galaxy-dev November 2009

galaxy-dev@lists.galaxyproject.org

26 participants
233 discussions

[hg] galaxy 2932: Page create fix
by Greg Von Kuster 08 Nov '09

08 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5d80e32d989b changeset: 2932:5d80e32d989b user: James Taylor <james(a)jamestaylor.org> date: Thu Oct 29 13:34:44 2009 -0400 description: Page create fix diffstat: lib/galaxy/web/controllers/page.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (14 lines): diff -r 86cc0b2b9e09 -r 5d80e32d989b lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Thu Oct 29 10:06:11 2009 -0400 +++ b/lib/galaxy/web/controllers/page.py Thu Oct 29 13:34:44 2009 -0400 @@ -138,8 +138,8 @@ session.save_or_update( page ) session.flush() # Display the management page - trans.set_message( "Page '%s' created" % page.title ) - return self.list( trans ) + ## trans.set_message( "Page '%s' created" % page.title ) + return trans.response.send_redirect( web.url_for( action='index' ) ) return trans.show_form( web.FormBuilder( web.url_for(), "Create new page", submit_text="Submit" ) .add_text( "page_title", "Page title", value=page_title, error=page_title_err )

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[hg] galaxy 2933: updated rgenetics test files
by Greg Von Kuster 08 Nov '09

08 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/28ec4708840f changeset: 2933:28ec4708840f user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Thu Oct 29 17:57:30 2009 -0400 description: updated rgenetics test files diffstat: test-data/tinywga.bed | 2 +- test-data/tinywga.bim | 35 ++++++++--- test-data/tinywga.fam | 130 +++++++++++++------------------------------ test-data/tinywga.map | 35 ++++++++--- test-data/tinywga.ped | 130 +++++++++++++------------------------------ test-data/tinywga.pphe | 42 ++++++++++++++ 6 files changed, 173 insertions(+), 201 deletions(-) diffs (400 lines): diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.bed --- a/test-data/tinywga.bed Thu Oct 29 13:34:44 2009 -0400 +++ b/test-data/tinywga.bed Thu Oct 29 17:57:30 2009 -0400 @@ -1,1 +1,1 @@ -lÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿï¾î¸ÿÿüþ¿ÿ¿ûú¿¿ï/ÿÿþÿï¯ê¸ëê°®¾î®ãê¸;ì/âïú¯ï¯Îê¼ïâ°¯þÏªã¯ø+ì?âÿú¯ïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïÿÿÿÿÿºÿÿþ¯þï¿ÿ»ÿÿþÿÿÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿÿÿÿÿþïÿÿÿþÿÿÿÿûÿûÿÿÿ»ÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïëÿê¾ÿºúïþ¯îë¿þ;¯>âïþ» \ No newline at end of file +lÿëþ¿¾+êóª¿ü £ïªîþ¨êÿïªûÿÿÿÿÿÿþï®¨ª"ëú £ïªîþ¨ÿÿ»ÿÿïïþÿèÿþ"ÿ«ïªîþ¨:*ÿïêüº.«ë:*ÿïêüº.«ëÿÿÿÿ¯ÿ¿ïþ¿ÿþªÿ¯û¿ïþ¿:*»ïêìª,«À:*»ïêìª,«Àÿëþ¿¾+êóª¿ÿÿÿÿûÿúÿÿÿÿÿÿÿÿÿ¿þ¿ÿëþ¿¾+êóª¿ºûÿÿ¿»ÿÿþ¿êÿÿªûÿÿÿÿÿºûÿÿ¿»ÿÿþ¿mÿÿÿýÿÿÿÿÿ ú¢ª±«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü( \ No newline at end of file diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.bim --- a/test-data/tinywga.bim Thu Oct 29 13:34:44 2009 -0400 +++ b/test-data/tinywga.bim Thu Oct 29 17:57:30 2009 -0400 @@ -1,10 +1,25 @@ -22 rs5992809 16.5965 16596539 0 C -22 rs12168131 16.6573 16657262 G A -22 rs390041 16.6629 16662916 T C -22 rs437633 16.6697 16669684 A G -22 rs450960 16.6909 16690858 T C -22 rs450975 16.6909 16690887 T C -22 rs451740 16.6912 16691174 T C -22 rs8139723 16.6917 16691696 T C -22 rs405490 16.6922 16692175 G A -22 rs415170 16.6935 16693517 G C +22 rs2283802 0 21784722 4 2 +22 rs2267000 0 21785366 4 2 +22 rs16997606 0 21794754 1 3 +22 rs4820537 0 21794810 1 3 +22 rs3788347 0 21797804 3 1 +22 rs756632 0 21799918 4 2 +22 rs4820539 0 21807970 1 3 +22 rs2283804 0 21820335 1 2 +22 rs2267006 0 21820990 3 1 +22 rs4822363 0 21821000 4 2 +22 rs5751592 0 21827674 4 2 +22 rs5759608 0 21832708 2 4 +22 rs5759612 0 21833170 3 1 +22 rs2267009 0 21860168 3 4 +22 rs2267010 0 21864366 3 1 +22 rs5759636 0 21868698 4 2 +22 rs2071436 0 21871488 4 2 +22 rs2267013 0 21875879 3 1 +22 rs6003566 0 21889806 3 1 +22 rs2256725 0 21892891 2 1 +22 rs12160770 0 21892925 1 3 +22 rs5751611 0 21896019 2 4 +22 rs762601 0 21898858 1 3 +22 rs2156921 0 21899063 3 1 +22 rs4822375 0 21905642 1 3 diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.fam --- a/test-data/tinywga.fam Thu Oct 29 13:34:44 2009 -0400 +++ b/test-data/tinywga.fam Thu Oct 29 17:57:30 2009 -0400 @@ -1,90 +1,40 @@ -CH18526 NA18526 0 0 2 1 -CH18524 NA18524 0 0 1 1 -CH18529 NA18529 0 0 2 1 -CH18558 NA18558 0 0 1 1 -CH18532 NA18532 0 0 2 1 -CH18561 NA18561 0 0 1 1 -CH18562 NA18562 0 0 1 1 -CH18537 NA18537 0 0 2 2 -CH18603 NA18603 0 0 1 2 -CH18540 NA18540 0 0 2 1 -CH18605 NA18605 0 0 1 1 -CH18542 NA18542 0 0 2 1 -CH18545 NA18545 0 0 2 1 -CH18572 NA18572 0 0 1 2 -CH18547 NA18547 0 0 2 2 -CH18609 NA18609 0 0 1 1 -CH18550 NA18550 0 0 2 1 -CH18608 NA18608 0 0 1 1 -CH18552 NA18552 0 0 2 1 -CH18611 NA18611 0 0 1 1 -CH18555 NA18555 0 0 2 1 -CH18564 NA18564 0 0 2 2 -CH18566 NA18566 0 0 2 1 -CH18563 NA18563 0 0 1 1 -CH18570 NA18570 0 0 2 1 -CH18612 NA18612 0 0 1 2 -CH18571 NA18571 0 0 2 1 -CH18620 NA18620 0 0 1 1 -CH18621 NA18621 0 0 1 1 -CH18594 NA18594 0 0 2 1 -CH18622 NA18622 0 0 1 2 -CH18573 NA18573 0 0 2 2 -CH18623 NA18623 0 0 1 1 -CH18576 NA18576 0 0 2 1 -CH18577 NA18577 0 0 2 1 -CH18624 NA18624 0 0 1 1 -CH18579 NA18579 0 0 2 1 -CH18632 NA18632 0 0 1 2 -CH18582 NA18582 0 0 2 1 -CH18633 NA18633 0 0 1 1 -CH18635 NA18635 0 0 1 2 -CH18592 NA18592 0 0 2 1 -CH18636 NA18636 0 0 1 1 -CH18593 NA18593 0 0 2 2 -CH18637 NA18637 0 0 1 1 -JA18942 NA18942 0 0 2 2 -JA18940 NA18940 0 0 1 2 -JA18951 NA18951 0 0 2 2 -JA18943 NA18943 0 0 1 2 -JA18947 NA18947 0 0 2 2 -JA18944 NA18944 0 0 1 2 -JA18945 NA18945 0 0 1 2 -JA18949 NA18949 0 0 2 2 -JA18948 NA18948 0 0 1 2 -JA18952 NA18952 0 0 1 2 -JA18956 NA18956 0 0 2 2 -JA18964 NA18964 0 0 2 2 -JA18953 NA18953 0 0 1 1 -JA18968 NA18968 0 0 2 2 -JA18959 NA18959 0 0 1 2 -JA18969 NA18969 0 0 2 1 -JA18960 NA18960 0 0 1 2 -JA18961 NA18961 0 0 1 2 -JA18972 NA18972 0 0 2 2 -JA18965 NA18965 0 0 1 2 -JA18973 NA18973 0 0 2 2 -JA18966 NA18966 0 0 1 2 -JA18975 NA18975 0 0 2 2 -JA18967 NA18967 0 0 1 2 -JA18976 NA18976 0 0 2 1 -JA18978 NA18978 0 0 2 2 -JA18970 NA18970 0 0 1 1 -JA18980 NA18980 0 0 2 2 -JA18995 NA18995 0 0 1 1 -JA18981 NA18981 0 0 2 2 -JA18971 NA18971 0 0 1 2 -JA18974 NA18974 0 0 1 1 -JA18987 NA18987 0 0 2 2 -JA18990 NA18990 0 0 1 1 -JA18991 NA18991 0 0 2 2 -JA18994 NA18994 0 0 1 2 -JA18992 NA18992 0 0 2 2 -JA18997 NA18997 0 0 2 2 -JA18998 NA18998 0 0 2 2 -JA19000 NA19000 0 0 1 2 -JA19005 NA19005 0 0 1 2 -JA18999 NA18999 0 0 2 2 -JA19007 NA19007 0 0 1 2 -JA19003 NA19003 0 0 2 2 -JA19012 NA19012 0 0 1 2 +101 1 3 2 2 2 +101 2 0 0 2 1 +101 3 0 0 1 1 +105 1 3 2 2 2 +105 2 0 0 2 1 +105 3 0 0 1 1 +112 1 3 2 1 2 +112 2 0 0 2 1 +112 3 0 0 1 1 +117 1 3 2 2 2 +117 2 0 0 2 1 +117 3 0 0 1 1 +12 1 3 2 1 2 +12 2 0 0 2 1 +12 3 0 0 1 1 +13 1 3 2 1 2 +13 2 0 0 2 1 +13 3 0 0 1 1 +1334 1 10 11 1 2 +1334 10 0 0 1 1 +1334 11 0 0 2 1 +1334 12 0 0 1 1 +1334 13 0 0 2 1 +1334 2 12 13 2 2 +1340 1 9 10 1 2 +1340 10 0 0 2 1 +1340 11 0 0 1 1 +1340 12 0 0 2 1 +1340 2 11 12 2 2 +1340 9 0 0 1 1 +1341 1 11 12 1 1 +1341 11 0 0 1 1 +1341 12 0 0 2 1 +1341 13 0 0 1 1 +1341 14 0 0 2 1 +1341 2 13 14 2 1 +1344 1 12 13 1 1 +1344 12 0 0 1 1 +1344 13 0 0 2 1 +1345 12 0 0 1 1 diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.map --- a/test-data/tinywga.map Thu Oct 29 13:34:44 2009 -0400 +++ b/test-data/tinywga.map Thu Oct 29 17:57:30 2009 -0400 @@ -1,10 +1,25 @@ -22 rs5992809 16.5965 16596539 -22 rs12168131 16.6573 16657262 -22 rs390041 16.6629 16662916 -22 rs437633 16.6697 16669684 -22 rs450960 16.6909 16690858 -22 rs450975 16.6909 16690887 -22 rs451740 16.6912 16691174 -22 rs8139723 16.6917 16691696 -22 rs405490 16.6922 16692175 -22 rs415170 16.6935 16693517 +22 rs2283802 0 21784722 +22 rs2267000 0 21785366 +22 rs16997606 0 21794754 +22 rs4820537 0 21794810 +22 rs3788347 0 21797804 +22 rs756632 0 21799918 +22 rs4820539 0 21807970 +22 rs2283804 0 21820335 +22 rs2267006 0 21820990 +22 rs4822363 0 21821000 +22 rs5751592 0 21827674 +22 rs5759608 0 21832708 +22 rs5759612 0 21833170 +22 rs2267009 0 21860168 +22 rs2267010 0 21864366 +22 rs5759636 0 21868698 +22 rs2071436 0 21871488 +22 rs2267013 0 21875879 +22 rs6003566 0 21889806 +22 rs2256725 0 21892891 +22 rs12160770 0 21892925 +22 rs5751611 0 21896019 +22 rs762601 0 21898858 +22 rs2156921 0 21899063 +22 rs4822375 0 21905642 diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.ped --- a/test-data/tinywga.ped Thu Oct 29 13:34:44 2009 -0400 +++ b/test-data/tinywga.ped Thu Oct 29 17:57:30 2009 -0400 @@ -1,90 +1,40 @@ -CH18526 NA18526 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18524 NA18524 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18529 NA18529 0 0 2 1 C C A A T C A G T C T C T C C C G A G C -CH18558 NA18558 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18532 NA18532 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18561 NA18561 0 0 1 1 C C A A C C G G T C C C T C C C G A G C -CH18562 NA18562 0 0 1 1 C C G A T C A G T C C C T C C C G A G C -CH18537 NA18537 0 0 2 2 C C A A T C A G C C C C C C C C A A C C -CH18603 NA18603 0 0 1 2 C C G A T C A G C C C C C C C C A A C C -CH18540 NA18540 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18605 NA18605 0 0 1 1 C C A A T T A A C C C C C C C C A A C C -CH18542 NA18542 0 0 2 1 C C G A T C G G C C C C C C C C A A C C -CH18545 NA18545 0 0 2 1 C C G A T C A G T C C C T C C C G A G C -CH18572 NA18572 0 0 1 2 C C A A T C A G C C C C C C C C A A G C -CH18547 NA18547 0 0 2 2 C C G A T C A G T C C C T C C C G A G C -CH18609 NA18609 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18550 NA18550 0 0 2 1 C C G G T T A A T C C C T C T C G A G C -CH18608 NA18608 0 0 1 1 C C G A T C G G C C C C C C C C A A C C -CH18552 NA18552 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18611 NA18611 0 0 1 1 C C G A T C A G T C C C T C C C G A G C -CH18555 NA18555 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18564 NA18564 0 0 2 2 C C A A T C G G C C C C C C C C A A C C -CH18566 NA18566 0 0 2 1 C C A A T C A G C C C C C C T C A A C C -CH18563 NA18563 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -CH18570 NA18570 0 0 2 1 C C A A T C A G T C T C T C C C G A G C -CH18612 NA18612 0 0 1 2 C C A A T C A A T C T C T C C C G A G C -CH18571 NA18571 0 0 2 1 C C A A T C A G C C C C C C C C A A C C -CH18620 NA18620 0 0 1 1 C C A A C C G G T C T C T C C C G A G C -CH18621 NA18621 0 0 1 1 C C G G T T A A T C C C T C C C G A G C -CH18594 NA18594 0 0 2 1 C C A A T T A A C C C C C C C C A A G C -CH18622 NA18622 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -CH18573 NA18573 0 0 2 2 C C A A T C A G C C C C C C C C A A C C -CH18623 NA18623 0 0 1 1 C C G A T C G G C C C C C C C C A A C C -CH18576 NA18576 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18577 NA18577 0 0 2 1 C C A A T C A G C C C C C C C C A A G C -CH18624 NA18624 0 0 1 1 C C A A T C A G C C C C C C C C A A C C -CH18579 NA18579 0 0 2 1 C C A A T C A G T C T C T C T C G A G C -CH18632 NA18632 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -CH18582 NA18582 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18633 NA18633 0 0 1 1 C C G A T C G G C C C C C C C C A A C C -CH18635 NA18635 0 0 1 2 C C A A T C G G C C C C C C C C A A C C -CH18592 NA18592 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -CH18636 NA18636 0 0 1 1 C C A A T C A A T C T C T C C C G A G C -CH18593 NA18593 0 0 2 2 C C A A C C G G T C T C T C C C G A G C -CH18637 NA18637 0 0 1 1 C C A A T C A G T C T C T C C C G A G C -JA18942 NA18942 0 0 2 2 C C A A C C A G C C C C C C C C A A C C -JA18940 NA18940 0 0 1 2 C C A A T C A G C C C C C C C C A A G C -JA18951 NA18951 0 0 2 2 C C G A T C A G C C C C C C C C A A C C -JA18943 NA18943 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA18947 NA18947 0 0 2 2 C C G A T T A A C C C C C C C C A A G C -JA18944 NA18944 0 0 1 2 C C A A T C A G T C T C T C C C G A G C -JA18945 NA18945 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA18949 NA18949 0 0 2 2 C C G A T C G G C C C C C C C C A A C C -JA18948 NA18948 0 0 1 2 C C G A T C G G C C C C C C C C A A C C -JA18952 NA18952 0 0 1 2 C C A A T C A G C C C C C C C C A A C C -JA18956 NA18956 0 0 2 2 C C A A C C A G T C T C T C C C G A G C -JA18964 NA18964 0 0 2 2 C C A A T T A A C C C C C C C C A A G C -JA18953 NA18953 0 0 1 1 C C A A T C A G C C C C C C T C A A C C -JA18968 NA18968 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18959 NA18959 0 0 1 2 C C G A T C G G C C C C C C C C A A C C -JA18969 NA18969 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -JA18960 NA18960 0 0 1 2 C C A A T C A G T C T C T C C C G A G C -JA18961 NA18961 0 0 1 2 C C A A C C A G C C C C C C C C A A C C -JA18972 NA18972 0 0 2 2 C C G A T T A A T T T C T T C C G G G G -JA18965 NA18965 0 0 1 2 C C A A T T A A C C C C C C C C A A C C -JA18973 NA18973 0 0 2 2 C C A A C C G G C C C C C C T C A A C C -JA18966 NA18966 0 0 1 2 C C G A T C A G T C C C T C C C G A G C -JA18975 NA18975 0 0 2 2 C C A A C C G G C C C C C C C C A A G C -JA18967 NA18967 0 0 1 2 C C A A C C G G C C C C C C C C A A G C -JA18976 NA18976 0 0 2 1 C C A A C C G G C C C C C C C C A A C C -JA18978 NA18978 0 0 2 2 C C G A T C G G C C C C C C C C A A C C -JA18970 NA18970 0 0 1 1 C C G G T T A A T T C C T T C C G G G G -JA18980 NA18980 0 0 2 2 C C A A T C A G T C T C T C C C G A G C -JA18995 NA18995 0 0 1 1 C C A A T T A A C C C C C C C C A A G G -JA18981 NA18981 0 0 2 2 C C A A T C A G C C C C C C C C A A G C -JA18971 NA18971 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA18974 NA18974 0 0 1 1 C C A A C C G G C C C C C C C C A A C C -JA18987 NA18987 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18990 NA18990 0 0 1 1 C C A A T C G G C C C C C C C C A A G C -JA18991 NA18991 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18994 NA18994 0 0 1 2 C C G A T C A G C C C C C C C C A A G C -JA18992 NA18992 0 0 2 2 C C A A T C A G C C C C C C T C A A C C -JA18997 NA18997 0 0 2 2 C C A A C C G G C C C C C C C C A A C C -JA18998 NA18998 0 0 2 2 C C A A C C G G C C C C C C T C A A C C -JA19000 NA19000 0 0 1 2 C C A A C C G G C C C C C C C C A A C C -JA19005 NA19005 0 0 1 2 C C A A C C G G C C C C C C C C A A G C -JA18999 NA18999 0 0 2 2 C C A A T C A G C C C C C C C C A A C C -JA19007 NA19007 0 0 1 2 C C A A T C A G C C C C C C C C A A G C -JA19003 NA19003 0 0 2 2 C C A A T C G G C C C C C C C C A A C C -JA19012 NA19012 0 0 1 2 C C A A 0 0 G G C C C C C C 0 0 A A C C +101 1 3 2 2 2 2 2 4 2 1 3 3 3 3 3 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 3 1 3 1 2 1 0 0 2 2 1 3 3 1 1 3 +101 2 0 0 2 1 2 2 4 2 1 3 3 3 3 3 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 3 1 3 1 2 1 3 3 2 2 1 3 3 1 1 3 +101 3 0 0 1 1 2 2 4 4 1 3 3 3 3 3 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 1 3 2 4 3 3 1 1 3 3 +105 1 3 2 2 2 2 2 4 2 3 3 3 3 3 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 3 1 1 1 2 1 0 0 2 2 1 1 3 3 1 1 +105 2 0 0 2 1 2 2 4 4 3 3 3 3 3 1 2 2 1 3 1 2 3 1 2 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +105 3 0 0 1 1 4 2 2 2 3 3 3 3 3 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +112 1 3 2 1 2 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +112 2 0 0 2 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +112 3 0 0 1 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 2 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +117 1 3 2 2 2 2 2 4 2 3 3 3 3 3 3 4 2 1 1 2 2 1 1 2 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1 +117 2 0 0 2 1 2 2 4 4 1 3 3 3 3 3 2 2 1 3 2 2 1 1 2 2 4 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +117 3 0 0 1 1 2 2 4 2 3 3 3 3 3 3 4 2 1 1 2 2 1 1 2 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +12 1 3 2 1 2 2 2 4 4 1 3 3 3 3 3 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3 +12 2 0 0 2 1 2 2 4 4 1 3 3 3 3 3 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3 +12 3 0 0 1 1 2 2 4 2 1 3 1 3 3 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3 +13 1 3 2 1 2 4 2 4 2 1 3 3 3 3 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 4 1 1 2 2 4 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3 +13 2 0 0 2 1 4 2 2 2 3 3 1 3 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 0 0 0 0 3 3 1 1 3 3 +13 3 0 0 1 1 2 2 4 4 1 3 3 3 3 3 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 3 1 2 2 2 2 1 1 3 1 1 1 3 3 2 2 3 3 1 1 3 3 +1334 1 10 11 1 2 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1334 10 0 0 1 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +1334 11 0 0 2 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1334 12 0 0 1 1 4 2 2 2 3 3 1 3 1 1 2 2 3 3 2 2 1 1 2 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +1334 13 0 0 2 1 4 2 4 2 3 3 1 3 3 1 4 2 1 3 2 2 1 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1334 2 12 13 2 2 4 4 2 2 3 3 1 3 1 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 3 1 1 2 2 4 4 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3 +1340 1 9 10 1 2 4 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 3 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1340 10 0 0 2 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 3 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1340 11 0 0 1 1 4 2 4 2 3 3 1 3 3 1 4 2 1 3 2 2 1 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1340 12 0 0 2 1 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 4 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1340 2 11 12 2 2 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1340 9 0 0 1 1 4 4 2 2 3 3 1 1 1 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 3 1 1 2 2 4 4 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1341 1 11 12 1 1 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 0 0 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1 +1341 11 0 0 1 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 4 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1341 12 0 0 2 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 4 2 4 2 3 1 1 1 2 1 3 3 2 2 1 1 3 3 1 1 +1341 13 0 0 1 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1341 14 0 0 2 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1341 2 13 14 2 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3 +1344 1 12 13 1 1 2 2 4 4 3 3 3 3 3 3 4 4 1 1 2 2 1 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1 +1344 12 0 0 1 1 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1344 13 0 0 2 1 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3 +1345 12 0 0 1 1 4 2 4 2 3 3 3 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 4 2 4 2 3 1 1 1 2 1 3 3 2 2 1 1 3 3 1 1 diff -r 5d80e32d989b -r 28ec4708840f test-data/tinywga.pphe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tinywga.pphe Thu Oct 29 17:57:30 2009 -0400 @@ -0,0 +1,42 @@ +FID IID c1 c2 +101 1 0.545103 0.918463 +101 2 0.491123 0.309616 +101 3 0.651988 0.048298 +105 1 0.424657 0.853486 +105 2 0.813036 0.767600 +105 3 0.042279 0.786226 +112 1 0.538062 0.116152 +112 2 0.038197 0.911567 +112 3 0.991881 0.647654 +117 1 0.553303 0.672842 +117 2 0.231171 0.197314 +117 3 0.245332 0.517846 +12 1 0.311838 0.108011 +12 2 0.764390 0.968887 +12 3 0.393993 0.857926 +13 1 0.291201 0.288068 +13 2 0.113351 0.782368 +13 3 0.130878 0.927257 +1334 1 0.539897 0.932499 +1334 10 0.204083 0.893518 +1334 11 0.441118 0.900758 +1334 12 0.325336 0.271307 +1334 13 0.910762 0.636606 +1334 2 0.630607 0.537458 +1340 1 0.598157 0.813064 +1340 10 0.162311 0.956523 +1340 11 0.891147 0.987962 +1340 12 0.302027 0.786424 +1340 2 0.375225 0.338616 +1340 9 0.691503 0.965552 +1341 1 0.971333 0.115437 +1341 11 0.171352 0.873480 +1341 12 0.778930 0.179902 +1341 13 0.092468 0.050435 +1341 14 0.898538 0.913943 +1341 2 0.969939 0.086483 +1344 1 0.318008 0.376770 +1344 12 0.290673 0.870879 +1344 13 0.716322 0.087859 +1345 12 0.886441 0.717204 +

1 0

[hg] galaxy 2934: trackster: fixed browser crashing (were drawin...
by Greg Von Kuster 08 Nov '09

08 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/979534de254d changeset: 2934:979534de254d user: Kanwei Li <kanwei(a)gmail.com> date: Thu Oct 29 18:28:11 2009 -0400 description: trackster: fixed browser crashing (were drawing huge canvas tiles because of resolution restriction), implemented simple LRU diffstat: static/scripts/lrucache.js | 238 --------------------------------------- static/scripts/packed/lrucache.js | 1 - static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 46 ++++++- templates/tracks/browser.mako | 2 +- 5 files changed, 39 insertions(+), 250 deletions(-) diffs (359 lines): diff -r 28ec4708840f -r 979534de254d static/scripts/lrucache.js --- a/static/scripts/lrucache.js Thu Oct 29 17:57:30 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,238 +0,0 @@ -/* -MIT LICENSE -Copyright (c) 2007 Monsur Hossain (http://www.monsur.com) - -Permission is hereby granted, free of charge, to any person -obtaining a copy of this software and associated documentation -files (the "Software"), to deal in the Software without -restriction, including without limitation the rights to use, -copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the -Software is furnished to do so, subject to the following -conditions: - -The above copyright notice and this permission notice shall be -included in all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES -OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR -OTHER DEALINGS IN THE SOFTWARE. -*/ - -// **************************************************************************** -// CachePriority ENUM -// An easier way to refer to the priority of a cache item -var CachePriority = { - Low: 1, - Normal: 2, - High: 4 -} - -// **************************************************************************** -// Cache constructor -// Creates a new cache object -// INPUT: maxSize (optional) - indicates how many items the cache can hold. -// default is -1, which means no limit on the -// number of items. -function Cache(maxSize) { - this.items = {}; - this.count = 0; - if (maxSize == null) - maxSize = -1; - this.maxSize = maxSize; - this.fillFactor = .75; - this.purgeSize = Math.round(this.maxSize * this.fillFactor); - - this.stats = {} - this.stats.hits = 0; - this.stats.misses = 0; -} - -// **************************************************************************** -// Cache.getItem -// retrieves an item from the cache, returns null if the item doesn't exist -// or it is expired. -// INPUT: key - the key to load from the cache -Cache.prototype.getItem = function(key) { - - // retrieve the item from the cache - var item = this.items[key]; - - if (item != null) { - if (!this._isExpired(item)) { - // if the item is not expired - // update its last accessed date - item.lastAccessed = new Date().getTime(); - } else { - // if the item is expired, remove it from the cache - this._removeItem(key); - item = null; - } - } - - // return the item value (if it exists), or null - var returnVal = null; - if (item != null) { - returnVal = item.value; - this.stats.hits++; - } else { - this.stats.misses++; - } - return returnVal; -} - -// **************************************************************************** -// Cache.setItem -// sets an item in the cache -// parameters: key - the key to refer to the object -// value - the object to cache -// options - an optional parameter described below -// the last parameter accepts an object which controls various caching options: -// expirationAbsolute: the datetime when the item should expire -// expirationSliding: an integer representing the seconds since -// the last cache access after which the item -// should expire -// priority: How important it is to leave this item in the cache. -// You can use the values CachePriority.Low, .Normal, or -// .High, or you can just use an integer. Note that -// placing a priority on an item does not guarantee -// it will remain in cache. It can still be purged if -// an expiration is hit, or if the cache is full. -// callback: A function that gets called when the item is purged -// from cache. The key and value of the removed item -// are passed as parameters to the callback function. -Cache.prototype.setItem = function(key, value, options) { - - function CacheItem(k, v, o) { - if ((k == null) || (k == '')) - throw new Error("key cannot be null or empty"); - this.key = k; - this.value = v; - if (o == null) - o = {}; - if (o.expirationAbsolute != null) - o.expirationAbsolute = o.expirationAbsolute.getTime(); - if (o.priority == null) - o.priority = CachePriority.Normal; - this.options = o; - this.lastAccessed = new Date().getTime(); - } - - // add a new cache item to the cache - if (this.items[key] != null) - this._removeItem(key); - this._addItem(new CacheItem(key, value, options)); - - // if the cache is full, purge it - if ((this.maxSize > 0) && (this.count > this.maxSize)) { - this._purge(); - } -} - -// **************************************************************************** -// Cache.clear -// Remove all items from the cache -Cache.prototype.clear = function() { - - // loop through each item in the cache and remove it - for (var key in this.items) { - this._removeItem(key); - } -} - -// **************************************************************************** -// Cache._purge (PRIVATE FUNCTION) -// remove old elements from the cache -Cache.prototype._purge = function() { - - var tmparray = new Array(); - - // loop through the cache, expire items that should be expired - // otherwise, add the item to an array - for (var key in this.items) { - var item = this.items[key]; - if (this._isExpired(item)) { - this._removeItem(key); - } else { - tmparray.push(item); - } - } - - if (tmparray.length > this.purgeSize) { - - // sort this array based on cache priority and the last accessed date - tmparray = tmparray.sort(function(a, b) { - if (a.options.priority != b.options.priority) { - return b.options.priority - a.options.priority; - } else { - return b.lastAccessed - a.lastAccessed; - } - }); - - // remove items from the end of the array - while (tmparray.length > this.purgeSize) { - var ritem = tmparray.pop(); - this._removeItem(ritem.key); - } - } -} - -// **************************************************************************** -// Cache._addItem (PRIVATE FUNCTION) -// add an item to the cache -Cache.prototype._addItem = function(item) { - this.items[item.key] = item; - this.count++; -} - -// **************************************************************************** -// Cache._removeItem (PRIVATE FUNCTION) -// Remove an item from the cache, call the callback function (if necessary) -Cache.prototype._removeItem = function(key) { - var item = this.items[key]; - delete this.items[key]; - this.count--; - - // if there is a callback function, call it at the end of execution - if (item.options.callback != null) { - var callback = function() { - item.options.callback(item.key, item.value); - } - setTimeout(callback, 0); - } -} - -// **************************************************************************** -// Cache._isExpired (PRIVATE FUNCTION) -// Returns true if the item should be expired based on its expiration options -Cache.prototype._isExpired = function(item) { - var now = new Date().getTime(); - var expired = false; - if ((item.options.expirationAbsolute) && (item.options.expirationAbsolute < now)) { - // if the absolute expiration has passed, expire the item - expired = true; - } - if ((expired == false) && (item.options.expirationSliding)) { - // if the sliding expiration has passed, expire the item - var lastAccess = item.lastAccessed + (item.options.expirationSliding * 1000); - if (lastAccess < now) { - expired = true; - } - } - return expired; -} - -Cache.prototype.toHtmlString = function() { - var returnStr = this.count + " item(s) in cache<br /><ul>"; - for (var key in this.items) { - var item = this.items[key]; - returnStr = returnStr + "<li>" + item.key.toString() + " = " + item.value.toString() + "</li>"; - } - returnStr = returnStr + "</ul>"; - return returnStr; -} diff -r 28ec4708840f -r 979534de254d static/scripts/packed/lrucache.js --- a/static/scripts/packed/lrucache.js Thu Oct 29 17:57:30 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -var CachePriority={Low:1,Normal:2,High:4};function Cache(a){this.items={};this.count=0;if(a==null){a=-1}this.maxSize=a;this.fillFactor=0.75;this.purgeSize=Math.round(this.maxSize*this.fillFactor);this.stats={};this.stats.hits=0;this.stats.misses=0}Cache.prototype.getItem=function(a){var c=this.items[a];if(c!=null){if(!this._isExpired(c)){c.lastAccessed=new Date().getTime()}else{this._removeItem(a);c=null}}var b=null;if(c!=null){b=c.value;this.stats.hits++}else{this.stats.misses++}return b};Cache.prototype.setItem=function(c,d,b){function a(f,e,g){if((f==null)||(f=="")){throw new Error("key cannot be null or empty")}this.key=f;this.value=e;if(g==null){g={}}if(g.expirationAbsolute!=null){g.expirationAbsolute=g.expirationAbsolute.getTime()}if(g.priority==null){g.priority=CachePriority.Normal}this.options=g;this.lastAccessed=new Date().getTime()}if(this.items[c]!=null){this._removeItem(c)}this._addItem(new a(c,d,b));if((this.maxSize>0)&&(this.count>this.maxSize)){this._purge()}} ;Cache.prototype.clear=function(){for(var a in this.items){this._removeItem(a)}};Cache.prototype._purge=function(){var d=new Array();for(var a in this.items){var b=this.items[a];if(this._isExpired(b)){this._removeItem(a)}else{d.push(b)}}if(d.length>this.purgeSize){d=d.sort(function(f,e){if(f.options.priority!=e.options.priority){return e.options.priority-f.options.priority}else{return e.lastAccessed-f.lastAccessed}});while(d.length>this.purgeSize){var c=d.pop();this._removeItem(c.key)}}};Cache.prototype._addItem=function(a){this.items[a.key]=a;this.count++};Cache.prototype._removeItem=function(a){var b=this.items[a];delete this.items[a];this.count--;if(b.options.callback!=null){var c=function(){b.options.callback(b.key,b.value)};setTimeout(c,0)}};Cache.prototype._isExpired=function(c){var a=new Date().getTime();var b=false;if((c.options.expirationAbsolute)&&(c.options.expirationAbsolute<a)){b=true}if((b==false)&&(c.options.expirationSliding)){var d=c.lastAccessed+(c.options. expirationSliding*1000);if(d<a){b=true}}return b};Cache.prototype.toHtmlString=function(){var b=this.count+" item(s) in cache<br /><ul>";for(var a in this.items){var c=this.items[a];b=b+"<li>"+c.key.toString()+" = "+c.value.toString()+"</li>"}b=b+"</ul>";return b}; \ No newline at end of file diff -r 28ec4708840f -r 979534de254d static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Thu Oct 29 17:57:30 2009 -0400 +++ b/static/scripts/packed/trackster.js Thu Oct 29 18:28:11 2009 -0400 @@ -1,1 +1,1 @@ -var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",CACHED_TILES=50,CACHED_DATA=20;function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).sh ow();$("#low").text(commatize(this.low));$("#high").text(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<5){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TI LES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,c=this.view.high,e=c-i;var b=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));b=Math.max(b,1);b=Math.min(b,100000);var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var j=this.content_div.width(),d=this.content_div.height(),m=j/e;var g;var a=Math.floor(i/b/DENSITY);while((a*DENSITY*b)<c){var k=this.view.zoom_level+"_"+a;if(this.tile_cache[k]){g=this.tile_cache[k];var f=a*DENSITY*b;g.css({left:(f-this.view.low)*m});l.append(g)}else{g=this.draw_tile(b,a,l,m,d)}if(g){this.tile_cache[k]=g}a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(b){if(!b||b=="error"){a.content_div.addClass("error").text(DATA_ERROR)}else{if(b=="no data"){a.content_div.addClass("nodata").text(DATA_NONE)}else{a.content_div.css("height",a.height_px+"px");a.min_value=b.min;a.max_value=b.max;a.vertical_range=a.max_value-a.min_value;a.view.redraw()}}})},get_data:f unction(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[e]=g;$(document).trigger("redraw")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);th is.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.content_div.addClass("error").text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.content_div.addClass("nodata").text(DATA_NONE)}else{a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}})},calc_slots:function(o){var c=[],b=this.container_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k=Math.floor(Math.max(e,(n.start-e)*g));k-=m.mea sureText(n.name).width;l=Math.ceil(Math.min(a,(n.end-e)*g))}else{k=Math.floor(Math.max(e,(n.start-e)*b));l=Math.ceil(Math.min(a,(n.end-e)*b))}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(t,y,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var z=y*DENSITY*t,b=(y+1)*DENSITY*t,o=DENSITY*t;var r=Math.ceil(o*n),q=this.height_px,p=$("<canvas class='tile'></canvas>");p.css({position:"absolute",top:0,left:(z-this.view.low)*n});p.get(0).width=r;p.get(0).height=q;var s=p.get(0).getContext("2d");s.fillStyle="#000";s.font="10px monospace";s.textAlign="right";var v=0;for(var w=0,x=this.values.length;w<x;w++){var f=this.values[w];if(f.start<=b&&f.end>=z){var e=Math.floor(Math.max(0,(f.start-z)*n)),h=Math.ceil(Math.min(r,(f.end-z)*n)),d=this.slots[f.name]*this.vertical_gap;s.fillRect(e,d+5,h-e,1);if(this.showing_labels&&s.fillText){s.fillText(f.name,e,d+8)}var c,D;if(f.exon_start&&f.exon_end){c=Math.floor(Math.max(0,(f.exon_start-z)*n));D=Math.ceil(Math.min(r,(f.exon_end-z)*n));s.fillRect(c,d+4,D-c,3)}if(f.blocks){for(var u=0,B=f.blocks.length;u<B;u++){var m=f.blocks[u],l=Math.floor(Math.max(0,(m[0]-z)*n)),A=Math.ceil(Math.min(r,(m[1]-z)*n));var a=3,C=4;if(c&&l>=c&&A<=D){a=5;C=3}s.fillRect(l,d+C,A-l,a)}}v++}}g.append(p);return p}}); \ No newline at end of file +var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=5,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/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="../images/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="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(l eft_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.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}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e =this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){thi s.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k)}if(g){this.tile_cache.set(i,g)}a+=1}}});var LabelTrack=function(a){Track.ca ll(this,null,a);this.container_div.addClass("label-track")};$.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 LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dat aset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[e]=g;$(document).trigger("redra w")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(FeatureTrack.prototype,TiledTrack.pro totype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.container_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k=Math.floor(Math.max(e,(n.star t-e)*g));k-=m.measureText(n.name).width;l=Math.ceil(Math.min(a,(n.end-e)*g))}else{k=Math.floor(Math.max(e,(n.start-e)*b));l=Math.ceil(Math.min(a,(n.end-e)*b))}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospac e";v.textAlign="right";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}els e{if(f.strand=="-"){v.fillStyle=LEFT_STRAND_INV}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}}}y++}}g.append(s);return s}}); \ No newline at end of file diff -r 28ec4708840f -r 979534de254d static/scripts/trackster.js --- a/static/scripts/trackster.js Thu Oct 29 17:57:30 2009 -0400 +++ b/static/scripts/trackster.js Thu Oct 29 18:28:11 2009 -0400 @@ -7,7 +7,7 @@ DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", DATA_LOADING = "Loading data...", - CACHED_TILES = 50, + CACHED_TILES = 5, CACHED_DATA = 20, CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), RIGHT_STRAND, LEFT_STRAND; @@ -42,6 +42,36 @@ } return number; } + +var Cache = function( num_elements ) { + this.num_elements = num_elements; + this.obj_cache = {}; + this.key_ary = []; +} +$.extend( Cache.prototype, { + get: function( key ) { + var index = this.key_ary.indexOf(key); + if (index != -1) { + // Move to the end + this.key_ary.splice(index, 1); + this.key_ary.push(key); + } + return this.obj_cache[key]; + }, + set: function( key, value ) { + if (!this.obj_cache[key]) { + if (this.key_ary.length >= this.num_elements) { + // Remove first element + var deleted_key = this.key_ary.shift(); + delete this.obj_cache[deleted_key]; + } + this.key_ary.push(key); + } + this.obj_cache[key] = value; + return value; + } +}); + var View = function( chrom, max_high ) { this.chrom = chrom; this.tracks = []; @@ -138,16 +168,14 @@ range = high - low; var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) ); - resolution = Math.max( resolution, 1 ); - resolution = Math.min( resolution, 100000 ); + resolution = Math.max( resolution, 0.1 ); + resolution = Math.min( resolution, 1000000 ); var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); this.content_div.append( parent_element ); - var w = this.content_div.width(), - h = this.content_div.height(), - w_scale = w / range; + var w_scale = this.content_div.width() / range; var tile_element; // Index of first tile that overlaps visible region @@ -155,7 +183,7 @@ while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache var key = this.view.zoom_level + "_" + tile_index; - var cached = this.tile_cache.getItem(key); + var cached = this.tile_cache.get(key); if ( cached ) { // console.log("cached tile"); var tile_low = tile_index * DENSITY * resolution; @@ -165,10 +193,10 @@ // Our responsibility to move the element to the new parent parent_element.append( cached ); } else { - tile_element = this.draw_tile( resolution, tile_index, parent_element, w_scale, h ); + tile_element = this.draw_tile( resolution, tile_index, parent_element, w_scale ); } if ( tile_element ) { - this.tile_cache.setItem(key, tile_element); + this.tile_cache.set(key, tile_element); } tile_index += 1; } diff -r 28ec4708840f -r 979534de254d templates/tracks/browser.mako --- a/templates/tracks/browser.mako Thu Oct 29 17:57:30 2009 -0400 +++ b/templates/tracks/browser.mako Thu Oct 29 18:28:11 2009 -0400 @@ -7,7 +7,7 @@ <%def name="javascripts()"> ${parent.javascripts()} -${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "lrucache", "trackster" )} +${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster" )} <script type="text/javascript">

1 0

[hg] galaxy 2927: trackster: y-axis labels for linetracks, thin/...
by Greg Von Kuster 08 Nov '09

08 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/edb48f2816b5 changeset: 2927:edb48f2816b5 user: Kanwei Li <kanwei(a)gmail.com> date: Tue Oct 27 22:34:30 2009 -0400 description: trackster: y-axis labels for linetracks, thin/thick blocks are correct for featuretracks, messages when data is loading and being indexed diffstat: lib/galaxy/visualization/tracks/data/interval_index.py | 4 +- static/scripts/trackster.js | 171 ++++++++++++--------- static/trackster.css | 10 + templates/tracks/browser.mako | 4 - 4 files changed, 110 insertions(+), 79 deletions(-) diffs (326 lines): diff -r ea0342f2df03 -r edb48f2816b5 lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Tue Oct 27 15:11:41 2009 -0400 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Tue Oct 27 22:34:30 2009 -0400 @@ -35,8 +35,8 @@ pass try: - payload['exon_start'] = int(feature[6]) - payload['exon_end'] = int(feature[7]) + payload['thick_start'] = int(feature[6]) + payload['thick_end'] = int(feature[7]) except IndexError: pass diff -r ea0342f2df03 -r edb48f2816b5 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Oct 27 15:11:41 2009 -0400 +++ b/static/scripts/trackster.js Tue Oct 27 22:34:30 2009 -0400 @@ -5,6 +5,8 @@ var DENSITY = 1000, DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig.", + DATA_PENDING = "Currently indexing... please wait", + DATA_LOADING = "Loading data...", CACHED_TILES = 50, CACHED_DATA = 20, CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), @@ -34,11 +36,11 @@ function commatize( number ) { number += ''; // Convert to string - var rgx = /(\d+)(\d{3})/; - while (rgx.test(number)) { - number = number.replace(rgx, '$1' + ',' + '$2'); - } - return number; + var rgx = /(\d+)(\d{3})/; + while (rgx.test(number)) { + number = number.replace(rgx, '$1' + ',' + '$2'); + } + return number; } var View = function( chrom, max_high ) { this.chrom = chrom; @@ -88,7 +90,7 @@ $("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>'); }, zoom_in: function ( point ) { - if (this.max_high === 0 || this.high - this.low < 5) { + if (this.max_high === 0 || this.high - this.low < 30) { return; } @@ -96,6 +98,7 @@ this.center = point / $(document).width() * (this.high - this.low) + this.low; } this.zoom_level += 1; + this.redraw(); }, zoom_out: function () { if (this.max_high === 0) { @@ -106,6 +109,7 @@ return; } this.zoom_level -= 1; + this.redraw(); } }); @@ -137,13 +141,13 @@ resolution = Math.max( resolution, 1 ); resolution = Math.min( resolution, 100000 ); - var parent_element = $("<div style='position: relative;'></div>"); + var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); this.content_div.append( parent_element ); var w = this.content_div.width(), h = this.content_div.height(), - w_scale = w / range; + w_scale = w / range; var tile_element; // Index of first tile that overlaps visible region @@ -211,21 +215,38 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { var track = this; + track.content_div.text(DATA_LOADING); $.getJSON( data_url, { stats: true, track_type: track.track_type, chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { if (!data || data == "error") { track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); + track.content_div.text(DATA_ERROR); } else if (data == "no data") { track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); + track.content_div.text(DATA_NONE); + } else if (data == "pending") { + track.container_div.addClass("pending"); + track.content_div.text(DATA_PENDING); + setTimeout(function() { track.init(); }, 5000); } else { + track.content_div.text(""); track.content_div.css( "height", track.height_px + "px" ); track.min_value = data.min; track.max_value = data.max; track.vertical_range = track.max_value - track.min_value; - track.view.redraw(); + + // Draw y-axis labels + var min_label = $("<div class='yaxislabel'>" + track.min_value + "</div>"); + var max_label = $("<div class='yaxislabel'>" + track.max_value + "</div>"); + + max_label.css({ position: "relative", top: "20px" }); + max_label.prependTo(track.container_div) + + min_label.css({ position: "relative", top: track.height_px + 50 + "px", }); + min_label.prependTo(track.container_div); + + track.draw(); } }); }, @@ -307,16 +328,22 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { var track = this; + track.content_div.text(DATA_LOADING); $.getJSON( data_url, { track_type: track.track_type, low: track.view.max_low, high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom }, function ( data ) { if (data == "error") { track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); + track.content_div.text(DATA_ERROR); } else if (data.length === 0 || data == "no data") { track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); + track.content_div.text(DATA_NONE); + } else if (data == "pending") { + track.container_div.addClass("pending"); + track.content_div.text(DATA_PENDING); + setTimeout(function() { track.init(); }, 5000); } else { + track.content_div.text(""); track.content_div.css( "height", track.height_px + "px" ); track.values = data; track.calc_slots(); @@ -412,68 +439,66 @@ f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), y_center = this.slots[feature.name] * this.vertical_gap; - if (feature.strand && this.showing_labels) { - if (feature.strand == "+") { - ctx.fillStyle = RIGHT_STRAND; - } else if (feature.strand == "-") { - ctx.fillStyle = LEFT_STRAND; + var thickness, y_start, thick_start = null, thick_end = null; + if (feature.thick_start && feature.thick_end) { + thick_start = Math.floor( Math.max(0, (feature.thick_start - tile_low) * w_scale) ); + thick_end = Math.ceil( Math.min(width, (feature.thick_end - tile_low) * w_scale) ); + } + if (!this.showing_labels) { + // Non-detail levels + ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); + } else { + // Showing labels, blocks, details + if (ctx.fillText) { + ctx.fillText(feature.name, f_start - 1, y_center + 8); } - ctx.fillRect(f_start, y_center, f_end - f_start, 10); - ctx.fillStyle = "#000"; - } else { - ctx.fillStyle = "#000"; - ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); - } - - if (this.showing_labels && ctx.fillText) { - ctx.fillText(feature.name, f_start - 1, y_center + 8); - } - - // If there is no thickStart/thickEnd, draw the whole thing - // as thick. - var exon_start, exon_end; - if (feature.exon_start && feature.exon_end) { - exon_start = Math.floor( Math.max(0, (feature.exon_start - tile_low) * w_scale) ); - exon_end = Math.ceil( Math.min(width, (feature.exon_end - tile_low) * w_scale) ); - } else { - exon_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ); - exon_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ); - } - - if (this.showing_labels) { - // If there are no blocks, we treat the feature as one - // big exon - var blocks = feature.blocks; - var arrows_in_blocks = false; - if ( ! blocks ) { - blocks = [[feature.start,feature.end]]; - arrows_in_blocks = true - } - for (var k = 0, k_len = blocks.length; k < k_len; k++) { - var block = blocks[k], - block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); - var thickness, y_start; - if (exon_start && block_start >= exon_start && block_end <= exon_end) { - thickness = 9; - y_start = 1; - ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); - if ( feature.strand && arrows_in_blocks ) { - if (feature.strand == "+") { - ctx.fillStyle = RIGHT_STRAND_INV; - } else if (feature.strand == "-") { - ctx.fillStyle = LEFT_STRAND_INV; - } - ctx.fillRect(block_start, y_center, block_end - block_start, 10); - ctx.fillStyle = "#000"; - } - } else { - thickness = 5; - y_start = 3; - ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); - } + var blocks = feature.blocks; + if (blocks) { + // Draw introns + if (feature.strand) { + if (feature.strand == "+") { + ctx.fillStyle = RIGHT_STRAND; + } else if (feature.strand == "-") { + ctx.fillStyle = LEFT_STRAND; + } + ctx.fillRect(f_start, y_center, f_end - f_start, 10); + ctx.fillStyle = "#000"; + } - // console.log(block_start, block_end); + for (var k = 0, k_len = blocks.length; k < k_len; k++) { + var block = blocks[k], + block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), + block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); + + // Draw the block + thickness = 5; + y_start = 3; + ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); + + if (thick_start && (block_start < thick_end || block_end > thick_start) ) { + thickness = 9; + y_start = 1; + var block_thick_start = Math.max(block_start, thick_start), + block_thick_end = Math.min(block_end, thick_end); + + ctx.fillRect(block_thick_start, y_center + y_start, block_thick_end - block_thick_start, thickness); + + } + } + } else { + // If there are no blocks, we treat the feature as one big exon + thickness = 9; + y_start = 1; + ctx.fillRect(f_start, y_center + y_start, f_end - f_start, thickness); + if ( feature.strand ) { + if (feature.strand == "+") { + ctx.fillStyle = RIGHT_STRAND_INV; + } else if (feature.strand == "-") { + ctx.fillStyle = LEFT_STRAND_INV; + } + ctx.fillRect(f_start, y_center, f_end - f_start, 10); + ctx.fillStyle = "#000"; + } } } j++; diff -r ea0342f2df03 -r edb48f2816b5 static/trackster.css --- a/static/trackster.css Tue Oct 27 15:11:41 2009 -0400 +++ b/static/trackster.css Tue Oct 27 22:34:30 2009 -0400 @@ -95,6 +95,16 @@ width: 100%; height: 100px; } + +.yaxislabel { + color: #777; +} +/* Line track needs borders to show range */ +.line-track .track-content { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; +} + .track { /* border-top: solid gray 1px; */ /* border-bottom: solid gray 1px; */ diff -r ea0342f2df03 -r edb48f2816b5 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue Oct 27 15:11:41 2009 -0400 +++ b/templates/tracks/browser.mako Tue Oct 27 22:34:30 2009 -0400 @@ -30,16 +30,13 @@ $(document).bind("mousewheel", function( e, delta ) { if (delta > 0) { view.zoom_in(e.pageX); - view.redraw(); } else { view.zoom_out(); - view.redraw(); } }); $(document).bind("dblclick", function( e ) { view.zoom_in(e.pageX); - view.redraw(); }); // To let the overview box be draggable @@ -96,7 +93,6 @@ }); }); })(); - view.redraw(); $(window).trigger("resize"); });

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Running Galaxy on another server
by Raghav Bhatnagar 06 Nov '09

06 Nov '09

Hi I installed a copy of Galaxy on my server under public_html Folder. I also modified the universe_wsgi.ini file and changed the host setting to 0.0.0.0. Invoking sh run.sh command, Galaxy tends to start starting : serving on 0.0.0.0:8080 view at http://127.0.0.1:8080 But http://127.0.0.1:8080 gives a "*page load error*" on viewing in browser. If I change host setting to the IP address of my server, it displays a bunch of errors and does not start Galaxy. Those errors are: - *Starting server in PID 29836. Traceback (most recent call last): File "./scripts/paster.py", line 32, in ? command.run() File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteScript-1.3.6-py2.4.egg/paste/script/command.py", line 78, in run invoke(command, command_name, options, args[1:]) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteScript-1.3.6-py2.4.egg/paste/script/command.py", line 117, in invoke exit_code = runner.run(args) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteScript-1.3.6-py2.4.egg/paste/script/command.py", line 212, in run result = self.command() File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteScript-1.3.6-py2.4.egg/paste/script/serve.py", line 232, in command server(app) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteDeploy-1.3.1-py2.4.egg/paste/deploy/loadwsgi.py", line 139, in server_wrapper wsgi_app, context.global_conf, File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/PasteDeploy-1.3.1-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1307, in server_runner serve(wsgi_app, **kwargs) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1257, in serve threadpool_options=threadpool_options) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1107, in __init__ RequestHandlerClass, ssl_context) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1087, in __init__ RequestHandlerClass, ssl_context) File "/nfs/home/raghav/public_html/galaxy/eggs/py2.4-noplatform/Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib/python2.4/SocketServer.py", line 330, in __init__ self.server_bind() File "/usr/lib/python2.4/BaseHTTPServer.py", line 99, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib/python2.4/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.gaierror: (-2, 'Name or service not known') galaxy.jobs INFO 2009-11-05 21:30:08,204 sending stop signal to worker thread galaxy.jobs INFO 2009-11-05 21:30:08,204 job queue stopped galaxy.jobs.runners.local INFO 2009-11-05 21:30:08,204 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2009-11-05 21:30:08,205 local job runner stopped galaxy.jobs INFO 2009-11-05 21:30:08,205 sending stop signal to worker thread galaxy.jobs INFO 2009-11-05 21:30:08,206 job stopper stopped * What changes do I have to make in order to run the Galaxy on my server? -- Raghav Bhatnagar Graduate Student (CS) Viterbi School of Engineering University of Southern California

2 1

Output Multiple Files in Galaxy
by Luqman Hakim B Abdul Hadi 05 Nov '09

05 Nov '09

Hi Galaxy team. Im pretty new to Galaxy and currently trying to put it into production. I was wondering if it is possible to have a program that outputs many output many results file and incorporate it into Galaxy? Can you give an example of how the XML looks like? Thanks loads! Luqman

2 1

Problems with URLs of Example pics
by Andreas Kuntzagk 05 Nov '09

05 Nov '09

Hi, we have a local galaxy installation behind a apache proxy. So far it's working flawless. But now we noticed that the images referenced in the example text of Operate on Genomic Intervals don't show. If I use the "real" address of the galaxy without proxy, it's working (no config change or restart!) The generated HTML contains: <img alt="../static/operation_icons/gops_complement.gif" src="../static/operation_icons/gops_complement.gif"> This are the settings in universe_wsgi.ini [filter:proxy-prefix] use=egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix regards, Andreas

2 1

Re: [galaxy-dev] Question
by Greg Von Kuster 05 Nov '09

05 Nov '09

Hello Rodolfo, I've cc'd the galaxy-dev mailing list as others may benefit from this exchange. On Nov 4, 2009, at 12:12 PM, Rodolfo Aramayo wrote: > Hi Greg, > > Thanks for replying. No we are not running into any problems with > Galaxy. In fact we LOVE IT! And students are asking to learn more > about it. In fact we had a little coup in here because students > refused to accept yet another Genomics Unix project, instead they > requested projects in Galaxy. This is great - so glad to hear this! > > Anyway, the reason I was contacting you guys is to ask guidance into > how to go about to load genomes that are not part of the current > Galaxy set up into Galaxy. For example I would like to know what > tables I would need to create for the genomes in question and how to > link them to MySQL. We are in the process of streamlining the process for supporting new genomes, but the current process is fairly simple. New database changes are needed. Since you are running your own local installation of Galaxy, new genomes can be specified by modifing the ${GALAXY_ROOT}/tool-data/shared/ucsc/builds.txt file. This file is generated using a script found at ${GALAXY_ROOT}/cron/updateucsc.sh. If this script is executed on a regular basis ( via cron perhaps ), it will be useful to instead add the required information to $ {GALAXY_ROOT}/tool-data/shared/ucsc/manual_builds.txt before running the script (otherwise each time the script is run, the changes to build.txt will be lost). See ${GALAXY_ROOT}/cron/README.txt for more information as well as the headers of each data file. > I have installed Galaxy locally without problems > and activated the EMBOSS part BUT, it is not clear to me how exactly > go about making Galaxy talk to MySQL. Any help in this area would be > GREATLY appreciated. Hooking up Galaxy to and installed postgres or mysql database is simply a config setting in universe_wsgi.ini ( look for the following section in this file in your galaxy root install directory ). The URL you'll use depends on the name and location of your database and the security you've implemented, but for mysql could look something like the following. See the mysql docs for details [app:main] # Specifies the factory for the universe WSGI application paste.app_factory = galaxy.web.buildapp:app_factory # By default, Galaxy uses a SQLite database found here #database_file = database/universe.sqlite # You may use a SQLAlchemy connection string to specify an external database # instead. PostgreSQL and MySQL are supported. database_connection = mysql://greg_test?unix_socket=/var/run/mysqld/ mysqld.sock > > Among other things, I am the director of the Laboratory for Genome > Bioinformatics here at Texas A&M University and I have been training > students in Bioinformatics/Genomics. I have access to very skillful > undergraduate students who are very computer savvy and are itching to > help Galaxy. We know a bit about Unix and MySQL but are not real > experts... > > Any help in this area would be great and would allow us to load the > fungal genomes we want to study into Galaxy > > Thanks for your help > > Rodolfo > > > > On Wed, Nov 4, 2009 at 09:12, Greg Von Kuster <greg(a)bx.psu.edu> wrote: >> Hello Rodolfo, >> Can you clarify what you would like to do? Are you running your >> own local >> Galaxy instance, or are you using our main public instance? Are >> you having >> problems uploading the files? >> Greg Von Kuster >> Galaxy Development Team >> >> On Oct 26, 2009, at 4:29 PM, Rodolfo Aramayo wrote: >> >> Hi, >> I teach Genomics and want to use Galaxy as a tool. I would like to >> upload a series of fungal genomes for this analysis. Who should I >> contact to talk about this? >> In other words, I need the name of a person who might help us or gude >> us through this process. >> Thank You for your help >> Rodolfo Aramayo, PhD >> Biology/Genetics >> Texas A&M University >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Re: [galaxy-dev] Experience with Loading NGS data on standalone instance of galaxy
by Nate Coraor 04 Nov '09

04 Nov '09

Hi Matthias, I've moved this thread over to galaxy-dev (I probably should've done this a while ago). Matthias Dodt wrote: > One more question according change set 2812: > > Add a new option, 'allow_library_path_paste' that adds a new upload page > ("Upload files from file system paths") to the admin-side library upload > pages. > > I am not sure where to add this option- i added to universe_wsgi.ini: > > allow_library_path_paste = True > allow_library_path_paste = /somepath/ > > both didnt work- how can i enable the "allow_library_path_paste" option? It goes in universe_wsgi.ini and 'True' is the correct value. Once restarting, you should see this link over on the admin side only, not the user side data libraries page. Is this not the case? --nate

1 0

galaxy data libraries
by Matthias Dodt 04 Nov '09

04 Nov '09

Hi there! Galaxy provides the upload of files from user directories via the user_library_import_dir tag in universe_wsgi.ini. 1. If i choose "upload from directory" in the data-libraries menu, first i have a list of folders to choose. How can i assign different folders to the same user? Normally it is only possible to upload files from the users home directory, which matches the username i guess- 2. There is an option: copy files into galaxy: yes/no. If i choose "no" it seems to me that the file gets copied still, because it takes ages to finish? 3. Assuming the "linking" of files into galaxy would work: If i choose once the users home directory for uploading files and link those into galaxy, and later i add more files to the folder and want to upload those, ALL files would be uplinked into galaxy again, no matter if they already exist? Is there a way to choose which files of the folder should be uploaded? Thanks in advance!

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galaxy-dev November 2009