File Changes for max

v283_base to v284_preview (2013-05-07 to 2013-05-14) v284

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 11, context: html, text, full: html, text
    new pubsBlat format allows to specify mouseover text and labels as part of primary table, without join. Also allows to define classes of papers and color them via a second table
  • lines changed 15, context: html, text, full: html, text
    adding publisher filter to pubs trackui
  • lines changed 3, context: html, text, full: html, text
    filters work on main table now if table is in new format, added publisher filter
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
  • lines changed 63, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
  • lines changed 2, context: html, text, full: html, text
    temporarily taking back a change as it proved deadly for bed3 files
  • lines changed 21, context: html, text, full: html, text
    fixing a bug where a bed3 file crashed the mouseOver mapItem method. Moved this method now into the linkedFeatures code, where it should have been from the start
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    moving the publication track code into its own .h/.c files
• src/hg/hgTracks/pubsTracks.c
  • lines changed 485, context: html, text, full: html, text
    moving the publication track code into its own .h/.c files
  • lines changed 42, context: html, text, full: html, text
    filters work on main table now if table is in new format, added publisher filter
  • lines changed 18, context: html, text, full: html, text
    change impact colors
  • lines changed 5, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
  • lines changed 9, context: html, text, full: html, text
    if impact coloring is activated, show impact factor in mouse over
  • lines changed 2, context: html, text, full: html, text
    forgot to init a variable
  • lines changed 0, context: html, text, full: html, text
    fixing a bug where a bed3 file crashed the mouseOver mapItem method. Moved this method now into the linkedFeatures code, where it should have been from the start
• src/hg/hgTracks/pubsTracks.h
  • lines changed 7, context: html, text, full: html, text
    moving the publication track code into its own .h/.c files
• src/hg/hgTracks/simpleTracks.c
  • lines changed 123, context: html, text, full: html, text
    new pubsBlat format allows to specify mouseover text and labels as part of primary table, without join. Also allows to define classes of papers and color them via a second table
  • lines changed 22, context: html, text, full: html, text
    trying to come up with better color shades for impact coloring
  • lines changed 18, context: html, text, full: html, text
    use only best color if several defined
  • lines changed 1, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
  • lines changed 480, context: html, text, full: html, text
    moving the publication track code into its own .h/.c files
  • lines changed 17, context: html, text, full: html, text
    fixing a bug where a bed3 file crashed the mouseOver mapItem method. Moved this method now into the linkedFeatures code, where it should have been from the start
  • lines changed 26, context: html, text, full: html, text
    last change broke hgGene links, temporarily taking it back
  • lines changed 21, context: html, text, full: html, text
    fixed linkedFeatures mouseOver text to work with hgGenes linkouts, tested on refseq, knownGenes, simple and extended bed files.
• src/hg/hgc/hgc.c
  • lines changed 34, context: html, text, full: html, text
    removed EXTRA_FIELDS_SUPPORT ifdef-blocks, as they made the code very hard to read, got OK from Tim by email
  • lines changed 119, context: html, text, full: html, text
    support for urls in bigBed+ fields via a new tdb statement "urls"
  • lines changed 1, context: html, text, full: html, text
    fixed one-off bug in disulf bind field
• src/hg/hgc/pubs.c
  • lines changed 32, context: html, text, full: html, text
    changing hgc page
  • lines changed 82, context: html, text, full: html, text
    many changes after review by krauthammer lab to adapt display to yif OCR images
  • lines changed 56, context: html, text, full: html, text
    added link to image page on yif server, after email from mate
  • lines changed 17, context: html, text, full: html, text
    additional debug statements
  • lines changed 37, context: html, text, full: html, text
    handling explicitly specified publisher names, adding the missing nature logo
  • lines changed 10, context: html, text, full: html, text
    better html layout of publisher logo
  • lines changed 27, context: html, text, full: html, text
    making it possible to link to hgc without t and o parameters (europmc)
  • lines changed 2, context: html, text, full: html, text
    correcting weird case where file desc is empty
  • lines changed 4, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
  • lines changed 2, context: html, text, full: html, text
    bugfix for europmc who want to link to hgc directly
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 25, context: html, text, full: html, text
    first try at "urls" statement documentation
  • lines changed 21, context: html, text, full: html, text
    adding mouse over statement doc
  • lines changed 7, context: html, text, full: html, text
    fixed linkedFeatures mouseOver text to work with hgGenes linkouts, tested on refseq, knownGenes, simple and extended bed files.
• src/hg/htdocs/images/pubs_asm.png
  • lines changed 0, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
• src/hg/htdocs/images/pubs_elsevier.png
  • lines changed 0, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
• src/hg/htdocs/images/pubs_nature.png
  • lines changed 0, context: html, text, full: html, text
    handling explicitly specified publisher names, adding the missing nature logo
• src/hg/htdocs/images/pubs_npg.png
  • lines changed 0, context: html, text, full: html, text
    handling explicitly specified publisher names, adding the missing nature logo
• src/hg/htdocs/images/pubs_oup.png
  • lines changed 0, context: html, text, full: html, text
    adding oup image for pubs track
• src/hg/htdocs/images/pubs_oxfordjournals.png
  • lines changed 0, context: html, text, full: html, text
    adding oup image for pubs track
• src/hg/htdocs/images/pubs_pmc.png
  • lines changed 0, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
• src/hg/htdocs/images/pubs_pnas.png
  • lines changed 0, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
• src/hg/htdocs/images/pubs_wiley.png
  • lines changed 0, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
• src/hg/makeDb/trackDb/human/lovd.html
  • lines changed 66, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
• src/hg/makeDb/trackDb/human/spMut.html
  • lines changed 56, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
  • lines changed 6, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
  • lines changed 3, context: html, text, full: html, text
    changes to html for spMut
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 20, context: html, text, full: html, text
    support for urls in bigBed+ fields via a new tdb statement "urls"
  • lines changed 11, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
  • lines changed 2, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    support for urls in bigBed+ fields via a new tdb statement "urls"
  • lines changed 1, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
• src/hg/utils/lovd/bedDetail4.sql
  • lines changed 16, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/hg/utils/lovd/check.sh
  • lines changed 47, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/hg/utils/lovd/download.sh
  • lines changed 24, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/hg/utils/lovd/load.sh
  • lines changed 21, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/hg/utils/uniprotMutations/README.txt
  • lines changed 30, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
  • lines changed 9, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
• src/hg/utils/uniprotMutations/bed12UniProtAnnot.as
  • lines changed 21, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
  • lines changed 1, context: html, text, full: html, text
    fixed same table name in different .as files
• src/hg/utils/uniprotMutations/bed12UniProtMut.as
  • lines changed 23, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
  • lines changed 2, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
• src/hg/utils/uniprotMutations/liftUniprotMut.py
  • lines changed 128, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
  • lines changed 2, context: html, text, full: html, text
    remove empty strings from output in two fields
  • lines changed 120, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
  • lines changed 3, context: html, text, full: html, text
    keep mutations with disease but no other comment
  • lines changed 33, context: html, text, full: html, text
    changed format to take into account new uniprot parser output, using disease codes now in bed3 field
• src/hg/utils/uniprotMutations/load.sh
  • lines changed 3, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
  • lines changed 5, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
• src/hg/utils/uniprotMutations/makeUniProtToHg.sh
  • lines changed 48, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/hg/utils/uniprotMutations/mapUniprot_doBlast
  • lines changed 18, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts