000210312113230321 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_5 0 phiX 5066 255 50M * 0 0 AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G22323002203102011012211230000101023211233231202001 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_6 0 phiX 1226 255 50M * 0 0 CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G31131003310112011211023030210213120202310111030313 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_7 0 phiX 1096 255 50M * 0 0 AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G20123122030103323321033212202023222310213303101033 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_8 0 phiX 535 255 50M * 0 0 CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G32231132231233213310122032013310033101313321021200 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_9 0 phiX 3669 255 50M * 0 0 CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G31003210022003121223310201032113212201012120321021 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_10 0 phiX 4887 255 50M * 0 0 TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G13112133130013233121023323111331202133200002113102 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_11 0 phiX 1849 255 50M * 0 0 TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G13311003122201333201102310002033023121332123002222 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_12 0 phiX 4145 255 50M * 0 0 AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G22222302211220002313313120033101221023233031011233 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_13 0 phiX 1853 255 50M * 0 0 TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G10031222013332011023100020330231213321230022223021 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_14 0 phiX 2800 255 50M * 0 0 CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G30300310330131003311010100213101001012230120031033 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_15 0 phiX 1910 255 50M * 0 0 AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G20133230020113200121203331032333013210332100211000 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_16 0 phiX 3366 255 50M * 0 0 GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G03030230012220321000022232031230003131012102110321 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_17 0 phiX 2165 255 50M * 0 0 CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G31312303312101211100201212031021210110131211020332 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_18 0 phiX 2051 255 50M * 0 0 TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G11013323103313330202313311002220213203321102022012 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- -random_phiX_region_19 0 phiX 5099 255 50M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G03211233231202001022023211021220321220312230331012 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_0 0 phiX174 553 255 50M * 0 0 TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G10122032013310033101313321021200111002331002233200 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_1 0 phiX174 3693 255 50M * 0 0 GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G01032113212201012120321021321231001331220321233013 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_2 0 phiX174 375 255 50M * 0 0 AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G20332013022003213122121021031212011032031313100201 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_3 0 phiX174 3168 255 50M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G00130020212022012020131310131203210311202213031002 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_4 0 phiX174 5254 255 50M * 0 0 ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G21331000022222231222301220321002000210312113230321 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_5 0 phiX174 5066 255 50M * 0 0 AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G22323002203102011012211230000101023211233231202001 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_6 0 phiX174 1226 255 50M * 0 0 CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G31131003310112011211023030210213120202310111030313 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_7 0 phiX174 1096 255 50M * 0 0 AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G20123122030103323321033212202023222310213303101033 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_8 0 phiX174 535 255 50M * 0 0 CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G32231132231233213310122032013310033101313321021200 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_9 0 phiX174 3669 255 50M * 0 0 CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G31003210022003121223310201032113212201012120321021 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_10 0 phiX174 4887 255 50M * 0 0 TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G13112133130013233121023323111331202133200002113102 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_11 0 phiX174 1849 255 50M * 0 0 TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G13311003122201333201102310002033023121332123002222 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_12 0 phiX174 4145 255 50M * 0 0 AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G22222302211220002313313120033101221023233031011233 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_13 0 phiX174 1853 255 50M * 0 0 TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G10031222013332011023100020330231213321230022223021 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_14 0 phiX174 2800 255 50M * 0 0 CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2300 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:11T38 CS:Z:G30300310330131003311010100213101001012230120031033 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_15 0 phiX174 1910 255 50M * 0 0 AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G20133230020113200121203331032333013210332100211000 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_16 0 phiX174 3366 255 50M * 0 0 GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G03030230012220321000022232031230003131012102110321 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_17 0 phiX174 2165 255 50M * 0 0 CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G31312303312101211100201212031021210110131211020332 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_18 0 phiX174 2051 255 50M * 0 0 TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G11013323103313330202313311002220213203321102022012 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- +random_phiX_region_19 0 phiX174 5099 255 50M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G03211233231202001022023211021220321220312230331012 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:-------------------------------------------------- --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bfast_out3.sam Thu Feb 17 13:46:40 2011 -0500 @@ -0,0 +1,23 @@ +@HD VN:0.1.2 SO:unsorted GO:none +@SQ SN:phiX LN:5386 +@PG ID:bfast VN:0.6.4d +random_phiX_region_0 0 phiX 553 255 50M * 0 0 TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_1 0 phiX 3693 255 50M * 0 0 GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_2 0 phiX 375 255 50M * 0 0 AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_3 0 phiX 3168 255 50M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_4 0 phiX 5254 255 50M * 0 0 ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_5 0 phiX 5066 255 50M * 0 0 AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_6 0 phiX 1226 255 50M * 0 0 CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_7 0 phiX 1096 255 50M * 0 0 AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_8 0 phiX 535 255 50M * 0 0 CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_9 0 phiX 3669 255 50M * 0 0 CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_10 0 phiX 4887 255 50M * 0 0 TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_11 0 phiX 1849 255 50M * 0 0 TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_12 0 phiX 4145 255 50M * 0 0 AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_13 0 phiX 1853 255 50M * 0 0 TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_14 0 phiX 2800 255 50M * 0 0 CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2300 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:11T38 XA:i:0 +random_phiX_region_15 0 phiX 1910 255 50M * 0 0 AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_16 0 phiX 3366 255 50M * 0 0 GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_17 0 phiX 2165 255 50M * 0 0 CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_18 0 phiX 2051 255 50M * 0 0 TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 +random_phiX_region_19 0 phiX 5099 255 50M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 --- a/tools/sr_mapping/bfast_wrapper.xml Thu Feb 17 12:05:39 2011 -0500 +++ b/tools/sr_mapping/bfast_wrapper.xml Thu Feb 17 13:46:40 2011 -0500 @@ -370,7 +370,7 @@ <param name="suppressHeader" value="False" /><param name="indexing_repeatmasker" value="" /><param name="indexing_option_selector" value="default" /> - <output name="output" ftype="sam" file="bfast_out1.sam" lines_diff="2" /> + <output name="output" ftype="sam" file="bfast_out3.sam" lines_diff="2" /></test></tests></tool> http://bitbucket.org/galaxy/galaxy-central/changeset/885f04ae671e/ changeset: r5081:885f04ae671e user: kellyv date: 2011-02-17 20:48:53 summary: merge affected #: 0 files (0 bytes) --- a/templates/library/common/ldda_info.mako Thu Feb 17 13:46:40 2011 -0500 +++ b/templates/library/common/ldda_info.mako Thu Feb 17 14:48:53 2011 -0500 @@ -117,14 +117,14 @@ </div> %if ldda.creating_job_associations: <% job = ldda.creating_job_associations[0].job %> - %if job.stdout.strip() != '': + %if job.stdout and job.stdout.strip() != '': <div class="form-row"><label>Job Standard Output</label><pre>${job.stdout}</pre><div style="clear: both"></div></div> %endif - %if job.stderr.strip() != '': + %if job.stderr and job.stderr.strip() != '': <div class="form-row"><label>Job Standard Error</label><pre>${job.stderr}</pre> --- a/tools/ngs_rna/cuffdiff_wrapper.xml Thu Feb 17 13:46:40 2011 -0500 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Thu Feb 17 14:48:53 2011 -0500 @@ -90,7 +90,7 @@ <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/><param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/> - <param name="min_alignment_count" type="integer" value="0" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/> + <param name="min_alignment_count" type="integer" value="1000" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/><param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts."><option value="No">No</option><option value="Yes">Yes</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Set default value for Cuffdiff's minimum alignment count parameter to reflect v0.9.3
by Bitbucket 17 Feb '11

17 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/144e064fa5c5/ changeset: r5079:144e064fa5c5 user: jgoecks date: 2011-02-17 20:25:56 summary: Set default value for Cuffdiff's minimum alignment count parameter to reflect v0.9.3 affected #: 1 file (3 bytes) --- a/tools/ngs_rna/cuffdiff_wrapper.xml Thu Feb 17 13:57:38 2011 -0500 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Thu Feb 17 14:25:56 2011 -0500 @@ -90,7 +90,7 @@ <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/><param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/> - <param name="min_alignment_count" type="integer" value="0" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/> + <param name="min_alignment_count" type="integer" value="1000" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/><param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts."><option value="No">No</option><option value="Yes">Yes</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fix displaying the stdout/stderr of a library upload when the stdout/stderr is None
by Bitbucket 17 Feb '11

17 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d83fa80e8321/ changeset: r5078:d83fa80e8321 user: natefoo date: 2011-02-17 19:57:38 summary: Fix displaying the stdout/stderr of a library upload when the stdout/stderr is None affected #: 1 file (30 bytes) --- a/templates/library/common/ldda_info.mako Thu Feb 17 12:05:39 2011 -0500 +++ b/templates/library/common/ldda_info.mako Thu Feb 17 13:57:38 2011 -0500 @@ -117,14 +117,14 @@ </div> %if ldda.creating_job_associations: <% job = ldda.creating_job_associations[0].job %> - %if job.stdout.strip() != '': + %if job.stdout and job.stdout.strip() != '': <div class="form-row"><label>Job Standard Output</label><pre>${job.stdout}</pre><div style="clear: both"></div></div> %endif - %if job.stderr.strip() != '': + %if job.stderr and job.stderr.strip() != '': <div class="form-row"><label>Job Standard Error</label><pre>${job.stderr}</pre> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Adjustment to dataset line estimation.
by Bitbucket 17 Feb '11

17 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2a3b27d59bd3/ changeset: r5077:2a3b27d59bd3 user: dannon date: 2011-02-17 18:05:39 summary: Adjustment to dataset line estimation. Estimate is now rounded to only the first two digits, like: ~65,000 lines, to make it clearer that it's an estimate. Will no longer try to estimate for small files, however they ended up without lines set. affected #: 3 files (757 bytes) --- a/lib/galaxy/datatypes/data.py Thu Feb 17 08:45:09 2011 -0500 +++ b/lib/galaxy/datatypes/data.py Thu Feb 17 12:05:39 2011 -0500 @@ -388,7 +388,23 @@ return 'text/plain' def set_meta( self, dataset, **kwd ): """ - Set the number of lines of data in dataset, + Set the number of lines of data in dataset. + """ + dataset.metadata.data_lines = self.count_data_lines(dataset) + def estimate_file_lines( self, dataset ): + """ + Perform a rough estimate by extrapolating number of lines from a small read. + """ + sample_size = 1048576 + dataset_fh = open( dataset.file_name ) + dataset_read = dataset_fh.read(sample_size) + dataset_fh.close() + sample_lines = dataset_read.count('\n') + est_lines = int(sample_lines * (float(dataset.get_size()) / float(sample_size))) + return est_lines + def count_data_lines(self, dataset): + """ + Count the number of lines of data in dataset, skipping all blank lines and comments. """ data_lines = 0 @@ -396,16 +412,7 @@ line = line.strip() if line and not line.startswith( '#' ): data_lines += 1 - dataset.metadata.data_lines = data_lines - def estimate_file_lines( self, dataset ): - # Perform a rough estimate by extrapolating number of lines from a small read. - sample_size = 1048576 - dataset_fh = open( dataset.file_name ) - dataset_read = dataset_fh.read(sample_size) - dataset_fh.close() - sample_lines = dataset_read.count('\n') - est_lines = int(sample_lines * (float(dataset.get_size()) / float(sample_size))) - return est_lines + return data_lines def set_peek( self, dataset, line_count=None, is_multi_byte=False ): if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method @@ -418,8 +425,13 @@ # Number of lines is not known ( this should not happen ), and auto-detect is # needed to set metadata # This can happen when the file is larger than max_optional_metadata_filesize. - est_lines = self.estimate_file_lines(dataset) - dataset.blurb = "~%s %s" % ( util.commaify(str(est_lines)), inflector.cond_plural(est_lines, "line") ) + if int(dataset.get_size()) <= 1048576: + #Small dataset, recount all lines and reset peek afterward. + dataset.metadata.data_lines = self.count_data_lines(dataset) + self.set_peek(dataset) + else: + est_lines = self.estimate_file_lines(dataset) + dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, "line") ) else: dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, "line") else: --- a/lib/galaxy/datatypes/interval.py Thu Feb 17 08:45:09 2011 -0500 +++ b/lib/galaxy/datatypes/interval.py Thu Feb 17 12:05:39 2011 -0500 @@ -71,7 +71,7 @@ else: # Number of lines is not known ( this should not happen ), and auto-detect is # needed to set metadata - dataset.blurb = "~%s regions" % util.commaify( str( self.estimate_file_lines(dataset) ) ) + dataset.blurb = "~%s regions" % util.commaify(util.roundify(str(self.estimate_file_lines(dataset)))) else: dataset.blurb = "%s regions" % util.commaify( str( line_count ) ) else: --- a/lib/galaxy/util/__init__.py Thu Feb 17 08:45:09 2011 -0500 +++ b/lib/galaxy/util/__init__.py Thu Feb 17 12:05:39 2011 -0500 @@ -298,7 +298,16 @@ return new else: return commaify(new) - + +def roundify(amount, sfs = 2): + """ + Take a number in string form and truncate to 'sfs' significant figures. + """ + if len(amount) <= sfs: + return amount + else: + return amount[0:sfs] + '0'*(len(amount) - sfs) + def object_to_string( obj ): return binascii.hexlify( pickle.dumps( obj, 2 ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add wc tool to tool_conf.xml.main
by Bitbucket 17 Feb '11

17 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/bae2fec3cb1b/ changeset: r5076:bae2fec3cb1b user: dan date: 2011-02-17 14:45:09 summary: Add wc tool to tool_conf.xml.main affected #: 1 file (38 bytes) --- a/tool_conf.xml.main Wed Feb 16 21:46:23 2011 -0500 +++ b/tool_conf.xml.main Thu Feb 17 08:45:09 2011 -0500 @@ -42,7 +42,8 @@ <tool file="filters/randomlines.xml" /><tool file="filters/headWrapper.xml" /><tool file="filters/tailWrapper.xml" /> - <tool file="filters/trimmer.xml" /> + <tool file="filters/trimmer.xml" /> + <tool file="filters/wc_gnu.xml" /></section><section name="Convert Formats" id="convert"><tool file="filters/bed2gff.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug in extract_genomic_dna to handle non-GFF files when interpret features is true. Tweak functional test to cover new behavior.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8ecfa22f0d98/ changeset: r5075:8ecfa22f0d98 user: jgoecks date: 2011-02-17 03:46:23 summary: Fix bug in extract_genomic_dna to handle non-GFF files when interpret features is true. Tweak functional test to cover new behavior. affected #: 2 files (16 bytes) --- a/tools/extract/extract_genomic_dna.py Wed Feb 16 13:50:30 2011 -0500 +++ b/tools/extract/extract_genomic_dna.py Wed Feb 16 21:46:23 2011 -0500 @@ -234,7 +234,7 @@ fout.write( "%s\n" % str( sequence[c:b] ) ) c = b else: # output_format == "interval" - if interpret_features: + if gff_format and interpret_features: # TODO: need better GFF Reader to capture all information needed # to produce this line. meta_data = "\t".join( --- a/tools/extract/extract_genomic_dna.xml Wed Feb 16 13:50:30 2011 -0500 +++ b/tools/extract/extract_genomic_dna.xml Wed Feb 16 21:46:23 2011 -0500 @@ -70,7 +70,7 @@ </test><test><param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> - <param name="interpret_features" value="no"/> + <param name="interpret_features" value="yes"/><param name="index_source" value="cached"/><param name="out_format" value="interval"/><output name="out_file1" file="extract_genomic_dna_out3.interval" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Quick fix for postgres9 JSONType/MetadataType hex decoding issues.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/89190bcd1ccf/ changeset: r5074:89190bcd1ccf user: dannon date: 2011-02-16 19:50:30 summary: Quick fix for postgres9 JSONType/MetadataType hex decoding issues. Todo: Postgres9 might be configurable to do this natively, postgres8 does not have the issue. affected #: 1 file (305 bytes) --- a/lib/galaxy/model/custom_types.py Wed Feb 16 13:48:14 2011 -0500 +++ b/lib/galaxy/model/custom_types.py Wed Feb 16 13:50:30 2011 -0500 @@ -4,6 +4,7 @@ import simplejson import pickle import copy +import binascii from galaxy.util.bunch import Bunch from galaxy.util.aliaspickler import AliasPickleModule @@ -14,8 +15,20 @@ json_encoder = simplejson.JSONEncoder( sort_keys=True ) json_decoder = simplejson.JSONDecoder( ) +def _sniffnfix_pg9_hex(value): + """ + Sniff for and fix postgres 9 hex decoding issue + """ + try: + if value[0] == 'x': + return binascii.unhexlify(value[1:]) + else: + return value + except Exception, ex: + return value + class JSONType( TypeDecorator ): - """ + """ Defines a JSONType for SQLAlchemy. Takes a primitive as input and JSONifies it. This should replace PickleType throughout Galaxy. """ @@ -29,16 +42,16 @@ def process_result_value( self, value, dialect ): if value is None: return None - return json_decoder.decode( str( value ) ) - + return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) + def copy_value( self, value ): # return json_decoder.decode( json_encoder.encode( value ) ) return copy.deepcopy( value ) def compare_values( self, x, y ): - # return json_encoder.encode( x ) == json_encoder.encode( y ) - return ( x == y ) - + # return json_encoder.encode( x ) == json_encoder.encode( y ) + return ( x == y ) + def is_mutable( self ): return True @@ -61,11 +74,11 @@ ret = dict( ret.__dict__ ) except: try: - ret = json_decoder.decode( str( value ) ) + ret = json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) except: ret = None return ret - + class TrimmedString( TypeDecorator ): impl = String def process_bind_param( self, value, dialect ): @@ -73,4 +86,4 @@ if self.impl.length and value is not None: value = value[0:self.impl.length] return value - + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fix unit tests failing on missing dependencies in job runners
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9a547a8f0d49/ changeset: r5073:9a547a8f0d49 user: natefoo date: 2011-02-16 19:48:14 summary: Fix unit tests failing on missing dependencies in job runners affected #: 1 file (86 bytes) --- a/run_unit_tests.sh Wed Feb 16 13:37:13 2011 -0500 +++ b/run_unit_tests.sh Wed Feb 16 13:48:14 2011 -0500 @@ -1,7 +1,9 @@ #!/bin/sh ## Excluding controllers due to the problematic genetrack dependency +## Excluding job runners due to various external dependencies python ./scripts/nosetests.py -v -w lib \ --with-nosehtml --html-report-file run_unit_tests.html \ - --with-doctest --exclude=functional --exclude="^get" --exclude=controllers + --with-doctest --exclude=functional --exclude="^get" \ + --exclude=controllers --exclude=runners Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Add test data repository setup directly to the buildbot setup script.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/53ea14cb5909/ changeset: r5072:53ea14cb5909 user: natefoo date: 2011-02-16 19:37:13 summary: Add test data repository setup directly to the buildbot setup script. affected #: 1 file (347 bytes) --- a/buildbot_setup.sh Wed Feb 16 12:56:18 2011 -0500 +++ b/buildbot_setup.sh Wed Feb 16 13:37:13 2011 -0500 @@ -115,4 +115,17 @@ cp test-data/wig_to_bigwig_hg17.len tool-data/shared/ucsc/chrom/hg17.len fi +if [ -d "test-data-repo" ]; then + echo "Updating test data repository" + cd test-data-repo + hg pull + hg update + cd .. +else + echo "Cloning test data repository" + hg clone http://bitbucket.org/natefoo/galaxy-test-data/ test-data-repo +fi +echo "Setting up test data location files" +python test-data-repo/location/make_location.py + python ./scripts/fetch_eggs.py all Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Bug fix: do not fix strand in extract_genomic_dna tool.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5f2047e0eb18/ changeset: r5071:5f2047e0eb18 user: jgoecks date: 2011-02-16 18:56:18 summary: Bug fix: do not fix strand in extract_genomic_dna tool. affected #: 1 file (1 byte) --- a/tools/extract/extract_genomic_dna.py Wed Feb 16 10:14:24 2011 -0500 +++ b/tools/extract/extract_genomic_dna.py Wed Feb 16 12:56:18 2011 -0500 @@ -120,7 +120,7 @@ twobitfile = None file_iterator = open( input_filename ) if gff_format and interpret_features: - file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=True ) + file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=False ) for i, feature in enumerate( file_iterator ): if gff_format and interpret_features: # Processing features. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: When rendering the contents of a data library, make sure a LibraryDataset has an associated LibraryDatasetDatasetAssociation. There should always be an ldda, but some users running their own instances have reported that some of their LibraryDatasets are missing these associations.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ca0c4ad2bb39/ changeset: r5070:ca0c4ad2bb39 user: greg date: 2011-02-16 16:14:24 summary: When rendering the contents of a data library, make sure a LibraryDataset has an associated LibraryDatasetDatasetAssociation. There should always be an ldda, but some users running their own instances have reported that some of their LibraryDatasets are missing these associations. affected #: 1 file (554 bytes) --- a/templates/library/common/browse_library.mako Wed Feb 16 09:54:49 2011 -0500 +++ b/templates/library/common/browse_library.mako Wed Feb 16 10:14:24 2011 -0500 @@ -438,9 +438,14 @@ %for library_dataset in library_datasets: <% ldda = library_dataset.library_dataset_dataset_association - selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + if ldda: + # There should always be an ldda, but some users running their own instances have reported that + # some of their LibraryDatasets have no associated lddas + selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids %> - ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} + %if ldda: + ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} + %endif %endfor %else: %for sub_folder in sub_folders: @@ -449,8 +454,13 @@ %for library_dataset in library_datasets: <% ldda = library_dataset.library_dataset_dataset_association - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset ) - selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + if ldda: + # There should always be an ldda, but some users running their own instances have reported that + # some of their LibraryDatasets have no associated lddas + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset ) + selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids + else: + can_access = False %> %if can_access: ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix bug when rendering the contents of a data library - render the options for acting on multiple datasets if the library includes accessible datasets at any level in the hierarchy rather than if it only includes them in the root folder.
by Bitbucket 16 Feb '11

16 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9754f81fd6c4/ changeset: r5069:9754f81fd6c4 user: greg date: 2011-02-16 15:54:49 summary: Fix bug when rendering the contents of a data library - render the options for acting on multiple datasets if the library includes accessible datasets at any level in the hierarchy rather than if it only includes them in the root folder. affected #: 2 files (354 bytes) --- a/lib/galaxy/webapps/reports/controllers/sample_tracking.py Tue Feb 15 19:20:39 2011 -0500 +++ b/lib/galaxy/webapps/reports/controllers/sample_tracking.py Wed Feb 16 09:54:49 2011 -0500 @@ -143,7 +143,6 @@ row.total, row.date.strftime( "%B" ), row.date.strftime( "%Y" ) ) ) - log.debug("#######In per_month_all, requests: %s" % str( requests )) return trans.fill_template( '/webapps/reports/requests_per_month_all.mako', requests=requests, message=message ) --- a/templates/library/common/browse_library.mako Tue Feb 15 19:20:39 2011 -0500 +++ b/templates/library/common/browse_library.mako Wed Feb 16 09:54:49 2011 -0500 @@ -20,6 +20,7 @@ self.message_box_visible=False self.active_view="user" self.overlay_visible=False + self.has_accessible_datasets = False %></%def> @@ -349,7 +350,9 @@ form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE info_association, inherited = folder.get_info_association( restrict=True ) - has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) + if not self.has_accessible_datasets: + # If we already know the library contains accessible datasets, no need to check again (and we may set it to False if we do). + self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) %> %if not root_folder and ( not folder.deleted or show_deleted ): <% encoded_id = trans.security.encode_id(folder.id) %> @@ -379,7 +382,7 @@ <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> %endif %if not branch_deleted( folder ): - %if has_accessible_datasets: + %if self.has_accessible_datasets: <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a> %endif %if can_modify: @@ -476,7 +479,7 @@ info_association, inherited = library.get_info_association() form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE - has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) + self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles ) tracked_datasets = {} @@ -523,7 +526,7 @@ %endif <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif - %if has_accessible_datasets: + %if self.has_accessible_datasets: <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a> %endif %elif can_modify and not library.purged: @@ -546,7 +549,7 @@ <br/> %endif - %if has_accessible_datasets: + %if self.has_accessible_datasets: <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post"> %endif %if has_accessible_folders: @@ -554,7 +557,7 @@ <thead><tr class="libraryTitle"><th> - %if has_accessible_datasets: + %if self.has_accessible_datasets: <input type="checkbox" id="checkAll" name=select_all_datasets_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_datasets_checkbox value="true"/> %endif Name @@ -568,18 +571,18 @@ <% row_counter = RowCounter() %> %if cntrller in [ 'library', 'requests' ]: ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} - %if not library.deleted and has_accessible_datasets: + %if not library.deleted and self.has_accessible_datasets: ${render_actions_on_multiple_items()} %endif %elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ): ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} - %if not library.deleted and not show_deleted and has_accessible_datasets: + %if not library.deleted and not show_deleted and self.has_accessible_datasets: ${render_actions_on_multiple_items()} %endif %endif </table> %endif - %if has_accessible_datasets: + %if self.has_accessible_datasets: </form> %endif @@ -591,7 +594,7 @@  %endif - %if has_accessible_datasets: + %if self.has_accessible_datasets: ${render_compression_types_help( comptypes )} %endif %if not has_accessible_folders: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: fix max chrom length.
by Bitbucket 15 Feb '11

15 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/88640d4ca8f5/ changeset: r5068:88640d4ca8f5 user: jgoecks date: 2011-02-16 01:20:39 summary: Trackster: fix max chrom length. affected #: 2 files (48 bytes) --- a/static/scripts/packed/trackster.js Tue Feb 15 19:09:38 2011 -0500 +++ b/static/scripts/packed/trackster.js Tue Feb 15 19:20:39 2011 -0500 @@ -1,1 +1,1 @@ -CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,PACK_SPACING=5,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. 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c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var k=$("<div class='form-row' />").appendTo(a);k.append($("<label />").attr("for",c).text(d.label+":"));if(d.type=="bool"){k.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type=="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var i=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(i);var j=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(i).appendTo(k).bind("click",function(l){i.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){i.hide();$(document).unbind("click.color-picker")});l.stopPropagation()})}else{k.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.name_div.data("menu_options")["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+a.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,j=g-m,c=this.view.container.width(),f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),r=c/j;this.content_div.append(p);this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=0;while((a*DENSITY*f)<g){var n=c+"_"+r+"_"+a;var e=this.tile_cache.get(n);var k=a*DENSITY*this.view.resolution;var q=k+DENSITY*this.view.resolution;if(!b&&e){this.show_tile(e,p,k,r)}else{this.delayed_draw(b,n,k,q,a,f,p,r)}a+=1}var d=this;var o=setInterval(function(){if(l===0){var u=d.content_div.children();var t=false;for(var v=u.length-1,s=0;v>=s;v--){var x=$(u[v]);if(t){x.remove()}else{if(x.children().length!==0){t=true}}}for(var w=0;w<d.filters.length;w++){d.filters[w].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(b)}},delayed_draw:function(b,g,f,i,c,e,h,j){var d=this;var a=setTimeout(function(){if(f<=d.view.high&&i>=d.view.low){var k;if(!b){k=d.tile_cache.get(g)}if(!k){k=d.draw_tile(e,c,h,j);if(k){var l=$("<div class='track-tile'>").prepend(k);if(k.hasClass(FILTERABLE_CLASS)){l.addClass(FILTERABLE_CLASS)}k=l}}if(k){d.tile_cache.set(g,k);d.show_tile(k,h,f,j)}}},50)},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>CHAR_WIDTH_PX){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.data_queue={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,j,d,q){var r=this.inc_slots[a];if(!r||(r.mode!==q)){r={};r.w_scale=a;r.mode=q;this.inc_slots[a]=r;this.start_end_dct[a]={}}var m=r.w_scale,x=[],y=[],k=0,o=this.view.max_low;for(var v=0,w=j.length;v<w;v++){var h=j[v],l=h[0];if(r[l]!==undefined){k=Math.max(k,r[l]);y.push(r[l])}else{x.push(v)}}var e=this.start_end_dct[a];var n=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=e[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var i=F[z];if(E>i[0]&&D<i[1]){A=true;break}}}if(!A){return C}}return -1};for(var v=0,w=x.length;v<w;v++){var h=j[x[v]],l=h[0],t=h[1],b=h[2],p=h[3],c=Math.floor((t-o)*m),g=Math.ceil((b-o)*m),u=CONTEXT.measureText(p).width,f;if(p!==undefined&&!d){u+=(LABEL_SPACING+PACK_SPACING);if(c-u>=0){c-=u;f="left"}else{g+=u;f="right"}}var s=n(c,g);if(s>=0){if(e[s]===undefined){e[s]=[]}e[s].push([c,g]);r[l]=s;k=Math.max(k,s)}else{}}return k},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>CHAR_WIDTH_PX){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ae,m,q,au){var K=m*DENSITY*ae,aj=(m+1)*DENSITY*ae,J=aj-K;var G=this.data_cache.get_data(K,aj,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[K,aj]]=true;this.get_data(K,aj);return}var a=Math.ceil(J*au),ag=this.prefs.label_color,g=this.prefs.block_color,p=this.mode,u=25,aa,V=this.left_offset,at,B,av;var o=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(o)}o=$(o);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(p==="Dense"){B=u;av=DENSE_TRACK_HEIGHT}else{if(p==="Squish"){av=SQUISH_TRACK_HEIGHT;aa=true}else{if(p==="Pack"){av=PACK_TRACK_HEIGHT;aa=false}else{if(G.extra_info==="no_detail"){av=(G.track_type==="bai"?SQUISH_TRACK_HEIGHT:NO_DETAIL_TRACK_HEIGHT);aa=true}else{av=PACK_TRACK_HEIGHT;aa=false}}}B=this.incremental_slots(au,G.data,aa,p)*av+u;at=this.inc_slots[au]}}o.get(0).width=a+V;o.get(0).height=B;if(G.dataset_type=="summary_tree"){o.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}q.parent().css("height",Math.max(this.height_px,B)+"px");var H=o.get(0).getContext("2d");H.fillStyle=g;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var v=B+LABEL_SPACING+CHAR_HEIGHT_PX;points=G.data,max=G.max,delta_x_px=Math.ceil(G.delta*au);var n=$("<div />").addClass("yaxislabel");n.text(max);n.css({position:"absolute",top:"22px",left:"10px"});n.prependTo(this.container_div);for(var an=0,F=points.length;an<F;an++){var Z=Math.floor((points[an][0]-K)*au);var Y=points[an][1];if(!Y){continue}var ak=Y/max*B;H.fillStyle="black";H.fillRect(Z+V,v-ak,delta_x_px,ak);var X=4;if(this.prefs.show_counts&&(H.measureText(Y).width+X)<delta_x_px){H.fillStyle="#666";H.textAlign="center";H.fillText(Y,Z+V+(delta_x_px/2),10)}}return o}if(G.message){o.css({"border-color":"red"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+V,av);if(!G.data){return o}}for(var aq=0;aq<this.filters.length;aq++){if(G.data.length&&this.filters[aq].applies_to(G.data[0])){o.addClass(FILTERABLE_CLASS);break}}var ar=G.data;var am=0;for(var an=0,F=ar.length;an<F;an++){var R=ar[an],O=R[0],ap=R[1],ac=R[2],L=R[3];if(this.mode!="Dense"&&at[O]===undefined){continue}var ab=false;var T;for(var aq=0;aq<this.filters.length;aq++){T=this.filters[aq];T.update_attrs(R);if(!T.keep(R)){ab=true;break}}if(ab){continue}if(ap<=aj&&ac>=K){if(G.dataset_type=="interval_index"){ac-=1}var ad=Math.floor(Math.max(0,(ap-K)*au)),I=Math.ceil(Math.min(a,Math.max(0,(ac-K)*au))),W=(p==="Dense"?1:(1+at[O]))*av;var E,ah,M=null,aw=null;if(G.dataset_type==="bai"){H.fillStyle=g;if(R[5] instanceof Array){var C=Math.floor(Math.max(0,(R[4][0]-K)*au)),N=Math.ceil(Math.min(a,Math.max(0,(R[4][1]-K)*au))),A=Math.floor(Math.max(0,(R[5][0]-K)*au)),t=Math.ceil(Math.min(a,Math.max(0,(R[5][1]-K)*au)));if(R[4][1]>=K&&R[4][0]<=aj&&R[4][2]){this.rect_or_text(H,au,K,aj,R[4][0],R[4][2],R[4][3],W)}if(R[5][1]>=K&&R[5][0]<=aj&&R[5][2]){this.rect_or_text(H,au,K,aj,R[5][0],R[5][2],R[5][3],W)}if(A>N){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(N+V,W+5,V+A,W+5)}}else{H.fillStyle=g;this.rect_or_text(H,au,K,aj,ap,R[4],R[5],W)}if(p!=="Dense"&&!aa&&ap>K){H.fillStyle=this.prefs.label_color;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}else{if(G.dataset_type==="interval_index"){if(p=="Auto"){if(R.length<=4){p="Squish"}else{p="Pack"}}if(p=="Dense"){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{if(R.length<=4){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{var D=R[5],U=R[6],af=R[7],e=R[8];if(U&&af){M=Math.floor(Math.max(0,(U-K)*au));aw=Math.ceil(Math.min(a,Math.max(0,(af-K)*au)))}var ao,P;if(p=="Squish"){ao=1;P=SQUISH_FEATURE_HEIGHT}else{ao=5;P=PACK_FEATURE_HEIGHT}if(!e){if(R.strand){if(R.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(R.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}}else{H.fillStyle=CONNECTOR_COLOR}H.fillRect(ad+V,W+(P-ao)/2+1,I-ad,P)}else{var z,Q;if(p=="Squish"){H.fillStyle=CONNECTOR_COLOR;z=W+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}else{if(D){var z=W;var Q=P;if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}}else{H.fillStyle=CONNECTOR_COLOR;z+=(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}}H.fillRect(ad+V,z,I-ad,Q);for(var al=0,d=e.length;al<d;al++){var s=e[al],c=Math.floor(Math.max(0,(s[0]-K)*au)),S=Math.ceil(Math.min(a,Math.max((s[1]-K)*au)));if(c>S){continue}H.fillStyle=g;H.fillRect(c+V,W+(P-ao)/2+1,S-c,ao);if(M!==undefined&&!(c>aw||S<M)){var ai=Math.max(c,M),w=Math.min(S,aw-1);H.fillRect(ai+V,W+1,w-ai,P)}}}if(p=="Pack"&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}}}else{if(G.dataset_type==="vcf"){if(aa){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,1)}else{var r=R[4],l=R[5],b=R[6];E=9;ah=1;H.fillRect(ad+V,W,I-ad,E);if(p!=="Dense"&&L!==undefined&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+2+V,W+8)}else{H.textAlign="right";H.fillText(L,ad-2+V,W+8)}H.fillStyle=g}var h=r+" / "+l;if(ap>K&&H.measureText(h).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(h,V+ad+(I-ad)/2,W+8);H.fillStyle=g}}}}}am++}}return o}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,PACK_SPACING=5,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var k=$("<div class='form-row' />").appendTo(a);k.append($("<label />").attr("for",c).text(d.label+":"));if(d.type=="bool"){k.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type=="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var i=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(i);var j=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(i).appendTo(k).bind("click",function(l){i.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){i.hide();$(document).unbind("click.color-picker")});l.stopPropagation()})}else{k.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.name_div.data("menu_options")["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+a.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,j=g-m,c=this.view.container.width(),f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),r=c/j;this.content_div.append(p);this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=0;while((a*DENSITY*f)<g){var n=c+"_"+r+"_"+a;var e=this.tile_cache.get(n);var k=a*DENSITY*this.view.resolution;var q=k+DENSITY*this.view.resolution;if(!b&&e){this.show_tile(e,p,k,r)}else{this.delayed_draw(b,n,k,q,a,f,p,r)}a+=1}var d=this;var o=setInterval(function(){if(l===0){var u=d.content_div.children();var t=false;for(var v=u.length-1,s=0;v>=s;v--){var x=$(u[v]);if(t){x.remove()}else{if(x.children().length!==0){t=true}}}for(var w=0;w<d.filters.length;w++){d.filters[w].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(b)}},delayed_draw:function(b,g,f,i,c,e,h,j){var d=this;var a=setTimeout(function(){if(f<=d.view.high&&i>=d.view.low){var k;if(!b){k=d.tile_cache.get(g)}if(!k){k=d.draw_tile(e,c,h,j);if(k){var l=$("<div class='track-tile'>").prepend(k);if(k.hasClass(FILTERABLE_CLASS)){l.addClass(FILTERABLE_CLASS)}k=l}}if(k){d.tile_cache.set(g,k);d.show_tile(k,h,f,j)}}},50)},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>CHAR_WIDTH_PX){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.data_queue={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,j,d,q){var r=this.inc_slots[a];if(!r||(r.mode!==q)){r={};r.w_scale=a;r.mode=q;this.inc_slots[a]=r;this.start_end_dct[a]={}}var m=r.w_scale,x=[],y=[],k=0,o=this.view.max_low;for(var v=0,w=j.length;v<w;v++){var h=j[v],l=h[0];if(r[l]!==undefined){k=Math.max(k,r[l]);y.push(r[l])}else{x.push(v)}}var e=this.start_end_dct[a];var n=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=e[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var i=F[z];if(E>i[0]&&D<i[1]){A=true;break}}}if(!A){return C}}return -1};for(var v=0,w=x.length;v<w;v++){var h=j[x[v]],l=h[0],t=h[1],b=h[2],p=h[3],c=Math.floor((t-o)*m),g=Math.ceil((b-o)*m),u=CONTEXT.measureText(p).width,f;if(p!==undefined&&!d){u+=(LABEL_SPACING+PACK_SPACING);if(c-u>=0){c-=u;f="left"}else{g+=u;f="right"}}var s=n(c,g);if(s>=0){if(e[s]===undefined){e[s]=[]}e[s].push([c,g]);r[l]=s;k=Math.max(k,s)}else{}}return k},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>CHAR_WIDTH_PX){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ae,m,q,au){var K=m*DENSITY*ae,aj=(m+1)*DENSITY*ae,J=aj-K;var G=this.data_cache.get_data(K,aj,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[K,aj]]=true;this.get_data(K,aj);return}var a=Math.ceil(J*au),ag=this.prefs.label_color,g=this.prefs.block_color,p=this.mode,u=25,aa,V=this.left_offset,at,B,av;var o=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(o)}o=$(o);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(p==="Dense"){B=u;av=DENSE_TRACK_HEIGHT}else{if(p==="Squish"){av=SQUISH_TRACK_HEIGHT;aa=true}else{if(p==="Pack"){av=PACK_TRACK_HEIGHT;aa=false}else{if(G.extra_info==="no_detail"){av=(G.track_type==="bai"?SQUISH_TRACK_HEIGHT:NO_DETAIL_TRACK_HEIGHT);aa=true}else{av=PACK_TRACK_HEIGHT;aa=false}}}B=this.incremental_slots(au,G.data,aa,p)*av+u;at=this.inc_slots[au]}}o.get(0).width=a+V;o.get(0).height=B;if(G.dataset_type=="summary_tree"){o.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}q.parent().css("height",Math.max(this.height_px,B)+"px");var H=o.get(0).getContext("2d");H.fillStyle=g;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var v=B+LABEL_SPACING+CHAR_HEIGHT_PX;points=G.data,max=G.max,delta_x_px=Math.ceil(G.delta*au);var n=$("<div 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ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file --- a/static/scripts/trackster.js Tue Feb 15 19:09:38 2011 -0500 +++ b/static/scripts/trackster.js Tue Feb 15 19:20:39 2011 -0500 @@ -523,7 +523,7 @@ view.intro_div.hide(); } view.chrom_select.val(view.chrom); - view.max_high = found.len; + view.max_high = found.len-1; // -1 because we're using 0-based indexing. view.reset(); view.redraw(true); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: trackster: For feature/bam tracks, new option in dropdown to list chroms/contigs that have data for that dataset. Tweak popup menu system to use a $.data variable that is bound to the anchor link, allowing options to be modified after the first initialization.
by Bitbucket 15 Feb '11

15 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/83b5c59076a5/ changeset: r5067:83b5c59076a5 user: kanwei date: 2011-02-16 01:09:38 summary: trackster: For feature/bam tracks, new option in dropdown to list chroms/contigs that have data for that dataset. Tweak popup menu system to use a $.data variable that is bound to the anchor link, allowing options to be modified after the first initialization. affected #: 6 files (1.2 KB) --- a/lib/galaxy/visualization/tracks/data_providers.py Tue Feb 15 17:24:24 2011 -0500 +++ b/lib/galaxy/visualization/tracks/data_providers.py Tue Feb 15 19:09:38 2011 -0500 @@ -47,6 +47,12 @@ """ # Override. pass + + def valid_chroms( self ): + """ + Returns chroms/contigs that the dataset contains + """ + return None # by default def has_data( self, chrom, start, end, **kwargs ): """ @@ -109,6 +115,11 @@ CACHE = LRUCache(20) # Store 20 recently accessed indices for performance + def valid_chroms( self ): + st = summary_tree_from_file( self.converted_dataset.file_name ) + return st.chrom_blocks.keys() + + def get_summary( self, chrom, start, end, **kwargs): filename = self.converted_dataset.file_name st = self.CACHE[filename] @@ -410,6 +421,10 @@ f = open( self.original_dataset.file_name ) return f + def valid_chroms( self ): + # No way to return this info as of now + return None + def has_data( self, chrom ): f = self._get_dataset() bw = BigWigFile(file=f) --- a/lib/galaxy/web/controllers/tracks.py Tue Feb 15 17:24:24 2011 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Tue Feb 15 19:09:38 2011 -0500 @@ -386,7 +386,7 @@ def reference( self, trans, dbkey, chrom, low, high, **kwargs ): if self.available_genomes is None: self._init_references(trans) - if dbkey not in self.available_genomes: + if dbkey not in self.available_genomes: return None try: @@ -434,10 +434,10 @@ return msg @web.json - def converted_datasets_state( self, trans, hda_ldda, dataset_id, chrom=None, low=None, high=None ): - """ - Returns state of dataset's converted datasets. If a genome window is - specified, method checks whether dataset has data in the window. + def converted_datasets_state( self, trans, hda_ldda, dataset_id, chrom=None ): + """ + Init-like method that returns state of dataset's converted datasets. Returns valid chroms + for that dataset as well. """ # TODO: this code is copied from data() -- should refactor. @@ -457,19 +457,24 @@ if msg: return msg + valid_chroms = None # Check for data in the genome window. if data_sources.get( 'index' ): tracks_dataset_type = data_sources['index']['name'] indexer = get_data_provider( tracks_dataset_type )( dataset.get_converted_dataset( trans, tracks_dataset_type ), dataset ) if not indexer.has_data( chrom ): return messages.NO_DATA + valid_chroms = indexer.valid_chroms() else: # Standalone data provider standalone_provider = get_data_provider(data_sources['data_standalone']['name'])( dataset ) kwargs = {"stats": True} if not standalone_provider.has_data( chrom ): return messages.NO_DATA - return messages.DATA + valid_chroms = standalone_provider.valid_chroms() + + # Have data if we get here + return { "status": messages.DATA, "valid_chroms": valid_chroms } @web.json def data( self, trans, hda_ldda, dataset_id, chrom, low, high, **kwargs ): --- a/static/scripts/galaxy.base.js Tue Feb 15 17:24:24 2011 -0500 +++ b/static/scripts/galaxy.base.js Tue Feb 15 19:09:38 2011 -0500 @@ -54,16 +54,21 @@ }); } -function make_popupmenu( button_element, options ) { +function make_popupmenu( button_element, initial_options ) { + + /* Use the $.data feature to store options with the link element. + This allows options to be changed at a later time + */ + button_element.data("menu_options", initial_options); button_element.bind("click.show_popup", function(e) { // Close existing visible menus $(".popmenu-wrapper").remove(); - // Need setTimeouts so clicks don't interfere with each other setTimeout( function() { // Dynamically generate the wrapper holding all the selectable options of the menu. var menu_element = $( "<ul id='" + button_element.attr('id') + "-menu'></ul>" ); + var options = button_element.data("menu_options"); if (obj_length(options) <= 0) { $("<li>No Options.</li>").appendTo(menu_element); } --- a/static/scripts/packed/galaxy.base.js Tue Feb 15 17:24:24 2011 -0500 +++ 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f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!==""){c.attr("value",m)}else{c.attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_to_values",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(l!==n&&n!==null&&n!==undefined){if(h!==undefined&&$.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window).trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function 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c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return 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false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var k=$("<div class='form-row' />").appendTo(a);k.append($("<label />").attr("for",c).text(d.label+":"));if(d.type=="bool"){k.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type=="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var i=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(i);var j=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(i).appendTo(k).bind("click",function(l){i.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){i.hide();$(document).unbind("click.color-picker")});l.stopPropagation()})}else{k.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,j=g-m,c=this.view.container.width(),f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),r=c/j;this.content_div.append(p);this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=0;while((a*DENSITY*f)<g){var n=c+"_"+r+"_"+a;var e=this.tile_cache.get(n);var k=a*DENSITY*this.view.resolution;var q=k+DENSITY*this.view.resolution;if(!b&&e){this.show_tile(e,p,k,r)}else{this.delayed_draw(b,n,k,q,a,f,p,r)}a+=1}var d=this;var o=setInterval(function(){if(l===0){var u=d.content_div.children();var t=false;for(var v=u.length-1,s=0;v>=s;v--){var x=$(u[v]);if(t){x.remove()}else{if(x.children().length!==0){t=true}}}for(var w=0;w<d.filters.length;w++){d.filters[w].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(b)}},delayed_draw:function(b,g,f,i,c,e,h,j){var d=this;var a=setTimeout(function(){if(f<=d.view.high&&i>=d.view.low){var k;if(!b){k=d.tile_cache.get(g)}if(!k){k=d.draw_tile(e,c,h,j);if(k){var l=$("<div class='track-tile'>").prepend(k);if(k.hasClass(FILTERABLE_CLASS)){l.addClass(FILTERABLE_CLASS)}k=l}}if(k){d.tile_cache.set(g,k);d.show_tile(k,h,f,j)}}},50)},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>CHAR_WIDTH_PX){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.data_queue={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,j,d,q){var r=this.inc_slots[a];if(!r||(r.mode!==q)){r={};r.w_scale=a;r.mode=q;this.inc_slots[a]=r;this.start_end_dct[a]={}}var m=r.w_scale,x=[],y=[],k=0,o=this.view.max_low;for(var v=0,w=j.length;v<w;v++){var h=j[v],l=h[0];if(r[l]!==undefined){k=Math.max(k,r[l]);y.push(r[l])}else{x.push(v)}}var e=this.start_end_dct[a];var n=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=e[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var i=F[z];if(E>i[0]&&D<i[1]){A=true;break}}}if(!A){return C}}return -1};for(var v=0,w=x.length;v<w;v++){var h=j[x[v]],l=h[0],t=h[1],b=h[2],p=h[3],c=Math.floor((t-o)*m),g=Math.ceil((b-o)*m),u=CONTEXT.measureText(p).width,f;if(p!==undefined&&!d){u+=(LABEL_SPACING+PACK_SPACING);if(c-u>=0){c-=u;f="left"}else{g+=u;f="right"}}var s=n(c,g);if(s>=0){if(e[s]===undefined){e[s]=[]}e[s].push([c,g]);r[l]=s;k=Math.max(k,s)}else{}}return k},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>CHAR_WIDTH_PX){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ae,m,q,au){var K=m*DENSITY*ae,aj=(m+1)*DENSITY*ae,J=aj-K;var G=this.data_cache.get_data(K,aj,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[K,aj]]=true;this.get_data(K,aj);return}var a=Math.ceil(J*au),ag=this.prefs.label_color,g=this.prefs.block_color,p=this.mode,u=25,aa,V=this.left_offset,at,B,av;var o=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(o)}o=$(o);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(p==="Dense"){B=u;av=DENSE_TRACK_HEIGHT}else{if(p==="Squish"){av=SQUISH_TRACK_HEIGHT;aa=true}else{if(p==="Pack"){av=PACK_TRACK_HEIGHT;aa=false}else{if(G.extra_info==="no_detail"){av=(G.track_type==="bai"?SQUISH_TRACK_HEIGHT:NO_DETAIL_TRACK_HEIGHT);aa=true}else{av=PACK_TRACK_HEIGHT;aa=false}}}B=this.incremental_slots(au,G.data,aa,p)*av+u;at=this.inc_slots[au]}}o.get(0).width=a+V;o.get(0).height=B;if(G.dataset_type=="summary_tree"){o.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}q.parent().css("height",Math.max(this.height_px,B)+"px");var H=o.get(0).getContext("2d");H.fillStyle=g;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var v=B+LABEL_SPACING+CHAR_HEIGHT_PX;points=G.data,max=G.max,delta_x_px=Math.ceil(G.delta*au);var n=$("<div />").addClass("yaxislabel");n.text(max);n.css({position:"absolute",top:"22px",left:"10px"});n.prependTo(this.container_div);for(var an=0,F=points.length;an<F;an++){var Z=Math.floor((points[an][0]-K)*au);var Y=points[an][1];if(!Y){continue}var ak=Y/max*B;H.fillStyle="black";H.fillRect(Z+V,v-ak,delta_x_px,ak);var X=4;if(this.prefs.show_counts&&(H.measureText(Y).width+X)<delta_x_px){H.fillStyle="#666";H.textAlign="center";H.fillText(Y,Z+V+(delta_x_px/2),10)}}return o}if(G.message){o.css({"border-color":"red"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+V,av);if(!G.data){return o}}for(var aq=0;aq<this.filters.length;aq++){if(G.data.length&&this.filters[aq].applies_to(G.data[0])){o.addClass(FILTERABLE_CLASS);break}}var ar=G.data;var am=0;for(var an=0,F=ar.length;an<F;an++){var R=ar[an],O=R[0],ap=R[1],ac=R[2],L=R[3];if(this.mode!="Dense"&&at[O]===undefined){continue}var ab=false;var T;for(var aq=0;aq<this.filters.length;aq++){T=this.filters[aq];T.update_attrs(R);if(!T.keep(R)){ab=true;break}}if(ab){continue}if(ap<=aj&&ac>=K){if(G.dataset_type=="interval_index"){ac-=1}var ad=Math.floor(Math.max(0,(ap-K)*au)),I=Math.ceil(Math.min(a,Math.max(0,(ac-K)*au))),W=(p==="Dense"?1:(1+at[O]))*av;var E,ah,M=null,aw=null;if(G.dataset_type==="bai"){H.fillStyle=g;if(R[5] instanceof Array){var C=Math.floor(Math.max(0,(R[4][0]-K)*au)),N=Math.ceil(Math.min(a,Math.max(0,(R[4][1]-K)*au))),A=Math.floor(Math.max(0,(R[5][0]-K)*au)),t=Math.ceil(Math.min(a,Math.max(0,(R[5][1]-K)*au)));if(R[4][1]>=K&&R[4][0]<=aj&&R[4][2]){this.rect_or_text(H,au,K,aj,R[4][0],R[4][2],R[4][3],W)}if(R[5][1]>=K&&R[5][0]<=aj&&R[5][2]){this.rect_or_text(H,au,K,aj,R[5][0],R[5][2],R[5][3],W)}if(A>N){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(N+V,W+5,V+A,W+5)}}else{H.fillStyle=g;this.rect_or_text(H,au,K,aj,ap,R[4],R[5],W)}if(p!=="Dense"&&!aa&&ap>K){H.fillStyle=this.prefs.label_color;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}else{if(G.dataset_type==="interval_index"){if(p=="Auto"){if(R.length<=4){p="Squish"}else{p="Pack"}}if(p=="Dense"){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{if(R.length<=4){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{var D=R[5],U=R[6],af=R[7],e=R[8];if(U&&af){M=Math.floor(Math.max(0,(U-K)*au));aw=Math.ceil(Math.min(a,Math.max(0,(af-K)*au)))}var ao,P;if(p=="Squish"){ao=1;P=SQUISH_FEATURE_HEIGHT}else{ao=5;P=PACK_FEATURE_HEIGHT}if(!e){if(R.strand){if(R.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(R.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}}else{H.fillStyle=CONNECTOR_COLOR}H.fillRect(ad+V,W+(P-ao)/2+1,I-ad,P)}else{var z,Q;if(p=="Squish"){H.fillStyle=CONNECTOR_COLOR;z=W+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}else{if(D){var z=W;var Q=P;if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}}else{H.fillStyle=CONNECTOR_COLOR;z+=(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}}H.fillRect(ad+V,z,I-ad,Q);for(var al=0,d=e.length;al<d;al++){var s=e[al],c=Math.floor(Math.max(0,(s[0]-K)*au)),S=Math.ceil(Math.min(a,Math.max((s[1]-K)*au)));if(c>S){continue}H.fillStyle=g;H.fillRect(c+V,W+(P-ao)/2+1,S-c,ao);if(M!==undefined&&!(c>aw||S<M)){var ai=Math.max(c,M),w=Math.min(S,aw-1);H.fillRect(ai+V,W+1,w-ai,P)}}}if(p=="Pack"&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}}}else{if(G.dataset_type==="vcf"){if(aa){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,1)}else{var r=R[4],l=R[5],b=R[6];E=9;ah=1;H.fillRect(ad+V,W,I-ad,E);if(p!=="Dense"&&L!==undefined&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+2+V,W+8)}else{H.textAlign="right";H.fillText(L,ad-2+V,W+8)}H.fillStyle=g}var h=r+" / "+l;if(ap>K&&H.measureText(h).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(h,V+ad+(I-ad)/2,W+8);H.fillStyle=g}}}}}am++}}return o}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,PACK_SPACING=5,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var k=$("<div class='form-row' />").appendTo(a);k.append($("<label />").attr("for",c).text(d.label+":"));if(d.type=="bool"){k.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type=="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var i=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(i);var j=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(i).appendTo(k).bind("click",function(l){i.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){i.hide();$(document).unbind("click.color-picker")});l.stopPropagation()})}else{k.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.name_div.data("menu_options")["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+a.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,j=g-m,c=this.view.container.width(),f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),r=c/j;this.content_div.append(p);this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=0;while((a*DENSITY*f)<g){var n=c+"_"+r+"_"+a;var e=this.tile_cache.get(n);var k=a*DENSITY*this.view.resolution;var q=k+DENSITY*this.view.resolution;if(!b&&e){this.show_tile(e,p,k,r)}else{this.delayed_draw(b,n,k,q,a,f,p,r)}a+=1}var d=this;var o=setInterval(function(){if(l===0){var u=d.content_div.children();var t=false;for(var v=u.length-1,s=0;v>=s;v--){var x=$(u[v]);if(t){x.remove()}else{if(x.children().length!==0){t=true}}}for(var w=0;w<d.filters.length;w++){d.filters[w].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(b)}},delayed_draw:function(b,g,f,i,c,e,h,j){var d=this;var a=setTimeout(function(){if(f<=d.view.high&&i>=d.view.low){var k;if(!b){k=d.tile_cache.get(g)}if(!k){k=d.draw_tile(e,c,h,j);if(k){var l=$("<div class='track-tile'>").prepend(k);if(k.hasClass(FILTERABLE_CLASS)){l.addClass(FILTERABLE_CLASS)}k=l}}if(k){d.tile_cache.set(g,k);d.show_tile(k,h,f,j)}}},50)},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>CHAR_WIDTH_PX){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.data_queue={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,j,d,q){var r=this.inc_slots[a];if(!r||(r.mode!==q)){r={};r.w_scale=a;r.mode=q;this.inc_slots[a]=r;this.start_end_dct[a]={}}var m=r.w_scale,x=[],y=[],k=0,o=this.view.max_low;for(var v=0,w=j.length;v<w;v++){var h=j[v],l=h[0];if(r[l]!==undefined){k=Math.max(k,r[l]);y.push(r[l])}else{x.push(v)}}var e=this.start_end_dct[a];var n=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=e[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var i=F[z];if(E>i[0]&&D<i[1]){A=true;break}}}if(!A){return C}}return -1};for(var v=0,w=x.length;v<w;v++){var h=j[x[v]],l=h[0],t=h[1],b=h[2],p=h[3],c=Math.floor((t-o)*m),g=Math.ceil((b-o)*m),u=CONTEXT.measureText(p).width,f;if(p!==undefined&&!d){u+=(LABEL_SPACING+PACK_SPACING);if(c-u>=0){c-=u;f="left"}else{g+=u;f="right"}}var s=n(c,g);if(s>=0){if(e[s]===undefined){e[s]=[]}e[s].push([c,g]);r[l]=s;k=Math.max(k,s)}else{}}return k},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>CHAR_WIDTH_PX){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ae,m,q,au){var K=m*DENSITY*ae,aj=(m+1)*DENSITY*ae,J=aj-K;var G=this.data_cache.get_data(K,aj,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[K,aj]]=true;this.get_data(K,aj);return}var a=Math.ceil(J*au),ag=this.prefs.label_color,g=this.prefs.block_color,p=this.mode,u=25,aa,V=this.left_offset,at,B,av;var o=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(o)}o=$(o);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(p==="Dense"){B=u;av=DENSE_TRACK_HEIGHT}else{if(p==="Squish"){av=SQUISH_TRACK_HEIGHT;aa=true}else{if(p==="Pack"){av=PACK_TRACK_HEIGHT;aa=false}else{if(G.extra_info==="no_detail"){av=(G.track_type==="bai"?SQUISH_TRACK_HEIGHT:NO_DETAIL_TRACK_HEIGHT);aa=true}else{av=PACK_TRACK_HEIGHT;aa=false}}}B=this.incremental_slots(au,G.data,aa,p)*av+u;at=this.inc_slots[au]}}o.get(0).width=a+V;o.get(0).height=B;if(G.dataset_type=="summary_tree"){o.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}q.parent().css("height",Math.max(this.height_px,B)+"px");var H=o.get(0).getContext("2d");H.fillStyle=g;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var v=B+LABEL_SPACING+CHAR_HEIGHT_PX;points=G.data,max=G.max,delta_x_px=Math.ceil(G.delta*au);var n=$("<div />").addClass("yaxislabel");n.text(max);n.css({position:"absolute",top:"22px",left:"10px"});n.prependTo(this.container_div);for(var an=0,F=points.length;an<F;an++){var Z=Math.floor((points[an][0]-K)*au);var Y=points[an][1];if(!Y){continue}var ak=Y/max*B;H.fillStyle="black";H.fillRect(Z+V,v-ak,delta_x_px,ak);var X=4;if(this.prefs.show_counts&&(H.measureText(Y).width+X)<delta_x_px){H.fillStyle="#666";H.textAlign="center";H.fillText(Y,Z+V+(delta_x_px/2),10)}}return o}if(G.message){o.css({"border-color":"red"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+V,av);if(!G.data){return o}}for(var aq=0;aq<this.filters.length;aq++){if(G.data.length&&this.filters[aq].applies_to(G.data[0])){o.addClass(FILTERABLE_CLASS);break}}var ar=G.data;var am=0;for(var an=0,F=ar.length;an<F;an++){var R=ar[an],O=R[0],ap=R[1],ac=R[2],L=R[3];if(this.mode!="Dense"&&at[O]===undefined){continue}var ab=false;var T;for(var aq=0;aq<this.filters.length;aq++){T=this.filters[aq];T.update_attrs(R);if(!T.keep(R)){ab=true;break}}if(ab){continue}if(ap<=aj&&ac>=K){if(G.dataset_type=="interval_index"){ac-=1}var ad=Math.floor(Math.max(0,(ap-K)*au)),I=Math.ceil(Math.min(a,Math.max(0,(ac-K)*au))),W=(p==="Dense"?1:(1+at[O]))*av;var E,ah,M=null,aw=null;if(G.dataset_type==="bai"){H.fillStyle=g;if(R[5] instanceof Array){var C=Math.floor(Math.max(0,(R[4][0]-K)*au)),N=Math.ceil(Math.min(a,Math.max(0,(R[4][1]-K)*au))),A=Math.floor(Math.max(0,(R[5][0]-K)*au)),t=Math.ceil(Math.min(a,Math.max(0,(R[5][1]-K)*au)));if(R[4][1]>=K&&R[4][0]<=aj&&R[4][2]){this.rect_or_text(H,au,K,aj,R[4][0],R[4][2],R[4][3],W)}if(R[5][1]>=K&&R[5][0]<=aj&&R[5][2]){this.rect_or_text(H,au,K,aj,R[5][0],R[5][2],R[5][3],W)}if(A>N){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(N+V,W+5,V+A,W+5)}}else{H.fillStyle=g;this.rect_or_text(H,au,K,aj,ap,R[4],R[5],W)}if(p!=="Dense"&&!aa&&ap>K){H.fillStyle=this.prefs.label_color;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}else{if(G.dataset_type==="interval_index"){if(p=="Auto"){if(R.length<=4){p="Squish"}else{p="Pack"}}if(p=="Dense"){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{if(R.length<=4){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,DENSE_FEATURE_HEIGHT)}else{var D=R[5],U=R[6],af=R[7],e=R[8];if(U&&af){M=Math.floor(Math.max(0,(U-K)*au));aw=Math.ceil(Math.min(a,Math.max(0,(af-K)*au)))}var ao,P;if(p=="Squish"){ao=1;P=SQUISH_FEATURE_HEIGHT}else{ao=5;P=PACK_FEATURE_HEIGHT}if(!e){if(R.strand){if(R.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(R.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}}else{H.fillStyle=CONNECTOR_COLOR}H.fillRect(ad+V,W+(P-ao)/2+1,I-ad,P)}else{var z,Q;if(p=="Squish"){H.fillStyle=CONNECTOR_COLOR;z=W+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}else{if(D){var z=W;var Q=P;if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}}else{H.fillStyle=CONNECTOR_COLOR;z+=(SQUISH_FEATURE_HEIGHT/2)+1;Q=1}}H.fillRect(ad+V,z,I-ad,Q);for(var al=0,d=e.length;al<d;al++){var s=e[al],c=Math.floor(Math.max(0,(s[0]-K)*au)),S=Math.ceil(Math.min(a,Math.max((s[1]-K)*au)));if(c>S){continue}H.fillStyle=g;H.fillRect(c+V,W+(P-ao)/2+1,S-c,ao);if(M!==undefined&&!(c>aw||S<M)){var ai=Math.max(c,M),w=Math.min(S,aw-1);H.fillRect(ai+V,W+1,w-ai,P)}}}if(p=="Pack"&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+V+LABEL_SPACING,W+8)}else{H.textAlign="right";H.fillText(L,ad+V-LABEL_SPACING,W+8)}H.fillStyle=g}}}}else{if(G.dataset_type==="vcf"){if(aa){H.fillStyle=g;H.fillRect(ad+V,W+5,I-ad,1)}else{var r=R[4],l=R[5],b=R[6];E=9;ah=1;H.fillRect(ad+V,W,I-ad,E);if(p!=="Dense"&&L!==undefined&&ap>K){H.fillStyle=ag;if(m===0&&ad-H.measureText(L).width<0){H.textAlign="left";H.fillText(L,I+2+V,W+8)}else{H.textAlign="right";H.fillText(L,ad-2+V,W+8)}H.fillStyle=g}var h=r+" / "+l;if(ap>K&&H.measureText(h).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(h,V+ad+(I-ad)/2,W+8);H.fillStyle=g}}}}}am++}}return o}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file --- a/static/scripts/trackster.js Tue Feb 15 17:24:24 2011 -0500 +++ b/static/scripts/trackster.js Tue Feb 15 19:09:38 2011 -0500 @@ -903,7 +903,7 @@ }); return container; }, - update_from_form : function( container ) { + update_from_form: function( container ) { var track_config = this; var changed = false; $.each( this.params, function( index, param ) { @@ -1002,8 +1002,7 @@ if ( track.view.chrom != null ) { // Get dataset state; if state is fine, enable and draw track. Otherwise, show message // about track status. - $.getJSON(this.dataset_check_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, - chrom: track.view.chrom, low: track.view.max_low, high: track.view.max_high}, + $.getJSON(converted_datasets_state_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, chrom: track.view.chrom}, function (result) { if (!result || result === "error" || result.kind === "error") { track.container_div.addClass("error"); @@ -1025,8 +1024,13 @@ track.container_div.addClass("pending"); track.content_div.text(DATA_PENDING); setTimeout(function() { track.init(); }, track.data_query_wait); - } else if (result === "data") { - // Only draw in user has selected a chromosome. + } else if (result['status'] === "data") { + if (result['valid_chroms']) { + track.valid_chroms = result['valid_chroms']; + track.name_div.data("menu_options")["List chrom/contigs with data"] = function() { + show_modal("Chrom/contigs with data", "<p>" + track.valid_chroms.join("<br/>") + "</p>", { "Close": function() { hide_modal(); } }); + }; + } track.content_div.text(DATA_OK); if (track.view.chrom) { track.content_div.text(""); @@ -1297,7 +1301,7 @@ "OK": ok_fn }); }; - + /* track_dropdown["Set as overview"] = function() { view.overview_viewport.find("canvas").remove(); track.is_overview = true; @@ -1307,7 +1311,7 @@ view.tracks[track_id].is_overview = false; } } - }; + };*/ if (track.filters.length > 0) { // Show/hide filters menu item. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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