kent: changes by commit

branch to review (2010-04-06 to 2010-04-13) v229

• Continued tuning of new font system.
  • src/hg/lib/hCytoBand.c 1.7 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgCourier10.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgCourier12.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgCourier14.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgCourier8.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgHelvetica10.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgHelvetica12.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgHelvetica18.c 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgHelvetica24.c 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgHelvetica8.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgHelveticaBold10.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgHelveticaBold12.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgHelveticaBold24.c 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgHelveticaBold8.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgSixhi6.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgTimes10.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgTimes12.c 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/lib/font/mgTimes8.c 1.4 - lines changed: 1, context: html, text, full: html, text
• Committing changes made a while back for last bits of mm9 known gene rebuild.
  • src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh 1.5 - lines changed: 42, context: html, text, full: html, text
• Expanding bigWig type docs a little.
  • src/hg/makeDb/trackDb/README 1.106 - lines changed: 3, context: html, text, full: html, text
• Adding mgTimes34Font()
  • src/inc/memgfx.h 1.28 - lines changed: 1, context: html, text, full: html, text
• Fixing max field in second and higher level zooms of bedGraphToBigWig and bedToBigBed.
  • src/inc/bbiFile.h 1.21 - lines changed: 2, context: html, text, full: html, text
  • src/lib/bbiWrite.c 1.13 - lines changed: 1, context: html, text, full: html, text
• Adding extra sig for detection of truncation at end of file.
  • src/inc/bbiFile.h 1.22 - lines changed: 2, context: html, text, full: html, text
  • src/lib/bwgCreate.c 1.23 - lines changed: 4, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/bedGraphToBigWig.c 1.26 - lines changed: 4, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c 1.23 - lines changed: 4, context: html, text, full: html, text
• Fixing indentation and putting function comment in right place. Code standards people!
  • src/hg/hgTracks/hgTracks.c 1.1637 - lines changed: 23, context: html, text, full: html, text
• Starting to work on makeItems type tracks.
  • src/hg/hgTracks/hgTracks.h 1.204 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTracks/makeItemsTrack.c 1.1 - lines changed: 32, context: html, text, full: html, text
  • src/hg/hgTracks/makefile 1.91 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.132 - lines changed: 4, context: html, text, full: html, text
  • src/hg/js/hgTracks.js 1.63 - lines changed: 20, context: html, text, full: html, text
• Making it so that list of makeItems tracks to initialize is determined at run time. Making hgTracks.c generate a javascript function hgTrackInitTracks() that gets called during the javascript init.
  • src/hg/hgTracks/hgTracks.c 1.1638 - lines changed: 18, context: html, text, full: html, text
  • src/hg/js/hgTracks.js 1.64 - lines changed: 2, context: html, text, full: html, text
• Starting to implement more of the makeItems track javascript/C interface.
  • src/hg/hgTracks/hgTracks.c 1.1639 - lines changed: 9, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.205 - lines changed: 1, context: html, text, full: html, text
• The makeItems drag now returns a proper track name, chrom, start, end.
  • src/hg/js/hgTracks.js 1.65 - lines changed: 44, context: html, text, full: html, text
• Refactoring so that ruler and makeItems share code to convert from pixel to chromosome coordinates.
  • src/hg/js/hgTracks.js 1.66 - lines changed: 69, context: html, text, full: html, text
• Adding makeItemsItem autoSql object.
  • src/hg/inc/makeItemsItem.h 1.1 - lines changed: 95, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.as 1.1 - lines changed: 13, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.c 1.1 - lines changed: 233, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.sql 1.1 - lines changed: 19, context: html, text, full: html, text
  • src/hg/lib/makefile 1.406 - lines changed: 2, context: html, text, full: html, text
• Updating comment and name.
  • src/hg/inc/makeItemsItem.h 1.2 - lines changed: 44, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.as 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.c 1.2 - lines changed: 40, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.sql 1.2 - lines changed: 2, context: html, text, full: html, text
• Starting to get makeItems to work as a custom track type.
  • src/hg/hgTracks/hgTracks.c 1.1640 - lines changed: 7, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.206 - lines changed: 15, context: html, text, full: html, text
  • src/hg/hgTracks/makeItemsTrack.c 1.2 - lines changed: 6, context: html, text, full: html, text
  • src/hg/lib/customFactory.c 1.119 - lines changed: 133, context: html, text, full: html, text
• Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections!
  • src/hg/hgTracks/hgTracks.c 1.1641 - lines changed: 36, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.207 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgTracks/makeItemsTrack.c 1.3 - lines changed: 67, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.133 - lines changed: 4, context: html, text, full: html, text
  • src/hg/inc/makeItemsItem.h 1.3 - lines changed: 6, context: html, text, full: html, text
  • src/hg/lib/customFactory.c 1.120 - lines changed: 19, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.as 1.3 - lines changed: 5, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.c 1.3 - lines changed: 33, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.sql 1.3 - lines changed: 5, context: html, text, full: html, text
• Replacing dummy first item with something better. Restoring click to details page, which is still sparse.
  • src/hg/hgTracks/makeItemsTrack.c 1.4 - lines changed: 40, context: html, text, full: html, text
• Adding id field to makeItemsItem.
  • src/hg/lib/customFactory.c 1.121 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.c 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.sql 1.4 - lines changed: 2, context: html, text, full: html, text
• Adding ID to makeItemsItem.
  • src/hg/hgTracks/makeItemsTrack.c 1.5 - lines changed: 23, context: html, text, full: html, text
• Adding some details page handling to makeItems.
  • src/hg/hgc/hgc.c 1.1610 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgc/hgc.h 1.51 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgc/makeItemsClick.c 1.1 - lines changed: 38, context: html, text, full: html, text
  • src/hg/hgc/makefile 1.66 - lines changed: 1, context: html, text, full: html, text
• Adding id column
  • src/hg/inc/makeItemsItem.h 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.as 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.c 1.5 - lines changed: 11, context: html, text, full: html, text
• Making it so can edit name and description of makeItems item.
  • src/hg/hgTracks/makeItemsTrack.c 1.6 - lines changed: 62, context: html, text, full: html, text
  • src/hg/hgc/makeItemsClick.c 1.2 - lines changed: 53, context: html, text, full: html, text
• Removing default values for name and description from makeItems.
  • src/hg/hgTracks/makeItemsTrack.c 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/customFactory.c 1.122 - lines changed: 1, context: html, text, full: html, text
• A little cleanup.
  • src/hg/hgTracks/makeItemsTrack.c 1.8 - lines changed: 6, context: html, text, full: html, text
• Adding makeItemsItemAutoSqlString.
  • src/hg/inc/makeItemsItem.h 1.5 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/makeItemsItem.c 1.6 - lines changed: 19, context: html, text, full: html, text
• Starting to get makeItems custom tracks to work. Schema page is made now, though links in it don't work.
  • src/hg/hgTables/schema.c 1.62 - lines changed: 28, context: html, text, full: html, text
• Making all fields output work with makeItems.
  • src/hg/hgTables/custom.c 1.44 - lines changed: 24, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c 1.191 - lines changed: 10, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.141 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgTables/joining.c 1.57 - lines changed: 14, context: html, text, full: html, text
• Some more progress in making makeItems tracks work in table browser. Selected fields output now works. Filter puts up UI, but filter is still ignored.
  • src/hg/hgTables/filterFields.c 1.80 - lines changed: 91, context: html, text, full: html, text
  • src/hg/hgTables/schema.c 1.63 - lines changed: 2, context: html, text, full: html, text
• Making filter work for makeItems. Hmm, what a complex piece of code!
  • src/hg/hgTables/custom.c 1.45 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/filterFields.c 1.81 - lines changed: 16, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c 1.192 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.142 - lines changed: 2, context: html, text, full: html, text
• Improving BED output for makeItems.
  • src/hg/hgTables/bedList.c 1.72 - lines changed: 25, context: html, text, full: html, text
  • src/hg/hgTables/custom.c 1.46 - lines changed: 12, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.143 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTables/joining.c 1.58 - lines changed: 10, context: html, text, full: html, text