November 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 9f172e4713ed: Support query anchored and HTML output
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286796719 -3600 # Node ID 9f172e4713edbf4d6a22f10ad01867710cce6b00 # Parent d8da4f7bb0f5e1d43b371e4e52fb688ad816e5bf Support query anchored and HTML output --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -15,7 +15,7 @@ blastn $adv_opts.filter_query $adv_opts.strand -out $output1 --outfmt $out_format +$out_format -num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments @@ -60,11 +60,16 @@ blastn </param><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"> - <option value="6">Tabular</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> + <option value="-outfmt 6" selected="True">Tabular</option> + <option value="-outfmt 5">BLAST XML</option> + <option value="-outfmt 0">Pairwise text</option> + <option value="-outfmt 0 -html">Pairwise HTML</option> + <option value="-outfmt 2">Query-anchored text</option> + <option value="-outfmt 2 -html">Query-anchored HTML</option> + <option value="-outfmt 4">Flat query-anchored text</option> + <option value="-outfmt 4 -html">Flat query-anchored HTML</option></param><conditional name="adv_opts"> @@ -102,10 +107,13 @@ blastn <outputs><data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"><change_format> - <when input="out_format" value="0" format="txt"/> - </change_format> - <change_format> - <when input="out_format" value="5" format="blastxml"/> + <when input="out_format" value="-outfmt 0" format="txt"/> + <when input="out_format" value="-outfmt 0 -html" format="html"/> + <when input="out_format" value="-outfmt 2" format="txt"/> + <when input="out_format" value="-outfmt 2 -html" format="html"/> + <when input="out_format" value="-outfmt 4" format="txt"/> + <when input="out_format" value="-outfmt 4 -html" format="html"/> + <when input="out_format" value="-outfmt 5" format="blastxml"/></change_format></data></outputs> @@ -147,7 +155,7 @@ Algorithms include blastn, megablast, an **Output format** -The default output of this tool is tabular, containing 12 columns: +Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: 1. Id of your sequence 2. GI of the database hit @@ -162,6 +170,14 @@ 10. End position in database hit 11. E-value 12. Bit score +The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + ------- **References** --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -15,7 +15,7 @@ blastp $adv_opts.filter_query $adv_opts.matrix -out $output1 --outfmt $out_format +$out_format -num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments @@ -55,11 +55,16 @@ blastp </param><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"> - <option value="6">Tabular</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> + <option value="-outfmt 6" selected="True">Tabular</option> + <option value="-outfmt 5">BLAST XML</option> + <option value="-outfmt 0">Pairwise text</option> + <option value="-outfmt 0 -html">Pairwise HTML</option> + <option value="-outfmt 2">Query-anchored text</option> + <option value="-outfmt 2 -html">Query-anchored HTML</option> + <option value="-outfmt 4">Flat query-anchored text</option> + <option value="-outfmt 4 -html">Flat query-anchored HTML</option></param><conditional name="adv_opts"> @@ -110,10 +115,13 @@ blastp <outputs><data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"><change_format> - <when input="out_format" value="0" format="txt"/> - </change_format> - <change_format> - <when input="out_format" value="5" format="blastxml"/> + <when input="out_format" value="-outfmt 0" format="txt"/> + <when input="out_format" value="-outfmt 0 -html" format="html"/> + <when input="out_format" value="-outfmt 2" format="txt"/> + <when input="out_format" value="-outfmt 2 -html" format="html"/> + <when input="out_format" value="-outfmt 4" format="txt"/> + <when input="out_format" value="-outfmt 4 -html" format="html"/> + <when input="out_format" value="-outfmt 5" format="blastxml"/></change_format></data></outputs> @@ -140,7 +148,7 @@ using the NCBI BLAST+ blastp command lin **Output format** -The default output of this tool is tabular, containing 12 columns: +Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: 1. Id of your sequence 2. GI of the database hit @@ -155,6 +163,14 @@ 10. End position in database hit 11. E-value 12. Bit score +The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + ------- **References** --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -15,7 +15,7 @@ tblastx $adv_opts.strand $adv_opts.matrix -out $output1 --outfmt $out_format +$out_format -num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments @@ -49,11 +49,16 @@ tblastx </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"> - <option value="6">Tabular</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> + <option value="-outfmt 6" selected="True">Tabular</option> + <option value="-outfmt 5">BLAST XML</option> + <option value="-outfmt 0">Pairwise text</option> + <option value="-outfmt 0 -html">Pairwise HTML</option> + <option value="-outfmt 2">Query-anchored text</option> + <option value="-outfmt 2 -html">Query-anchored HTML</option> + <option value="-outfmt 4">Flat query-anchored text</option> + <option value="-outfmt 4 -html">Flat query-anchored HTML</option></param><conditional name="adv_opts"> @@ -100,10 +105,13 @@ tblastx <outputs><data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}"><change_format> - <when input="out_format" value="0" format="txt"/> - </change_format> - <change_format> - <when input="out_format" value="5" format="blastxml"/> + <when input="out_format" value="-outfmt 0" format="txt"/> + <when input="out_format" value="-outfmt 0 -html" format="html"/> + <when input="out_format" value="-outfmt 2" format="txt"/> + <when input="out_format" value="-outfmt 2 -html" format="html"/> + <when input="out_format" value="-outfmt 4" format="txt"/> + <when input="out_format" value="-outfmt 4 -html" format="html"/> + <when input="out_format" value="-outfmt 5" format="blastxml"/></change_format></data></outputs> @@ -122,7 +130,7 @@ tblastx --><param name="evalue_cutoff" value="10.0" /><param name="filter_query" value="yes" /> - <param name="out_format" value="6" /> + <param name="out_format" value="-outfmt 6" /><output name="output1" file="megablast_wrapper_test1.out"/></test></tests> @@ -143,7 +151,7 @@ using the NCBI BLAST+ tblastx command li **Output format** -The default output of this tool is tabular, containing 12 columns: +Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: 1. Id of your sequence 2. GI of the database hit @@ -158,6 +166,14 @@ 10. End position in database hit 11. E-value 12. Bit score +The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + ------- **References** --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -15,7 +15,7 @@ blastx $adv_opts.strand $adv_opts.matrix -out $output1 --outfmt $out_format +$out_format -num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments @@ -50,11 +50,16 @@ blastx </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"> - <option value="6">Tabular</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> + <option value="-outfmt 6" selected="True">Tabular</option> + <option value="-outfmt 5">BLAST XML</option> + <option value="-outfmt 0">Pairwise text</option> + <option value="-outfmt 0 -html">Pairwise HTML</option> + <option value="-outfmt 2">Query-anchored text</option> + <option value="-outfmt 2 -html">Query-anchored HTML</option> + <option value="-outfmt 4">Flat query-anchored text</option> + <option value="-outfmt 4 -html">Flat query-anchored HTML</option></param><conditional name="adv_opts"> @@ -103,10 +108,13 @@ blastx <outputs><data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}"><change_format> - <when input="out_format" value="0" format="txt"/> - </change_format> - <change_format> - <when input="out_format" value="5" format="blastxml"/> + <when input="out_format" value="-outfmt 0" format="txt"/> + <when input="out_format" value="-outfmt 0 -html" format="html"/> + <when input="out_format" value="-outfmt 2" format="txt"/> + <when input="out_format" value="-outfmt 2 -html" format="html"/> + <when input="out_format" value="-outfmt 4" format="txt"/> + <when input="out_format" value="-outfmt 4 -html" format="html"/> + <when input="out_format" value="-outfmt 5" format="blastxml"/></change_format></data></outputs> @@ -133,7 +141,7 @@ using the NCBI BLAST+ blastx command lin **Output format** -The default output of this tool is tabular, containing 12 columns: +Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: 1. Id of your sequence 2. GI of the database hit @@ -148,6 +156,14 @@ 10. End position in database hit 11. E-value 12. Bit score +The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + ------- **References** --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -14,7 +14,7 @@ tblastn $adv_opts.filter_query $adv_opts.matrix -out $output1 --outfmt $out_format +$out_format -num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments @@ -50,11 +50,16 @@ tblastn </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"> - <option value="6">Tabular</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> + <option value="-outfmt 6" selected="True">Tabular</option> + <option value="-outfmt 5">BLAST XML</option> + <option value="-outfmt 0">Pairwise text</option> + <option value="-outfmt 0 -html">Pairwise HTML</option> + <option value="-outfmt 2">Query-anchored text</option> + <option value="-outfmt 2 -html">Query-anchored HTML</option> + <option value="-outfmt 4">Flat query-anchored text</option> + <option value="-outfmt 4 -html">Flat query-anchored HTML</option></param><conditional name="adv_opts"> @@ -105,10 +110,13 @@ tblastn <outputs><data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"><change_format> - <when input="out_format" value="0" format="txt"/> - </change_format> - <change_format> - <when input="out_format" value="5" format="blastxml"/> + <when input="out_format" value="-outfmt 0" format="txt"/> + <when input="out_format" value="-outfmt 0 -html" format="html"/> + <when input="out_format" value="-outfmt 2" format="txt"/> + <when input="out_format" value="-outfmt 2 -html" format="html"/> + <when input="out_format" value="-outfmt 4" format="txt"/> + <when input="out_format" value="-outfmt 4 -html" format="html"/> + <when input="out_format" value="-outfmt 5" format="blastxml"/></change_format></data></outputs> @@ -135,7 +143,7 @@ using the NCBI BLAST+ tblastn command li **Output format** -The default output of this tool is tabular, containing 12 columns: +Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: 1. Id of your sequence 2. GI of the database hit @@ -150,6 +158,14 @@ 10. End position in database hit 11. E-value 12. Bit score +The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + ------- **References**

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galaxy-dist commit 5f4ad3738071: trackster: Fix ReferenceTrack not drawing, summary_tree display is now histogram and more fine grained. Small overview fix, UI tweaks
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1287007196 14400 # Node ID 5f4ad373807158f8b2ac0bcaafab9f57b972e562 # Parent 76f09e5ccb85569b56e66676e4c761f4348336fc trackster: Fix ReferenceTrack not drawing, summary_tree display is now histogram and more fine grained. Small overview fix, UI tweaks --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -292,7 +292,7 @@ var View = function( container, chrom, t view.low = Math.max(low, 0); view.high = Math.min(high, view.max_high); } - view.overview_viewport.find("canvas").remove(); + view.reset_overview(); view.redraw(); }, @@ -438,6 +438,13 @@ var View = function( container, chrom, t this.low = Math.round(cur_center - new_half); this.high = Math.round(cur_center + new_half); 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(); } }); @@ -648,8 +655,6 @@ var TiledTrack = function() { }, 50); }, set_overview: function() { var view = this.view; - view.overview_viewport.height(view.default_overview_height); - view.overview_box.height(view.default_overview_height); if (this.initial_canvas && this.is_overview) { view.overview_close.show(); @@ -695,6 +700,7 @@ var ReferenceTrack = function (view) { Track.call( this, null, view, view.top_labeltrack ); TiledTrack.call( this ); + this.left_offset = 200; this.height_px = 12; this.container_div.addClass( "reference-track" ); this.dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"); @@ -752,8 +758,9 @@ var ReferenceTrack = function (view) { }); for (var c = 0, str_len = seq.length; c < str_len; c++) { - var c_start = Math.round(c * w_scale); - ctx.fillText(seq[c], c_start + this.left_offset, 10); + var c_start = Math.round(c * w_scale), + gap = Math.round(w_scale / 2); + ctx.fillText(seq[c], c_start + this.left_offset + gap, 10); } parent_element.append(canvas); return canvas; @@ -991,7 +998,7 @@ var FeatureTrack = function ( name, view this.showing_details = false; this.vertical_detail_px = 10; this.vertical_nodetail_px = 2; - this.summary_draw_height = 20; + this.summary_draw_height = 30; this.default_font = "9px Monaco, Lucida Console, monospace"; this.inc_slots = {}; this.data_queue = {}; @@ -1194,32 +1201,25 @@ var FeatureTrack = function ( name, view ctx.textAlign = "right"; if (result.dataset_type == "summary_tree") { - var color, - min_color = 55, - color_span = 255 - min_color, - color_cutoff = color_span*2/3, // Where text switches from black to white - points = result.data, + var points = result.data, max = result.max, avg = result.avg, delta_x_px = Math.ceil(result.delta * w_scale); - + for ( var i = 0, len = points.length; i < len; i++ ) { var x = Math.floor( (points[i][0] - tile_low) * w_scale ); var y = points[i][1]; - + if (!y) { continue; } - color = Math.floor( color_span - (y / max) * color_span ); - ctx.fillStyle = "rgb(" +color+ "," +color+ "," +color+ ")"; - ctx.fillRect(x + left_offset, 0, delta_x_px, this.summary_draw_height); - + var y_px = y / max * this.summary_draw_height; + + ctx.fillStyle = "black"; + ctx.fillRect(x + left_offset, this.summary_draw_height - y_px, delta_x_px, y_px); + if (this.prefs.show_counts && ctx.measureText(y).width < delta_x_px) { - if (color > color_cutoff) { - ctx.fillStyle = "black"; - } else { - ctx.fillStyle = "#ddd"; - } + ctx.fillStyle = "#bbb"; ctx.textAlign = "center"; - ctx.fillText(y, x + left_offset + (delta_x_px/2), 12); + ctx.fillText(y, x + left_offset + (delta_x_px/2), this.summary_draw_height - 5); } } cur_mode = "Summary"; @@ -1252,18 +1252,19 @@ var FeatureTrack = function ( name, view y_center = (mode === "Dense" ? 1 : (1 + slots[feature_uid])) * y_scale; if (result.dataset_type === "bai") { + var cigar = feature[4]; ctx.fillStyle = block_color; - if (feature[4] instanceof Array) { - var b1_start = Math.floor( Math.max(0, (feature[4][0] - tile_low) * w_scale) ), - b1_end = Math.ceil( Math.min(width, Math.max(0, (feature[4][1] - tile_low) * w_scale)) ), - b2_start = Math.floor( Math.max(0, (feature[5][0] - tile_low) * w_scale) ), - b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) ); + if (feature[5] instanceof Array) { + var b1_start = Math.floor( Math.max(0, (feature[5][0] - tile_low) * w_scale) ), + b1_end = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) ), + b2_start = Math.floor( Math.max(0, (feature[6][0] - tile_low) * w_scale) ), + b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[6][1] - tile_low) * w_scale)) ); - if (feature[4][1] >= tile_low && feature[4][0] <= tile_high) { - this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], b1_start + left_offset, b1_end - b1_start, y_center); + if (feature[5][1] >= tile_low && feature[5][0] <= tile_high) { + this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], b1_start + left_offset, b1_end - b1_start, y_center); } - if (feature[5][1] >= tile_low && feature[5][0] <= tile_high) { - this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], b2_start + left_offset, b2_end - b2_start, y_center); + if (feature[6][1] >= tile_low && feature[6][0] <= tile_high) { + this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[6][0], feature[6][2], b2_start + left_offset, b2_end - b2_start, y_center); } if (b2_start > b1_end) { ctx.fillStyle = "#999"; --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -97,7 +97,7 @@ class SummaryTreeDataProvider( TracksDat resolution = max(1, ceil(float(kwargs['resolution']))) - level = ceil( log( resolution, st.block_size ) ) + level = ceil( log( resolution, st.block_size ) ) - 1 level = int(max( level, 0 )) if level <= 0: return None @@ -167,6 +167,7 @@ class BamDataProvider( TracksDataProvide Fetch intervals in the region """ start, end = int(start), int(end) + no_detail = "no_detail" in kwargs # Attempt to open the BAM file with index bamfile = csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', index_filename=self.converted_dataset.file_name ) message = None @@ -189,16 +190,20 @@ class BamDataProvider( TracksDataProvide message = "Only the first %s pairs are being displayed." % MAX_VALS break qname = read.qname + if no_detail: + seq = len(read.seq) + else: + seq = read.seq if read.is_proper_pair: if qname in paired_pending: # one in dict is always first pair = paired_pending[qname] - results.append( [ qname, pair['start'], read.pos + read.rlen, read.seq, [pair['start'], pair['end'], pair['seq']], [read.pos, read.pos + read.rlen, read.seq] ] ) + results.append( [ qname, pair['start'], read.pos + read.rlen, seq, read.cigar, [pair['start'], pair['end'], pair['seq']], [read.pos, read.pos + read.rlen, seq] ] ) # results.append( [read.qname, pair['start'], read.pos + read.rlen, qname, [pair['start'], pair['end']], [read.pos, read.pos + read.rlen] ] ) del paired_pending[qname] else: - paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read.rlen, 'seq': read.seq, 'mate_start': read.mpos, 'rlen': read.rlen } + paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read.rlen, 'seq': seq, 'mate_start': read.mpos, 'rlen': read.rlen, 'cigar': read.cigar } else: - results.append( [qname, read.pos, read.pos + read.rlen, read.seq] ) + results.append( [qname, read.pos, read.pos + read.rlen, seq, read.cigar] ) # take care of reads whose mates are out of range for qname, read in paired_pending.iteritems(): if read['mate_start'] < read['start']: @@ -212,7 +217,7 @@ class BamDataProvider( TracksDataProvide r1 = [read['start'], read['end'], read['seq']] r2 = [read['mate_start'], read['mate_start'] + read['rlen']] - results.append( [ qname, start, end, read['seq'], r1, r2 ] ) + results.append( [ qname, start, end, read['seq'], read['cigar'], r1, r2 ] ) bamfile.close() return { 'data': results, 'message': message } --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -6,7 +6,7 @@ .nav-controls a{padding:0 0.4em;} .nav-input{font-size:12px;width:30em;z-index:1000;} .location{display:inline-block;width:15em;margin:0px 10px;} -.draghandle{float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;margin-right:5px;} +.draghandle{cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;} .intro{z-index:1000;margin-left:auto;margin-right:auto;color:#555;text-align:center;font-size:16px;} .overview{width:100%;margin:0px;color:white;} .overview-viewport{position:relative;height:14px;background:white;border-bottom:solid gray 1px;margin:0;} @@ -18,11 +18,12 @@ .viewport-canvas{width:100%;height:100px;} .yaxislabel{color:#777;} .line-track .track-content{border-top:1px solid #ddd;border-bottom:1px solid #ddd;} -.track{background:white;} +.track{background:white;margin-bottom:1px;} .track-header{text-align:left;padding:4px 0px;color:#666;} +.track-header .menubutton{margin-left:3px;} .track-content{overflow:hidden;text-align:center;} -.track.error{margin-bottom:2px;background-color:#ECB4AF;} -.track.nodata{margin-bottom:2px;background-color:#ddd;} +.track.error{background-color:#ECB4AF;} +.track.nodata{background-color:#ddd;} .loading{min-height:100px;} .label-track{} .label-track .label{border-left:solid #999 1px;padding:1px;display:inline-block;} --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -35,11 +35,11 @@ margin: 0px 10px; } .draghandle { + cursor: move; float: left; background: transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat; width: 10px; height: 12px; - margin-right: 5px; } .intro { z-index: 1000; @@ -127,6 +127,7 @@ /* border-top: solid #DDDDDD 1px; */ /* border-bottom: solid #DDDDDD 1px; */ background: white; + margin-bottom: 1px; } .track-header { @@ -135,17 +136,19 @@ color: #666; } +.track-header .menubutton { + margin-left: 3px; +} + .track-content { overflow: hidden; text-align: center; } .track.error { - margin-bottom: 2px; background-color: #ECB4AF; } .track.nodata { - margin-bottom: 2px; background-color: #ddd; } --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,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_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;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()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this. min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);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_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);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=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<inp ut/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<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/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info ;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.origin al_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a. low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g i n c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.overview_viewport.find("canvas").remove();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(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();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();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,widt h: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(var 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()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track");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=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name)}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){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");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Erro r","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_m odes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configuration"]=function(){var k=function(){hide_modal()};var j=function(){d.update_options(d.track_id);hide_modal()};show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:k,OK:j})};b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(d.name_div,b)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d) <e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;a.overview_viewport.height(a.default_overview_height);a.overview_box.h eight(a.default_overview_height);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())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.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.content_div.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.trac k_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.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;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){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;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefi ned;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();a.container_div.css("position","relative");var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.cont ainer_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=M ath.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs .max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(j).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=20;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_ca che.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y [0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ae,o,r,ar){var L=o*DENSITY*ae,ak=(o+1)*DENSITY*ae,K=ak-L;var al=(!this.initial_canvas?"initial":L+"_"+ak);var G=this.data_cache.get(al);var e;if(G===undefined||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ak]]=true;this.get_data(L,ak);return}var a=Math.ceil(K*ar),S=$("<canvas class='tile'></canvas>"),ag=this.pr efs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ac=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),W=this.left_offset,aq,B,at;if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ac?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/view.zoom_res:ar);B=this.incremental_slots(w,G.data,ac,q)*at+v;aq=this.inc_slots[w]}}S.css({position:"absolute",top:0,left:(L-this.view.low)*ar-W});S.get(0).width=a+W;S.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=S.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";if(G.dataset_type=="summary_tree"){var R,O=55,aj=255-O,n=aj*2/3,Y=G.data,J=G.max,p=G.avg,b=Math.ceil(G.delta*ar);for(var an=0,F=Y.length;an<F;an++){var aa=Math.floor((Y[an][0]-L)*ar);var Z=Y[an][1];if(!Z){continue}R=Math.floor(aj-(Z/J)*aj);H.fillStyle="rgb("+R+","+R+","+R+")";H.fillRect(aa+W,0,b,this.su mmary_draw_height);if(this.prefs.show_counts&&H.measureText(Z).width<b){if(R>n){H.fillStyle="black"}else{H.fillStyle="#ddd"}H.textAlign="center";H.fillText(Z,aa+W+(b/2),12)}}e="Summary";r.append(S);return S}if(G.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+W,at)}var ap=G.data;var am=0;for(var an=0,F=ap.length;an<F;an++){var T=ap[an],Q=T[0],ao=T[1],ab=T[2],M=T[3];if(ao<=ak&&ab>=L){var ad=Math.floor(Math.max(0,(ao-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(ab-L)*ar))),X=(q==="Dense"?1:(1+aq[Q]))*at;if(G.dataset_type==="bai"){H.fillStyle=h;if(T[4] instanceof Array){var C=Math.floor(Math.max(0,(T[4][0]-L)*ar)),P=Math.ceil(Math.min(a,Math.max(0,(T[4][1]-L)*ar))),A=Math.floor(Math.max(0,(T[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-L)*ar)));if(T[4][1]>=L&&T[4][0]<=ak){this.rect_or_text(H,ar,L,ak,T[4][0],T[4][2],C+W,P-C,X)}if(T[5][1]>=L&&T[5][0]<=ak){this.rect_or_text(H,ar,L,ak,T[5] [0],T[5][2],A+W,u-A,X)}if(A>P){H.fillStyle="#999";H.fillRect(P+W,X+5,A-P,1)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ak,ao,M,ad+W,I-ad,X)}if(q!=="Dense"&&!ac&&ao>L){H.fillStyle=this.prefs.label_color;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(Q,I+2+W,X+8)}else{H.textAlign="right";H.fillText(Q,ad-2+W,X+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ac){H.fillStyle=h;H.fillRect(ad+W,X+5,I-ad,1)}else{var E=T[4],V=T[5],af=T[6],g=T[7];var D,ah,N=null,au=null;if(V&&af){N=Math.floor(Math.max(0,(V-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(af-L)*ar)))}if(q!=="Dense"&&M!==undefined&&ao>L){H.fillStyle=ag;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+W,X+8)}else{H.textAlign="right";H.fillText(M,ad-2+W,X+8)}H.fillStyle=h}if(g){if(E){if(E=="+"){H.fillStyle=RIGHT_STRAND}else{if(E=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ad+W,X,I-ad,10);H.fillStyle=h}for(var al=0,f=g.length;al<f;al++){var t=g[al],d=Math.floor(Mat h.max(0,(t[0]-L)*ar)),U=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>U){continue}D=5;ah=3;H.fillRect(d+W,X+ah,U-d,D);if(N!==undefined&&!(d>au||U<N)){D=9;ah=1;var ai=Math.max(d,N),z=Math.min(U,au);H.fillRect(ai+W,X+ah,z-ai,D)}}}else{D=9;ah=1;H.fillRect(ad+W,X+ah,I-ad,D);if(T.strand){if(T.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ad+W,X,I-ad,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ac){H.fillStyle=h;H.fillRect(ad+W,X+5,I-ad,1)}else{var s=T[4],m=T[5],c=T[6];D=9;ah=1;H.fillRect(ad+W,X,I-ad,D);if(q!=="Dense"&&M!==undefined&&ao>L){H.fillStyle=ag;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+W,X+8)}else{H.textAlign="right";H.fillText(M,ad-2+W,X+8)}H.fillStyle=h}var l=s+" / "+m;if(ao>L&&H.measureText(l).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(l,W+ad+(I-ad)/2,X+8);H.fillStyle=h}}}}}am++}}r.append(S);return S},gen_options:function(j){var a=$("<div / >").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs .show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;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()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this. min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);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_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);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=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<inp ut/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<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/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info ;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.origin al_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a. low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g i n c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(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();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();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_locatio n(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(var 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()},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 Track=function(b,a,c){this.name=b;this.parent_ element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track");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=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name)}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){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");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(D ATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class= 'right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configuration"]=function(){var k=function(){hide_modal()};var j=function(){d.update_options(d.track_id);hide_modal()};show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:k,OK:j})};b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(d.name_div,b)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution ;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element); c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},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())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.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.content_div.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.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.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;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).get Context("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){thi s.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();a.container_div.css("position","relative");var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.cs s({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false ,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input ></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(j).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show _labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data _queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}v ar v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ac,n,q,ap){var L=n*DENSITY*ac,ah=(n+1)*DENSITY*ac,K=ah-L;var aj=(!this.initial_canvas?"initial":L+"_"+ah);var G=this.data_cache.get(aj);var e;if(G===undefined||(this.mode!=="Auto"&& G.dataset_type==="summary_tree")){this.data_queue[[L,ah]]=true;this.get_data(L,ah);return}var a=Math.ceil(K*ap),Q=$("<canvas class='tile'></canvas>"),ae=this.prefs.label_color,h=this.prefs.block_color,p=this.mode,v=25,aa=(p==="Squish")||(p==="Dense")&&(p!=="Pack")||(p==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,ao,B,aq;if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(p==="Dense"){B=v;aq=10}else{aq=(aa?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ap<0.0001?1/view.zoom_res:ap);B=this.incremental_slots(w,G.data,aa,p)*aq+v;ao=this.inc_slots[w]}}Q.css({position:"absolute",top:0,left:(L-this.view.low)*ap-U});Q.get(0).width=a+U;Q.get(0).height=B;q.parent().css("height",Math.max(this.height_px,B)+"px");var H=Q.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,o=G.avg,b=Math.ceil(G.delta*ap);for(var al=0,F=W.length;al<F;al++){var Y=Math.floor((W[a l][0]-L)*ap);var X=W[al][1];if(!X){continue}var ai=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-ai,b,ai);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}e="Summary";q.append(Q);return Q}if(G.message){Q.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,aq)}var an=G.data;var ak=0;for(var al=0,F=an.length;al<F;al++){var R=an[al],P=R[0],am=R[1],Z=R[2],M=R[3];if(am<=ah&&Z>=L){var ab=Math.floor(Math.max(0,(am-L)*ap)),I=Math.ceil(Math.min(a,Math.max(0,(Z-L)*ap))),V=(p==="Dense"?1:(1+ao[P]))*aq;if(G.dataset_type==="bai"){var t=R[4];H.fillStyle=h;if(R[5] instanceof Array){var C=Math.floor(Math.max(0,(R[5][0]-L)*ap)),O=Math.ceil(Math.min(a,Math.max(0,(R[5][1]-L)*ap))),A=Math.floor(Math.max(0,(R[6][0]-L)*ap)),u=Math.ceil(Math.min(a,Math.max(0,(R[6][1]-L)*ap)));if(R[5][1]>=L&& R[5][0]<=ah){this.rect_or_text(H,ap,L,ah,R[5][0],R[5][2],C+U,O-C,V)}if(R[6][1]>=L&&R[6][0]<=ah){this.rect_or_text(H,ap,L,ah,R[6][0],R[6][2],A+U,u-A,V)}if(A>O){H.fillStyle="#999";H.fillRect(O+U,V+5,A-O,1)}}else{H.fillStyle=h;this.rect_or_text(H,ap,L,ah,am,M,ab+U,I-ab,V)}if(p!=="Dense"&&!aa&&am>L){H.fillStyle=this.prefs.label_color;if(n===0&&ab-H.measureText(M).width<0){H.textAlign="left";H.fillText(P,I+2+U,V+8)}else{H.textAlign="right";H.fillText(P,ab-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(aa){H.fillStyle=h;H.fillRect(ab+U,V+5,I-ab,1)}else{var E=R[4],T=R[5],ad=R[6],g=R[7];var D,af,N=null,ar=null;if(T&&ad){N=Math.floor(Math.max(0,(T-L)*ap));ar=Math.ceil(Math.min(a,Math.max(0,(ad-L)*ap)))}if(p!=="Dense"&&M!==undefined&&am>L){H.fillStyle=ae;if(n===0&&ab-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ab-2+U,V+8)}H.fillStyle=h}if(g){if(E){if(E=="+"){H.fillStyle=RIGHT_STRAND}else{if(E=="-"){H .fillStyle=LEFT_STRAND}}H.fillRect(ab+U,V,I-ab,10);H.fillStyle=h}for(var aj=0,f=g.length;aj<f;aj++){var s=g[aj],d=Math.floor(Math.max(0,(s[0]-L)*ap)),S=Math.ceil(Math.min(a,Math.max((s[1]-L)*ap)));if(d>S){continue}D=5;af=3;H.fillRect(d+U,V+af,S-d,D);if(N!==undefined&&!(d>ar||S<N)){D=9;af=1;var ag=Math.max(d,N),z=Math.min(S,ar);H.fillRect(ag+U,V+af,z-ag,D)}}}else{D=9;af=1;H.fillRect(ab+U,V+af,I-ab,D);if(R.strand){if(R.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(R.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ab+U,V,I-ab,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(aa){H.fillStyle=h;H.fillRect(ab+U,V+5,I-ab,1)}else{var r=R[4],m=R[5],c=R[6];D=9;af=1;H.fillRect(ab+U,V,I-ab,D);if(p!=="Dense"&&M!==undefined&&am>L){H.fillStyle=ae;if(n===0&&ab-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ab-2+U,V+8)}H.fillStyle=h}var l=r+" / "+m;if(am>L&&H.measureText(l).width<(I-ab)){H.fillStyle="white";H.textAlig n="center";H.fillText(l,U+ab+(I-ab)/2,V+8);H.fillStyle=h}}}}}ak++}}q.append(Q);return Q},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.b lock_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});

1 0

galaxy-dist commit 76f09e5ccb85: sample tracking UI fixes
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287002139 14400 # Node ID 76f09e5ccb85569b56e66676e4c761f4348336fc # Parent c0feb970e48de8b713a9a516cad61950ed0641b5 sample tracking UI fixes --- a/templates/requests/common/manage_request.mako +++ b/templates/requests/common/manage_request.mako @@ -132,38 +132,38 @@ <div class="grid-header"><h2>Sequencing Request "${request.name}"</h2> + + <ul class="manage-table-actions"> + <li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li> + <div popupmenu="seqreq-${request.id}-popup"> + %if request.is_unsubmitted and request.samples: + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> + %endif + <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">History</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> + %if is_admin: + %if request.is_submitted: + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + %endif + %endif + </div> + <li><a class="action-button" href="${h.url_for( controller=cntrller, action='browse_requests' )}">Browse requests</a></li> + </ul> + <div class="toolParamHelp" style="clear: both;"> - <b>Sequencer</b>: ${request.type.name} - %if is_admin: - | <b>User</b>: ${request.user.email} - %endif - %if request.is_submitted: - | <b>State</b>: <i>${request.state}</i> - %else: - | <b>State</b>: ${request.state} - %endif + <b>Sequencer</b>: ${request.type.name} + %if is_admin: + | <b>User</b>: ${request.user.email} + %endif + %if request.is_submitted: + | <b>State</b>: <i>${request.state}</i> + %else: + | <b>State</b>: ${request.state} + %endif </div></div> -<br/><br/> -<ul class="manage-table-actions"> - <li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li> - <div popupmenu="seqreq-${request.id}-popup"> - %if request.is_unsubmitted and request.samples: - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> - %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">History</a> - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> - %if is_admin: - %if request.is_submitted: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> - %endif - %endif - </div> - <li><a class="action-button" href="${h.url_for( controller=cntrller, action='browse_requests' )}">Browse requests</a></li> -</ul> - %if request.has_samples_without_library_destinations: ${render_msg( "Select a target data library and folder for all the samples before starting the sequence run", "warning" )} %endif --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -393,7 +393,8 @@ class RequestsAdmin( BaseController, Use # get the sample these datasets are associated with try: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( selected_sample_id ) ) - sample.library.id and sample.folder.id + if sample.name in sample.request.has_samples_without_library_destinations: + raise Exception() except: # if no sample (with associated library & folder) has been selected status = 'error'

1 0

galaxy-dist commit 77e13329ab8b: No longer try to display Image type (including PDF) datasets within browser. Clicking on eye icon for binary and image types will now invoke save action.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1286945049 14400 # Node ID 77e13329ab8b9e69089400259eb70cda9525ec80 # Parent 9f172e4713edbf4d6a22f10ad01867710cce6b00 No longer try to display Image type (including PDF) datasets within browser. Clicking on eye icon for binary and image types will now invoke save action. --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -324,56 +324,56 @@ class DatasetInterface( BaseController, if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) current_user_roles = trans.get_current_user_roles() - if trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): - if data.state == trans.model.Dataset.states.UPLOAD: - return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) + if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): + return trans.show_error_message( "You are not allowed to access this dataset" ) + + if data.state == trans.model.Dataset.states.UPLOAD: + return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) + + if filename and filename != "index": + # For files in extra_files_path + file_path = os.path.join( data.extra_files_path, filename ) + if os.path.exists( file_path ): + mime, encoding = mimetypes.guess_type( file_path ) + if not mime: + try: + mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) + except: + mime = "text/plain" - if filename and filename != "index": - # For files in extra_files_path - file_path = os.path.join( data.extra_files_path, filename ) - if os.path.exists( file_path ): - mime, encoding = mimetypes.guess_type( file_path ) - if not mime: - try: - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) - except: - mime = "text/plain" - - trans.response.set_content_type( mime ) - return open( file_path ) - else: - return "Could not find '%s' on the extra files path %s." % (filename,file_path) - - mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) - trans.response.set_content_type(mime) - trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) - - if to_ext: # Saving the file - if data.ext in composite_extensions: - return self.archive_composite_dataset( trans, data, **kwd ) - else: - trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) - if to_ext[0] != ".": - to_ext = "." + to_ext - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = data.name - fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s]%s" % (data.hid, fname, to_ext) - return open( data.file_name ) - if os.path.exists( data.file_name ): - max_peek_size = 1000000 # 1 MB - if preview and (not isinstance(data.datatype, datatypes.binary.Binary)) and os.stat( data.file_name ).st_size > max_peek_size: - trans.response.set_content_type( "text/html" ) - return trans.stream_template_mako( "/dataset/large_file.mako", - truncated_data = open( data.file_name ).read(max_peek_size), - data = data ) - else: - return open( data.file_name ) + trans.response.set_content_type( mime ) + return open( file_path ) else: - raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) + return "Could not find '%s' on the extra files path %s." % (filename,file_path) + + mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) + trans.response.set_content_type(mime) + trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) + + if to_ext or isinstance(data.datatype, datatypes.binary.Binary) or isinstance(data.datatype, datatypes.images.Image): # Saving the file, or binary/image file + if data.extension in composite_extensions: + return self.archive_composite_dataset( trans, data, **kwd ) + else: + trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) + if not to_ext: + to_ext = data.extension + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = data.name + fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] + trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, to_ext) + return open( data.file_name ) + if not os.path.exists( data.file_name ): + raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) + + max_peek_size = 1000000 # 1 MB + if preview and os.stat( data.file_name ).st_size > max_peek_size: + trans.response.set_content_type( "text/html" ) + return trans.stream_template_mako( "/dataset/large_file.mako", + truncated_data = open( data.file_name ).read(max_peek_size), + data = data ) else: - return trans.show_error_message( "You are not allowed to access this dataset" ) - + return open( data.file_name ) + @web.expose @web.require_login( "see all available datasets" ) def list( self, trans, **kwargs ):

1 0

galaxy-dist commit c0feb970e48d: sample tracking bug fixes
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287000426 14400 # Node ID c0feb970e48de8b713a9a516cad61950ed0641b5 # Parent 77e13329ab8b9e69089400259eb70cda9525ec80 sample tracking bug fixes --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -3,15 +3,14 @@ <% from galaxy.web.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> -<br/><br/> -<font color="red"><b><i>A dataset can be renamed only if its status is "Not Started"</i></b></font> +<h3>Rename datasets for Sample "${sample.name}"</h3><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li><li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller='requests_admin', id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li></ul> @@ -19,40 +18,39 @@ ${render_msg( message, status )} %endif +${render_msg( 'A dataset can be renamed only if it is in <b>Not Started</b> state.', 'warning' )} <div class="toolForm"> - <div class="toolFormTitle">Rename datasets for Sample "${sample.name}"</div> - <div class="toolFormBody"> - <form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > - <table class="grid"> - <thead> - <tr> - <th>Prepend directory name</th> - <th>Name</th> - <th>Path on sequencer</th> - </tr> - <thead> - <tbody> - %for sample_dataset in sample_datasets: - %if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: - <tr> - <td> - <% rename_datasets_for_sample_select_field = build_rename_datasets_for_sample_select_field( trans, sample_dataset ) %> - ${rename_datasets_for_sample_select_field} - </td> - <td> - <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id} )" value="${sample_dataset.name}" size="100"/> - </td> - <td>${sample_dataset.file_path}</td> - </tr> - %endif - %endfor - </tbody> - </table> - <br/> - <div class="form-row"> - <input type="submit" name="rename_datasets_button" value="Save"/> - <input type="submit" name="cancel_rename_datasets_button" value="Close"/> - </div> - </form> - </div> + <form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > + <table class="grid"> + <thead> + <tr> + <th>Prepend directory name</th> + <th>Name</th> + <th>Path on sequencer</th> + </tr> + <thead> + <tbody> + %for id in id_list: + <% sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) %> + %if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: + <tr> + <td> + <% rename_datasets_for_sample_select_field = build_rename_datasets_for_sample_select_field( trans, sample_dataset ) %> + ${rename_datasets_for_sample_select_field.get_html()} + </td> + <td> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> + </td> + <td>${sample_dataset.file_path}</td> + </tr> + %endif + %endfor + </tbody> + </table> + <br/> + <div class="form-row"> + <input type="submit" name="rename_datasets_button" value="Save"/> + <input type="submit" name="cancel_rename_datasets_button" value="Close"/> + </div> + </form></div> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -105,8 +105,7 @@ class RequestsGrid( grids.Grid ): class RequestsCommon( BaseController, UsesFormDefinitionWidgets ): @web.json - def sample_state_updates( self, trans, ids=None, states=None, cntrller=None ): - # TODO fix this mthod - cntrller is required in the signature. + def sample_state_updates( self, trans, cntrller, ids=None, states=None ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' @@ -424,13 +423,19 @@ class RequestsCommon( BaseController, Us except: invalid_id_redirect( trans, cntrller, folder_id ) for sample_id in selected_samples: - sample = trans.sa_session.query( trans.model.Sample ).get( sample_id ) + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) sample.library = library sample.folder = folder trans.sa_session.add( sample ) trans.sa_session.flush() trans.sa_session.refresh( request ) message = 'Changes made to the selected samples have been saved. ' + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='manage_request', + cntrller=cntrller, + id=request_id, + status=status, + message=message ) ) elif params.get( 'cancel_change_lib_button', False ): return trans.response.send_redirect( web.url_for( controller='requests_common', action='manage_request', @@ -859,7 +864,7 @@ class RequestsCommon( BaseController, Us # The user has selected a sample to copy. library_id = current_samples[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) folder_id = current_samples[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True ) - name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( index+1 ) + name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( len( current_samples ) + 1 ) library_id = 'none' folder_id = 'none' field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ] @@ -867,7 +872,7 @@ class RequestsCommon( BaseController, Us # The user has not selected a sample to copy (may just be adding a sample). library_id = None folder_id = None - name = 'Sample_%i' % ( sample_index+1 ) + name = 'Sample_%i' % ( len( current_samples ) + 1 ) field_values = [ '' for field in request.type.sample_form.fields ] # Build the library_select_field and folder_select_field for the new sample being added. library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -9,11 +9,13 @@ import logging, os, pexpect, ConfigParse log = logging.getLogger( __name__ ) -class UserColumn( grids.TextColumn ): - def get_value( self, trans, grid, request ): - return request.user.email + class AdminRequestsGrid( RequestsGrid ): + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, request ): + return request.user.email + # Grid definition columns = [ col for col in RequestsGrid.columns ] columns.append( UserColumn( "User", model_class=model.User, @@ -180,7 +182,7 @@ class RequestsAdmin( BaseController, Use @web.json def get_file_details( self, trans, id, folder_path ): def print_ticks( d ): - # TODO: why is this method here? Add comments! + # pexpect timeout method pass # Avoid caching trans.response.headers['Pragma'] = 'no-cache' @@ -243,16 +245,20 @@ class RequestsAdmin( BaseController, Use if not sample_dataset_id: return invalid_id_redirect( trans, 'requests_admin', sample_dataset_id ) id_list = util.listify( sample_dataset_id ) + selected_sample_datasets = [] + for sample_dataset_id in id_list: + try: + selected_sample_datasets.append( trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) ) + except: + return invalid_id_redirect( trans, 'requests_admin', sample_dataset_id ) if operation == "view": - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) return trans.fill_template( '/admin/requests/dataset.mako', - sample_dataset=sample_dataset ) + sample_dataset=selected_sample_datasets[0] ) elif operation == "delete": not_deleted = [] - for sample_dataset_id in id_list: - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) - sample_id = sample_dataset.sample_id - if sample_dataset.status == sample_dataset.sample.transfer_status.NOT_STARTED: + for sample_dataset in selected_sample_datasets: + sample_id = sample_dataset.sample.id + if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: trans.sa_session.delete( sample_dataset ) trans.sa_session.flush() else: @@ -267,13 +273,26 @@ class RequestsAdmin( BaseController, Use status=status, message=message ) ) elif operation == "rename": - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) + # if none of the selected sample datasets are in the NOT_STARTED state, + # then display error message + flag = True + for sd in selected_sample_datasets: + if sd.status == trans.app.model.Sample.transfer_status.NOT_STARTED: + flag = False + break + if flag: + status = 'error' + message = 'A dataset can be renamed only if it is in the <b>Not Started</b> state.' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_datasets', + sample_id=trans.security.encode_id( selected_sample_datasets[0].sample.id ), + status=status, + message=message ) ) return trans.fill_template( '/admin/requests/rename_datasets.mako', - sample=sample_dataset.sample, + sample=selected_sample_datasets[0].sample, id_list=id_list ) elif operation == "start transfer": - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) - self.__start_datatx( trans, sample_dataset.sample, id_list ) + self.__start_datatx( trans, selected_sample_datasets[0].sample, selected_sample_datasets ) # Render the grid view sample_id = params.get( 'sample_id', None ) try: @@ -340,7 +359,7 @@ class RequestsAdmin( BaseController, Use message = 'Changes saved successfully.' return trans.fill_template( '/admin/requests/rename_datasets.mako', sample=sample, - sample_datasets=sample_datasets, + id_list=id_list, message=message, status=status ) return trans.response.send_redirect( web.url_for( controller='requests_admin', @@ -353,38 +372,48 @@ class RequestsAdmin( BaseController, Use message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) request_id = kwd.get( 'request_id', None ) + files = [] try: request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', request_id ) - files_list = util.listify( params.get( 'files_list', [] ) ) + selected_files = util.listify( params.get( 'files_list', [] ) ) folder_path = util.restore_text( params.get( 'folder_path', request.type.datatx_info[ 'data_dir' ] ) ) - selected_value = kwd.get( 'sample_id', 'none' ) - sample_id_select_field = self.__build_sample_id_select_field( request, selected_value ) + selected_sample_id = kwd.get( 'sample_id', 'none' ) + sample_id_select_field = self.__build_sample_id_select_field( trans, request, selected_sample_id ) # The __get_files() method redirects here with a status of 'error' and a message if there # was a problem retrieving the files. if folder_path and status != 'error': folder_path = self.__check_path( folder_path ) - sample_id = params.get( 'sample_id', None ) - try: - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', sample_id ) - # Get the filenames from the remote host - files = self.__get_files( trans, request, folder_path ) - if params.get( 'open_folder', False ): - if len( files_list ) == 1: - folder_path = os.path.join( folder_path, files_list[0] ) - folder_path = self.__check_path( folder_path ) + if params.get( 'folder_up', False ): + if folder_path[-1] == os.sep: + folder_path = os.path.dirname(folder_path[:-1]) + folder_path = self.__check_path( folder_path ) elif params.get( 'select_show_datasets_button', False ) or params.get( 'select_more_button', False ): - sample_dataset_file_names = self.__save_sample_datasets( trans, sample, files_list, folder_path ) + # get the sample these datasets are associated with + try: + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( selected_sample_id ) ) + sample.library.id and sample.folder.id + except: + # if no sample (with associated library & folder) has been selected + status = 'error' + message = 'Select a sample with associated data library and folder before selecting the dataset(s).' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='get_data', + request_id=trans.security.encode_id( request.id ), + folder_path=folder_path, + status=status, + message=message ) ) + # save the sample datasets + sample_dataset_file_names = self.__save_sample_datasets( trans, sample, selected_files, folder_path ) if sample_dataset_file_names: message = 'Datasets (%s) have been selected for sample (%s)' % \ ( str( sample_dataset_file_names )[1:-1].replace( "'", "" ), sample.name ) if params.get( 'select_show_datasets_button', False ): return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', - sample_id=sample_id, + request_id=request_id, + sample_id=trans.security.encode_id( sample.id ), message=message, status=status ) ) else: # 'select_more_button' was clicked @@ -392,11 +421,13 @@ class RequestsAdmin( BaseController, Use action='get_data', request_id=request_id, folder_path=folder_path, - sample_id=sample_id, + sample_id=sample.id, open_folder=True, message=message, status=status ) ) - return trans.fill_template( '/admin/requests/dataset_transfer.mako', + # Get the filenames from the remote host + files = self.__get_files( trans, request, folder_path ) + return trans.fill_template( '/admin/requests/get_data.mako', cntrller='requests_admin', request=request, sample_id_select_field=sample_id_select_field, @@ -434,20 +465,20 @@ class RequestsAdmin( BaseController, Use if ok: return output.splitlines() return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='get_data', - request_id=trans.security.encode_id( request.id ), - folder_path=folder_path, - status=status, - message=message ) ) + action='get_data', + request_id=trans.security.encode_id( request.id ), + folder_path=folder_path, + status=status, + message=message ) ) def __check_path( self, a_path ): # Return a valid folder_path if a_path and not a_path.endswith( os.sep ): a_path += os.sep return a_path - def __save_sample_datasets( self, trans, sample, files_list, folder_path ): + def __save_sample_datasets( self, trans, sample, selected_files, folder_path ): sample_dataset_file_names = [] - if files_list: - for f in files_list: + if selected_files: + for f in selected_files: filepath = os.path.join( folder_path, f ) if f[-1] == os.sep: # FIXME: The selected item is a folder so transfer all the folder contents @@ -522,7 +553,7 @@ class RequestsAdmin( BaseController, Use trans.sa_session.add( lfp ) trans.sa_session.flush() return datatx_user - def __send_message( self, trans, datatx_info, sample, id_list ): + def __send_message( self, trans, datatx_info, sample, selected_sample_datasets ): """Ceates an xml message and sends it to the rabbitmq server""" # Create the xml message based on the following template xml = \ @@ -542,8 +573,7 @@ class RequestsAdmin( BaseController, Use <file>%(FILE)s</file></dataset>''' datasets = '' - for id in id_list: - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) + for sample_dataset in selected_sample_datasets: if sample_dataset.status == sample.transfer_status.NOT_STARTED: datasets = datasets + dataset_xml % dict( ID=str( sample_dataset.id ), NAME=sample_dataset.name, @@ -574,7 +604,7 @@ class RequestsAdmin( BaseController, Use routing_key=trans.app.config.amqp['routing_key'] ) chan.close() conn.close() - def __start_datatx( self, trans, sample, id_list ): + def __start_datatx( self, trans, sample, selected_sample_datasets ): datatx_user = self.__setup_datatx_user( trans, sample.library, sample.folder ) # Validate sequencer information datatx_info = sample.request.type.datatx_info @@ -582,8 +612,8 @@ class RequestsAdmin( BaseController, Use message = "Error in sequencer login information." status = "error" else: - self.__send_message( trans, datatx_info, sample, id_list ) - message = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to see the latest transfer status." % len( id_list ) + self.__send_message( trans, datatx_info, sample, selected_sample_datasets ) + message = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to see the latest transfer status." % len( selected_sample_datasets ) status = "done" return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', @@ -599,6 +629,14 @@ class RequestsAdmin( BaseController, Use obj_id = kwd.get( 'id', None ) if operation == "view_form_definition": return self.view_form_definition( trans, **kwd ) + elif operation == "view": + return self.view_request_type( trans, **kwd ) + elif operation == "delete": + return self.delete_request_type( trans, **kwd ) + elif operation == "undelete": + return self.undelete_request_type( trans, **kwd ) + elif operation == "permissions": + return self.request_type_permissions( trans, **kwd ) # Render the grid view return self.requesttype_grid( trans, **kwd ) @web.expose @@ -655,26 +693,26 @@ class RequestsAdmin( BaseController, Use message=message, status=status ) def __create_request_type_form( self, trans, **kwd ): - request_form_definitionss = self.get_all_forms( trans, + request_form_definitions = self.get_all_forms( trans, filter=dict( deleted=False ), form_type=trans.model.FormDefinition.types.REQUEST ) sample_form_definitions = self.get_all_forms( trans, filter=dict( deleted=False ), form_type=trans.model.FormDefinition.types.SAMPLE ) - if not request_form_definitionss or not sample_form_definitions: + if not request_form_definitions or not sample_form_definitions: return [],[] params = util.Params( kwd ) request_form_id = params.get( 'request_form_id', 'none' ) sample_form_id = params.get( 'sample_form_id', 'none' ) request_form_id_select_field = build_select_field( trans, - objs=request_form_definitionss, - label_attr='id', + objs=request_form_definitions, + label_attr='name', select_field_name='request_form_id', selected_value=request_form_id, refresh_on_change=False ) sample_form_id_select_field = build_select_field( trans, objs=sample_form_definitions, - label_attr='id', + label_attr='name', select_field_name='sample_form_id', selected_value=sample_form_id, refresh_on_change=False ) @@ -826,7 +864,7 @@ class RequestsAdmin( BaseController, Use status=status, message=message ) # ===== Methods for building SelectFields used on various admin_requests forms - def __build_sample_id_select_field( self, request, selected_value ): + def __build_sample_id_select_field( self, trans, request, selected_value ): return build_select_field( trans, request.samples, 'name', 'sample_id', selected_value=selected_value, refresh_on_change=False ) def __build_rename_dataset_select_field( self, trans, request_type=None ): if request_type: --- a/templates/admin/requests/get_data.mako +++ b/templates/admin/requests/get_data.mako @@ -68,13 +68,6 @@ } </script> -<style type="text/css"> -.msg_head { - padding: 0px 0px; - cursor: pointer; -} -</style> - <br/><br/><ul class="manage-table-actions"> @@ -92,7 +85,7 @@ <div class="toolForm"><div class="toolFormTitle">Select files for transfer</div> - <form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', cntrller=cntrller, request_id=trans.security.encode_id( request.id )}" method="post" > + <form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', cntrller=cntrller, request_id=trans.security.encode_id( request.id ))}" method="post" ><div class="form-row"><label>Sample:</label> ${sample_id_select_field.get_html()} --- a/templates/requests/common/manage_request.mako +++ b/templates/requests/common/manage_request.mako @@ -62,7 +62,7 @@ // Build request data var ids = [] var states = [] - $.each( sample_states, function ( id, state ) { + $.each( sample_states, function ( id, state, cntrller ) { ids.push( id ); states.push( state ); }); @@ -73,7 +73,7 @@ dataType: "json", data: { ids: ids.join( "," ), states: states.join( "," ) }, success : function ( data ) { - $.each( data, function(id, val, cntrller ) { + $.each( data, function( cntrller, id, val ) { // Replace HTML var cell1 = $("#sampleState-" + id); cell1.html( val.html_state ); @@ -146,8 +146,6 @@ </div><br/><br/> -<font color="red"><b><i>A dataset can be renamed only if its status is "Not Started"</i></b></font> - <ul class="manage-table-actions"><li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li><div popupmenu="seqreq-${request.id}-popup">

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galaxy-dist commit 4d5b00b6fe74: Show Image type datasets inline in browser
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1287007951 14400 # Node ID 4d5b00b6fe741a35320a572302d1fb8bb7eb6971 # Parent 5f4ad373807158f8b2ac0bcaafab9f57b972e562 Show Image type datasets inline in browser --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -350,7 +350,7 @@ class DatasetInterface( BaseController, trans.response.set_content_type(mime) trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) - if to_ext or isinstance(data.datatype, datatypes.binary.Binary) or isinstance(data.datatype, datatypes.images.Image): # Saving the file, or binary/image file + if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file if data.extension in composite_extensions: return self.archive_composite_dataset( trans, data, **kwd ) else: @@ -366,13 +366,13 @@ class DatasetInterface( BaseController, raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) max_peek_size = 1000000 # 1 MB - if preview and os.stat( data.file_name ).st_size > max_peek_size: + if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size: + return open( data.file_name ) + else: trans.response.set_content_type( "text/html" ) return trans.stream_template_mako( "/dataset/large_file.mako", truncated_data = open( data.file_name ).read(max_peek_size), data = data ) - else: - return open( data.file_name ) @web.expose @web.require_login( "see all available datasets" )

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galaxy-dist commit c8173a50bc9b: sample_tracking fixes
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287030296 14400 # Node ID c8173a50bc9bdb0c8e07807c1b73be746557647f # Parent 4d5b00b6fe741a35320a572302d1fb8bb7eb6971 sample_tracking fixes --- a/templates/requests/common/sample_datasets.mako +++ b/templates/requests/common/sample_datasets.mako @@ -1,5 +1,5 @@ -<%def name="render_sample_datasets( cntrller, sample )"> - <a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.transferred_dataset_files} / ${len( sample.datasets )}</a> +<%def name="render_sample_datasets( sample )"> + ${sample.transferred_dataset_files} / ${len( sample.datasets )} </%def> -${render_sample_datasets( cntrller, sample )} +${render_sample_datasets( sample )} --- a/test/functional/test_forms_and_requests.py +++ b/test/functional/test_forms_and_requests.py @@ -160,8 +160,8 @@ class TestFormsAndRequests( TwillTestCas name = 'Test Requestype' self.create_request_type( name, "test sequencer configuration", - str( request_form.id ), - str( sample_form.id ), + self.security.encode_id( request_form.id ), + self.security.encode_id( sample_form.id ), sample_states, strings_displayed=[ 'Create a new sequencer configuration' ], strings_displayed_after_submit=[ "Sequencer configuration (%s) has been created" % name ] ) --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -88,7 +88,7 @@ class RequestsGrid( grids.Grid ): StateColumn( "State", key='state', filterable="advanced", - link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) ) + link=( lambda item: iff( item.deleted, None, dict( operation="request_events", id=item.id ) ) ) ) ] columns.append( grids.MulticolFilterColumn( "Search", @@ -105,7 +105,7 @@ class RequestsGrid( grids.Grid ): class RequestsCommon( BaseController, UsesFormDefinitionWidgets ): @web.json - def sample_state_updates( self, trans, cntrller, ids=None, states=None ): + def sample_state_updates( self, trans, ids=None, states=None ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' @@ -120,12 +120,10 @@ class RequestsCommon( BaseController, Us rval[ id ] = { "state": sample.state.name, "datasets": len( sample.datasets ), "html_state": unicode( trans.fill_template( "requests/common/sample_state.mako", - sample=sample, - cntrller=cntrller ), + sample=sample), 'utf-8' ), "html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako", - sample=sample, - cntrller=cntrller ), + sample=sample ), 'utf-8' ) } return rval @web.expose @@ -865,8 +863,6 @@ class RequestsCommon( BaseController, Us library_id = current_samples[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) folder_id = current_samples[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True ) name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( len( current_samples ) + 1 ) - library_id = 'none' - folder_id = 'none' field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ] else: # The user has not selected a sample to copy (may just be adding a sample). --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -52,6 +52,12 @@ class Requests( BaseController ): action='undelete_request', cntrller='requests', **kwd ) ) + if operation == "request_events": + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='request_events', + cntrller='requests', + **kwd ) ) + # If there are requests that have been rejected, show a message as a reminder to the user rejected = 0 for request in trans.sa_session.query( trans.app.model.Request ) \ --- a/templates/admin/requests/view_request_type.mako +++ b/templates/admin/requests/view_request_type.mako @@ -11,7 +11,7 @@ <div class="toolForm"><div class="toolFormTitle">Sequencer configuration information</div> - <form name="view_request_type" action="${h.url_for( controller='requests_admin', action='create_request_type', rt_id=request_type.id)}" method="post" > + <form name="view_request_type" action="${h.url_for( controller='requests_admin', action='create_request_type', rt_id=trans.security.encode_id( request_type.id ))}" method="post" ><div class="form-row"><label>Name</label> ${request_type.name} --- a/templates/requests/common/manage_request.mako +++ b/templates/requests/common/manage_request.mako @@ -62,7 +62,7 @@ // Build request data var ids = [] var states = [] - $.each( sample_states, function ( id, state, cntrller ) { + $.each( sample_states, function ( id, state ) { ids.push( id ); states.push( state ); }); @@ -73,7 +73,7 @@ dataType: "json", data: { ids: ids.join( "," ), states: states.join( "," ) }, success : function ( data ) { - $.each( data, function( cntrller, id, val ) { + $.each( data, function( id, val ) { // Replace HTML var cell1 = $("#sampleState-" + id); cell1.html( val.html_state ); @@ -140,7 +140,6 @@ <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> %endif <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">History</a> - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> %if is_admin: %if request.is_submitted: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> @@ -178,6 +177,13 @@ <h4><img src="/static/images/fugue/toggle-expand.png" alt="Show" onclick="showContent(this);" style="cursor:pointer;"/> Request Information</h4><div style="display:none;"> + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit request informaton</a> + </li> + </ul> + </div><table class="grid" border="0"><tbody><tr> @@ -452,7 +458,7 @@ %if sample.request.is_unsubmitted: <td>Unsubmitted</td> %else: - <td id="sampleState-${sample.id}">${render_sample_state( cntrller, sample )}</td> + <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if info['library']: %if cntrller == 'requests': @@ -469,9 +475,9 @@ <td></td> %endif %if request.is_submitted or request.is_complete: - <td id="sampleDatasets-${sample.id}"> - ${render_sample_datasets( cntrller, sample )} - </td> + <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}"> + ${render_sample_datasets( sample )} + </a></td> %endif %else: ${show_basic_info_form( sample_index, sample, info )} --- a/templates/requests/common/sample_state.mako +++ b/templates/requests/common/sample_state.mako @@ -1,5 +1,5 @@ -<%def name="render_sample_state( cntrller, sample )"> - <a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a> +<%def name="render_sample_state( sample )"> + ${sample.state.name} </%def> -${render_sample_state( cntrller, sample )} +${render_sample_state( sample )} --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -163,6 +163,11 @@ class RequestsAdmin( BaseController, Use action='manage_request', cntrller='requests_admin', **kwd ) ) + if operation == "request_events": + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='request_events', + cntrller='requests_admin', + **kwd ) ) if operation == "reject": return self.reject_request( trans, **kwd ) if operation == "view_type": @@ -423,7 +428,6 @@ class RequestsAdmin( BaseController, Use request_id=request_id, folder_path=folder_path, sample_id=sample.id, - open_folder=True, message=message, status=status ) ) # Get the filenames from the remote host @@ -590,21 +594,31 @@ class RequestsAdmin( BaseController, Use FOLDER_ID=str(sample.folder.id), DATASETS=datasets ) # Send the message - conn = amqp.Connection( host=trans.app.config.amqp['host'] + ":" + trans.app.config.amqp['port'], - userid=trans.app.config.amqp['userid'], - password=trans.app.config.amqp['password'], - virtual_host=trans.app.config.amqp['virtual_host'], - insist=False ) - chan = conn.channel() - msg = amqp.Message( data.replace( '\n', '' ).replace( '\r', '' ), - content_type='text/plain', - application_headers={'msg_type': 'data_transfer'} ) - msg.properties["delivery_mode"] = 2 - chan.basic_publish( msg, - exchange=trans.app.config.amqp['exchange'], - routing_key=trans.app.config.amqp['routing_key'] ) - chan.close() - conn.close() + try: + conn = amqp.Connection( host=trans.app.config.amqp['host'] + ":" + trans.app.config.amqp['port'], + userid=trans.app.config.amqp['userid'], + password=trans.app.config.amqp['password'], + virtual_host=trans.app.config.amqp['virtual_host'], + insist=False ) + chan = conn.channel() + msg = amqp.Message( data.replace( '\n', '' ).replace( '\r', '' ), + content_type='text/plain', + application_headers={'msg_type': 'data_transfer'} ) + msg.properties["delivery_mode"] = 2 + chan.basic_publish( msg, + exchange=trans.app.config.amqp['exchange'], + routing_key=trans.app.config.amqp['routing_key'] ) + chan.close() + conn.close() + except Exception, e: + message = "Error in sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e) + status = "error" + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_datasets', + sample_id=trans.security.encode_id( sample.id ), + status=status, + message=message) ) + def __start_datatx( self, trans, sample, selected_sample_datasets ): datatx_user = self.__setup_datatx_user( trans, sample.library, sample.folder ) # Validate sequencer information

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galaxy-dist commit 1c8a5958c748: Use dropdown (default) rather than radio for BLAST databases as could be lots of them
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285945041 -3600 # Node ID 1c8a5958c7481e53e862dbdf44d5367b6f3fc271 # Parent 477eb3cceae79d93be845a8540572033f208ae73 Use dropdown (default) rather than radio for BLAST databases as could be lots of them --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -24,7 +24,7 @@ <option value="file">FASTA file</option></param><when value="db"> - <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <param name="database" type="select" label="Nucleotide BLAST database"><options from_file="blastdb.loc"><column name="name" index="0"/><column name="value" index="1"/> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -23,7 +23,7 @@ <option value="file">FASTA file</option></param><when value="db"> - <param name="database" type="select" display="radio" label="Protein BLAST database"> + <param name="database" type="select" label="Protein BLAST database"><options from_file="blastdb_p.loc"><column name="name" index="0"/><column name="value" index="1"/> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -23,7 +23,7 @@ <option value="file">FASTA file</option></param><when value="db"> - <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <param name="database" type="select" label="Nucleotide BLAST database"><options from_file="blastdb.loc"><column name="name" index="0"/><column name="value" index="1"/> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -23,7 +23,7 @@ <option value="file">FASTA file</option></param><when value="db"> - <param name="database" type="select" display="radio" label="Protein BLAST database"> + <param name="database" type="select" label="Protein BLAST database"><options from_file="blastdb_p.loc"><column name="name" index="0"/><column name="value" index="1"/> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -22,7 +22,7 @@ <option value="file">FASTA file</option></param><when value="db"> - <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <param name="database" type="select" label="Nucleotide BLAST database"><options from_file="blastdb.loc"><column name="name" index="0"/><column name="value" index="1"/>

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galaxy-dist commit 9bf65ebafa8f: Reduce whitespace in <command> tag (there are OS limits on command line length)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286366018 -3600 # Node ID 9bf65ebafa8fc89115a5b42ebb9865ed99c1cf84 # Parent 6273161e76c33f807145d9b12eafa0a6e414bbf1 Reduce whitespace in <command> tag (there are OS limits on command line length) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -1,20 +1,21 @@ <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.1"><description>Search nucleotide database with nucleotide query sequence(s)</description><command> - blastn - -query "$query" +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastn -query "$query" #if $db_opts.db_opts_selector == "db": - -db "$db_opts.database" + -db "$db_opts.database" #else: - -subject "$db_opts.subject" + -subject "$db_opts.subject" #end if - -task $blast_type - -evalue $evalue_cutoff - $adv_opts.filter_query - $adv_opts.strand - -out $output1 - -outfmt $out_format - -num_threads 8 +-task $blast_type +-evalue $evalue_cutoff +$adv_opts.filter_query +$adv_opts.strand +-out $output1 +-outfmt $out_format +-num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -1,20 +1,22 @@ <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.1"><description>Search protein database with protein query sequence(s)</description><command> - blastp - -query "$query" +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastp +-query "$query" #if $db_opts.db_opts_selector == "db": - -db "$db_opts.database" + -db "$db_opts.database" #else: - -subject "$db_opts.subject" + -subject "$db_opts.subject" #end if - -task $blast_type - -evalue $evalue_cutoff - $adv_opts.filter_query - $adv_opts.matrix - -out $output1 - -outfmt $out_format - -num_threads 8 +-task $blast_type +-evalue $evalue_cutoff +$adv_opts.filter_query +$adv_opts.matrix +-out $output1 +-outfmt $out_format +-num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -1,20 +1,22 @@ <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.1"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description><command> - tblastx - -query "$query" +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +tblastx +-query "$query" #if $db_opts.db_opts_selector == "db": - -db "$db_opts.database" + -db "$db_opts.database" #else: - -subject "$db_opts.subject" + -subject "$db_opts.subject" #end if - -evalue $evalue_cutoff - $adv_opts.filter_query - $adv_opts.strand - $adv_opts.matrix - -out $output1 - -outfmt $out_format - -num_threads 8 +-evalue $evalue_cutoff +$adv_opts.filter_query +$adv_opts.strand +$adv_opts.matrix +-out $output1 +-outfmt $out_format +-num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -1,20 +1,22 @@ <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.1"><description>Search protein database with translated nucleotide query sequence(s)</description><command> - blastx - -query "$query" +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastx +-query "$query" #if $db_opts.db_opts_selector == "db": - -db "$db_opts.database" + -db "$db_opts.database" #else: - -subject "$db_opts.subject" + -subject "$db_opts.subject" #end if - -evalue $evalue_cutoff - $adv_opts.filter_query - $adv_opts.strand - $adv_opts.matrix - -out $output1 - -outfmt $out_format - -num_threads 8 +-evalue $evalue_cutoff +$adv_opts.filter_query +$adv_opts.strand +$adv_opts.matrix +-out $output1 +-outfmt $out_format +-num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -1,19 +1,21 @@ <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.1"><description>Search translated nucleotide database with protein query sequence(s)</description><command> - tblastn - -query "$query" +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +tblastn +-query "$query" #if $db_opts.db_opts_selector == "db": - -db "$db_opts.database" + -db "$db_opts.database" #else: - -subject "$db_opts.subject" + -subject "$db_opts.subject" #end if - -evalue $evalue_cutoff - $adv_opts.filter_query - $adv_opts.matrix - -out $output1 - -outfmt $out_format - -num_threads 8 +-evalue $evalue_cutoff +$adv_opts.filter_query +$adv_opts.matrix +-out $output1 +-outfmt $out_format +-num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>

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galaxy-dist commit c4c2b6eea3e1: Added support for BLAST+ -max_target_seqs option
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286381268 -3600 # Node ID c4c2b6eea3e11ee8a024b32f58419f7b1d36f114 # Parent 9bf65ebafa8fc89115a5b42ebb9865ed99c1cf84 Added support for BLAST+ -max_target_seqs option --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -3,7 +3,8 @@ <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces -blastn -query "$query" +blastn +-query "$query" #if $db_opts.db_opts_selector == "db": -db "$db_opts.database" #else: @@ -16,6 +17,11 @@ blastn -query "$query" -out $output1 -outfmt $out_format -num_threads 8 +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -62,6 +68,7 @@ blastn -query "$query" <when value="basic"><param name="filter_query" type="hidden" value="" /><param name="strand" type="hidden" value="" /> + <param name="max_hits" type="hidden" value="" /></when><when value="advanced"> @@ -71,6 +78,10 @@ blastn -query "$query" <option value="-strand plus">Plus (forward)</option><option value="-strand minus">Minus (reverse complement)</option></param> +  + <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -17,6 +17,11 @@ blastp -out $output1 -outfmt $out_format -num_threads 8 +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -60,6 +65,7 @@ blastp <when value="basic"><param name="filter_query" type="hidden" value="" /><param name="matrix" type="hidden" value="" /> + <param name="max_hits" type="hidden" value="" /></when><when value="advanced"> @@ -74,6 +80,10 @@ blastp <option value="-matrix PAM70">PAM70</option><option value="-matrix PAM30">PAM30</option></param> +  + <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -17,6 +17,11 @@ tblastx -out $output1 -outfmt $out_format -num_threads 8 +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -57,6 +62,7 @@ tblastx <param name="filter_query" type="hidden" value="" /><param name="strand" type="hidden" value="" /><param name="matrix" type="hidden" value="" /> + <param name="max_hits" type="hidden" value="" /></when><when value="advanced"> @@ -76,6 +82,10 @@ tblastx <option value="-matrix PAM70">PAM70</option><option value="-matrix PAM30">PAM30</option></param> +  + <param name="max_hits" type="integer" value="0" lable="Maximum hits to show (in plain text output)" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -17,6 +17,11 @@ blastx -out $output1 -outfmt $out_format -num_threads 8 +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -57,6 +62,7 @@ blastx <param name="filter_query" type="hidden" value="" /><param name="strand" type="hidden" value="" /><param name="matrix" type="hidden" value="" /> + <param name="max_hits" type="hidden" value="" /></when><when value="advanced"> @@ -76,7 +82,10 @@ blastx <option value="-matrix PAM70">PAM70</option><option value="-matrix PAM30">PAM30</option></param> - +  + <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -16,6 +16,11 @@ tblastn -out $output1 -outfmt $out_format -num_threads 8 +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -55,6 +60,7 @@ tblastn <when value="basic"><param name="filter_query" type="hidden" value="" /><param name="matrix" type="hidden" value="" /> + <param name="max_hits" type="hidden" value="" /></when><when value="advanced"> @@ -69,6 +75,10 @@ tblastn <option value="-matrix PAM70">PAM70</option><option value="-matrix PAM30">PAM30</option></param> +  + <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs>

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