Commits for max
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v283_base to v284_preview (2013-05-07 to 2013-05-14) v284
- changing hgc page
- many changes after review by krauthammer lab to adapt display to yif OCR images
- 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
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 11, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c - lines changed 123, context: html, text, full: html, text
- added link to image page on yif server, after email from mate
- trying to come up with better color shades for impact coloring
- src/hg/hgTracks/simpleTracks.c - lines changed 22, context: html, text, full: html, text
- use only best color if several defined
- src/hg/hgTracks/simpleTracks.c - lines changed 18, context: html, text, full: html, text
- adding publisher filter to pubs trackui
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 15, context: html, text, full: html, text
- additional debug statements
- lovd and uniprot mutation tracks scripts
- src/hg/utils/lovd/bedDetail4.sql - lines changed 16, context: html, text, full: html, text
- src/hg/utils/lovd/check.sh - lines changed 47, context: html, text, full: html, text
- src/hg/utils/lovd/download.sh - lines changed 24, context: html, text, full: html, text
- src/hg/utils/lovd/load.sh - lines changed 21, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/README.txt - lines changed 30, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/bed12UniProtMut.as - lines changed 23, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/liftUniprotMut.py - lines changed 128, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/load.sh - lines changed 3, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/makeUniProtToHg.sh - lines changed 48, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/mapUniprot_doBlast - lines changed 18, 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
- support for urls in bigBed+ fields via a new tdb statement "urls"
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 20, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
- remove empty strings from output in two fields
- src/hg/utils/uniprotMutations/liftUniprotMut.py - lines changed 2, context: html, text, full: html, text
- first try at "urls" statement documentation
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 25, context: html, text, full: html, text
- uniprot variants track also can generate annotations now
- src/hg/hgTracks/bigBedTrack.c - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lovd.html - lines changed 66, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/spMut.html - lines changed 56, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 11, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/README.txt - lines changed 9, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/bed12UniProtAnnot.as - lines changed 21, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/bed12UniProtMut.as - lines changed 2, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/liftUniprotMut.py - lines changed 120, context: html, text, full: html, text
- src/hg/utils/uniprotMutations/load.sh - lines changed 5, context: html, text, full: html, text
- adding mouseOverField to trackDb for bigBed and using it for the spMut track
- src/hg/hgTracks/bigBedTrack.c - lines changed 63, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.h - lines changed 2, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/spMut.html - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
- Merge branch 'master' into upLovdBbLinks
- Merge branch 'master' into pubs2
- keep mutations with disease but no other comment
- src/hg/utils/uniprotMutations/liftUniprotMut.py - lines changed 3, context: html, text, full: html, text
- moving the publication track code into its own .h/.c files
- src/hg/hgTracks/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/pubsTracks.c - lines changed 485, context: html, text, full: html, text
- src/hg/hgTracks/pubsTracks.h - lines changed 7, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c - lines changed 480, context: html, text, full: html, text
- filters work on main table now if table is in new format, added publisher filter
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgTracks/pubsTracks.c - lines changed 42, context: html, text, full: html, text
- handling explicitly specified publisher names, adding the missing nature logo
- src/hg/htdocs/images/pubs_nature.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/pubs_npg.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- better html layout of publisher logo
- making it possible to link to hgc without t and o parameters (europmc)
- adding oup image for pubs track
- src/hg/htdocs/images/pubs_oup.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/pubs_oxfordjournals.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- correcting weird case where file desc is empty
- adding mouse over statement doc
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 21, context: html, text, full: html, text
- change impact colors
- src/hg/hgTracks/pubsTracks.c - lines changed 18, 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/liftUniprotMut.py - lines changed 33, context: html, text, full: html, text
- fixed publisher filter and publisher logo bugs
- src/hg/hgTracks/pubsTracks.c - lines changed 5, context: html, text, full: html, text
- src/hg/htdocs/images/pubs_asm.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/pubs_elsevier.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/pubs_pmc.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/pubs_pnas.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/pubs_wiley.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- changes to html for spMut
- src/hg/makeDb/trackDb/human/spMut.html - lines changed 3, context: html, text, full: html, text
- Merge branch 'upLovdBbLinks'
- fixed one-off bug in disulf bind field
- Merge branch 'pubs2'
- if impact coloring is activated, show impact factor in mouse over
- src/hg/hgTracks/pubsTracks.c - lines changed 9, context: html, text, full: html, text
- bugfix for europmc who want to link to hgc directly
- forgot to init a variable
- src/hg/hgTracks/pubsTracks.c - lines changed 2, context: html, text, full: html, text
- temporarily taking back a change as it proved deadly for bed3 files
- src/hg/hgTracks/bigBedTrack.c - lines changed 2, 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/bigBedTrack.c - lines changed 21, context: html, text, full: html, text
- src/hg/hgTracks/pubsTracks.c - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/hgTracks/simpleTracks.c - lines changed 17, context: html, text, full: html, text
- fixed same table name in different .as files
- src/hg/utils/uniprotMutations/bed12UniProtAnnot.as - lines changed 1, context: html, text, full: html, text
- last change broke hgGene links, temporarily taking it back
- src/hg/hgTracks/simpleTracks.c - lines changed 26, 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/hgTracks/simpleTracks.c - lines changed 21, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 7, context: html, text, full: html, text
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