Commits for angie

v372_preview2 to v372_base (2018-09-24 to 2018-10-01) v372

3ecfb8deb165083b0d3df5081aeb5dda2c4b6ff1 Mon Sep 24 10:53:38 2018 -0700

• Libifying JS module autocompleteCat (autocomplete with optional category labels) from hgGateway.
  • src/hg/hgGateway/hgGateway.c - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/style/HGStyle.css - lines changed 14, context: html, text, full: html, text
  • src/hg/htdocs/style/jWest.css - lines changed 13, context: html, text, full: html, text
  • src/hg/js/autocompleteCat.js - lines changed 118, context: html, text, full: html, text
  • src/hg/js/hgGateway.js - lines changed 119, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text

bffbb000a3df4b88a8117ea5f852ab3abeea6e17 Mon Sep 24 14:42:01 2018 -0700

• Added a new mode to hgSuggest: altOrPatch, to match alt haplo or fix patch sequence names. Use it in hgTracks' multi-region dialog. Make the dialog inputs activate their respective radio buttons. refs #18854
  • src/hg/hgSuggest/hgSuggest.c - lines changed 162, context: html, text, full: html, text
  • src/hg/hgTracks/config.c - lines changed 22, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 4, context: html, text, full: html, text
  • src/hg/js/hgTracks.js - lines changed 13, context: html, text, full: html, text

13827887c45cb6ba7da05276cf0c703ec7627c17 Tue Sep 25 13:29:25 2018 -0700

• Add 'show this sequence placed on its chromosome' link to fixLocations in addition to altLocations, and chop ':start-end' from item names to get just the sequence name for singleAltHaplo mode. refs #18854
  • src/hg/hgc/hgc.c - lines changed 13, context: html, text, full: html, text

3446d0006f2c776afd02a36d351d79611383615e Tue Sep 25 13:26:29 2018 -0700

• Chop at ':', if there is one, in {alt,fix}Locations.name when matching an alt or fix sequence name. refs #18854
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text

31d76baa5576bc0fe479c2b9ae3d06a6df875cc1 Tue Sep 25 13:32:17 2018 -0700

• In the multi-region position pop-up, when viewing just a subregion of a large virt, add a hint about the full region size to make it clear that it's a subregion not the whole thing.
  • src/hg/js/hgTracks.js - lines changed 9, context: html, text, full: html, text

d86d0030a9eb8ebce064d942456b42e6f82874cf Tue Sep 25 14:11:18 2018 -0700

• In altOrPatch mode, if prefix matching yields no results, then try matching any part of sequence names. Treat '.' as a single-char wildcard so 'KI270857.1' can match chr17_KI270857v1_alt. refs #18854
  • src/hg/hgSuggest/hgSuggest.c - lines changed 26, context: html, text, full: html, text

f70c2b18fe16f73ae6faee21e006eabcf5fd9aa6 Wed Sep 26 10:05:16 2018 -0700

• Tweak to prevent symmetrical _alt and _fix mappings from causing alt results in fix searches and vice versa. refs #18854
  • src/hg/hgSuggest/hgSuggest.c - lines changed 4, context: html, text, full: html, text

e4406bcd83a67929f2c980c338eba9071818d461 Wed Sep 26 10:54:01 2018 -0700

• Add chromAlias to multi-region alt/fix autocomplete, so we can match RefSeq accessions and Assembly names. refs #18854
  • src/hg/hgSuggest/hgSuggest.c - lines changed 46, context: html, text, full: html, text

fca9df21f4b3dfbb1191a0fe13d1d1bb100252c3 Wed Sep 26 11:20:36 2018 -0700

• In multi-region dialog, mention fix patches if applicable, and make alt/fix input wider to accommodate long aliases and autocomplete labels. refs #18854
  • src/hg/hgTracks/config.c - lines changed 5, context: html, text, full: html, text

57d1068b88c6255f3530cb981bf97bb127a459f9 Wed Sep 26 11:42:17 2018 -0700

• Fixing typo in regex for ignoring stuff after the colon and position range in altLocations names. refs #18854
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text

60e7358ad9239e80827ee2a9d95151ef5fc57946 Wed Sep 26 12:17:25 2018 -0700

• Add fuzzy search of chromAlias to multi-region alt/fix autocomplete, so common haplotype name components like 'cox', 'apd', 'kir' can be matched. refs #18544
  • src/hg/hgSuggest/hgSuggest.c - lines changed 9, context: html, text, full: html, text

a4234f184e880692939c7dfe967d1d3b220399e6 Wed Sep 26 12:25:10 2018 -0700

• In multi-region alt/fix autocomplete, escape search terms in the same way for chromAlias search as for {alt,fix}SeqLiftOverPsl. refs #18544
  • src/hg/hgSuggest/hgSuggest.c - lines changed 20, context: html, text, full: html, text

9c6ef86df0c2a4358634bcd9dae49093e300ff29 Wed Sep 26 15:28:10 2018 -0700

• For multi-region alt/fix autocomplete, use {alt,fix}Locations insteaf of {alt,fix}SeqLiftOverPsl because the former are more stable at this point, and the *Locations tables are used by hgTracks. refs #22144
  • src/hg/hgSuggest/hgSuggest.c - lines changed 14, context: html, text, full: html, text