Commits for kate

v332_base to v333_preview (2016-05-02 to 2016-05-09) v333

b46d372807d2ffc6fd3d03ec2ad71dd72a361672 Thu Apr 28 11:15:14 2016 -0700

• Refactor GTEx boxplot code in preparation for moving to library for shared use with hgGene
  
  • src/hg/hgc/gtexClick.c - lines changed 32, context: html, text, full: html, text
  • src/hg/inc/gtexInfo.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.c - lines changed 8, context: html, text, full: html, text

000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700

• Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
  
  • src/hg/hgGene/gtex.c - lines changed 62, context: html, text, full: html, text
  • src/hg/hgGene/hgGene.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGene.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg19/section.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg38/section.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/links.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/hgGene/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/gtexClick.c - lines changed 146, context: html, text, full: html, text
  • src/hg/inc/gtexUi.h - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/gtexUi.c - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text

b3bbb2830441deb68f6645938db234d0ce7f170d Thu Apr 28 13:17:13 2016 -0700

• Cleanup for readability.
  
  • src/hg/hgc/gtexClick.c - lines changed 11, context: html, text, full: html, text

c32415cfb3e0d34c6c21ad9b10dbd66c7ef2b76b Mon May 2 10:44:28 2016 -0700

• Add link to browser with GTEX track on to hgGene GTEX section. refs #17244
  
  • src/hg/hgGene/gtex.c - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/gtexUi.c - lines changed 1, context: html, text, full: html, text

2226ef649b0fbb80ce771caeda16c71ccc290eac Mon May 2 10:46:16 2016 -0700

• Add link to browser with GTEX track on to hgGene GTEX section. refs #17244
  
  • src/hg/hgc/gtexClick.c - lines changed 2, context: html, text, full: html, text

114bd9cc108feeb8b20ad0b98b35454ea3fde8e0 Mon May 2 11:45:50 2016 -0700

• Add details page info to show highest expressed tissue with scores. refs #17244
  
  • src/hg/hgc/gtexClick.c - lines changed 6, context: html, text, full: html, text
  • src/hg/inc/gtexGeneBed.h - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/gtexTissue.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/gtexGeneBed.c - lines changed 18, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.c - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/gtexTissue.c - lines changed 11, context: html, text, full: html, text

c4da827b5b232b002a32e2ec07cdb6b2494df4e4 Mon May 2 14:23:26 2016 -0700

• Add highest and total median expression info to section panel. refs #17244
  
  • src/hg/hgGene/gtex.c - lines changed 29, context: html, text, full: html, text

04b40eb81c2e19a60a7f36033ef920c734f72536 Mon May 2 14:32:28 2016 -0700

• Merge branch 'gtexHggene'
  

ba9c4b8c144df33072d58154549b7cf531d15bde Tue May 3 09:14:22 2016 -0700

• Libifying GTEx boxplot for use by hgGene (as well as hgc). refs #17244
  
  • src/hg/lib/gtexBoxplot.c - lines changed 160, context: html, text, full: html, text

6eb7b642e4d1286b4662ea3d527a9bc09b17db70 Wed May 4 10:53:50 2016 -0700

• Performance work: Add measureTiming support. Also, restructure GTEx to move heavy lifting to print routine so closing section will save time. Also, a few label changes for expression sections. refs #17244
  
  • src/hg/hgGene/gtex.c - lines changed 43, context: html, text, full: html, text
  • src/hg/hgGene/hgGene.c - lines changed 35, context: html, text, full: html, text
  • src/hg/hgGene/hgGene.h - lines changed 2, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg19/section.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg38/section.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/section.ra - lines changed 1, context: html, text, full: html, text

527dfbba9bc27ffed6fe82f446911a0f817ee1f9 Wed May 4 10:54:07 2016 -0700

• Merge branch 'hggenePerf'
  

ddafb30c2f0d5489f4a56c280f56fabf0b08c161 Wed May 4 12:45:18 2016 -0700

• Add default visibility feature to hgGene sections. Setting 'visiblity hide' in section.ra will cause section to be collapsed as default. Using this to set microarray sections to default closed when GTEx data is present (perf boost). refs #17244
  
  • src/hg/hgGene/hgGene.c - lines changed 21, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg19/section.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg38/section.ra - lines changed 11, context: html, text, full: html, text

69c5a5974e76178684d43c58cfef2c3eccdc81fd Wed May 4 12:45:27 2016 -0700

• Merge branch 'hggenePerf'
  

58f241185a4522bb0dd6bac6df5b1abe4f5d6a4f Wed May 4 13:22:25 2016 -0700

• Shift alleles section code from exists to print routine to allow hide of section to speed up hgGene which is slow on hg19. Part of perf improvements when adding GTEx to hgGene. refs #17244
  
  • src/hg/hgGene/alleles.c - lines changed 39, context: html, text, full: html, text

f000e65b9a032c4bdf2375199627a6c8b8a17964 Wed May 4 13:22:54 2016 -0700

• Merge branch 'hggenePerf'
  

c9f540c357130c039f10a9da275891a461b99cae Wed May 4 14:07:11 2016 -0700

• Set Gene Alleles section to default off. Saves 500-1000 msec. By request of JK. Part of perf improvements motivated by adding GTEx section. refs #17244
  
  • src/hg/hgGene/hgGeneData/Human/hg19/section.ra - lines changed 1, context: html, text, full: html, text

7ab16d909d9bbd6b55565c87f7ad7b645caa90a2 Thu May 5 19:54:36 2016 -0700

• Tweak the new darkerLabels setting to further darken extra pale colors.
  
  • src/hg/hgTracks/hgTracks.c - lines changed 6, context: html, text, full: html, text