6e303eeb45dbabb0e9b38bb6eaa24f3948d4908f
angie
  Fri Feb 4 09:40:36 2011 -0800
Track #34 (dbVar for human): Color switch agreed on by NCBI, DGV andother parties: Gain is now blue, Loss is now red.

diff --git src/hg/hgTracks/gvfTrack.c src/hg/hgTracks/gvfTrack.c
index 12aa558..cdfd100 100644
--- src/hg/hgTracks/gvfTrack.c
+++ src/hg/hgTracks/gvfTrack.c
@@ -1,122 +1,122 @@
 /* gvfTrack.c - display variants from GVF (http://www.sequenceontology.org/gvf.html) */
 
 #include "common.h"
 #include "hgTracks.h"
 #include "imageV2.h"
 #include "hdb.h"
 #include "bed8Attrs.h"
 
 static Color gvfColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* Color item by var_type attribute, according to Deanna Church's document
  * SvRepresentation2.doc attached to redmine #34. */
 {
 struct bed8Attrs *gvf = item;
 Color dbVarUnknown = hvGfxFindColorIx(hvg, 0xb2, 0xb2, 0xb2);
 int ix = stringArrayIx("var_type", gvf->attrTags, gvf->attrCount);
 if (ix < 0)
     return dbVarUnknown;
 char *varType = gvf->attrVals[ix];
 if (sameString(varType, "CNV"))
     return MG_BLACK;
 else if (sameString(varType, "Gain"))
-    return hvGfxFindColorIx(hvg, 0xcc, 0x66, 0x00);
-else if (sameString(varType, "Loss"))
     return hvGfxFindColorIx(hvg, 0x00, 0x00, 0xff);
+else if (sameString(varType, "Loss"))
+    return hvGfxFindColorIx(hvg, 0xff, 0x00, 0x00);
 else if (sameString(varType, "Insertion"))
     return hvGfxFindColorIx(hvg, 0xff, 0xcc, 0x00);
 else if (sameString(varType, "Complex"))
     return hvGfxFindColorIx(hvg, 0x99, 0xcc, 0xff);
 else if (sameString(varType, "Unknown"))
     return dbVarUnknown;
 else if (sameString(varType, "Other"))
     return hvGfxFindColorIx(hvg, 0xcc, 0x99, 0xff);
 else if (sameString(varType, "Inversion"))
     return hvGfxFindColorIx(hvg, 0x99, 0x33, 0xff); // Needs pattern
 else if (sameString(varType, "LOH"))
     return hvGfxFindColorIx(hvg, 0x00, 0x00, 0xff); // Needs pattern
 else if (sameString(varType, "Everted"))
     return hvGfxFindColorIx(hvg, 0x66, 0x66, 0x66); // Needs pattern
 else if (sameString(varType, "Transchr"))
     return hvGfxFindColorIx(hvg, 0xb2, 0xb2, 0xb2); // Plus black vert. bar at broken end
 else if (sameString(varType, "UPD"))
     return hvGfxFindColorIx(hvg, 0x00, 0xff, 0xff); // Needs pattern
 return dbVarUnknown;
 }
 
 // Globals used for sorting:
 static struct hash *nameHash = NULL;
 
 static char *getAttributeVal(const struct bed8Attrs *gvf, char *tag)
 /* Return value corresponding to tag or NULL.  Don't free result. */
 {
 int ix = stringArrayIx(tag, gvf->attrTags, gvf->attrCount);
 if (ix >= 0)
     return(gvf->attrVals[ix]);
 return NULL;
 }
 
 static int gvfHierCmp(const void *va, const void *vb)
 /* Sort GVF so that children follow their parents, and children of the same parent 
  * are sorted by var_type -- otherwise things are sorted by size,chromStart,name. */
 {
 const struct bed8Attrs *a = *((struct bed8Attrs **)va);
 const struct bed8Attrs *b = *((struct bed8Attrs **)vb);
 char *aParentName = getAttributeVal(a, "Parent");
 char *bParentName = getAttributeVal(b, "Parent");
 if (bParentName != NULL && sameString(bParentName, a->name))
     return -1;
 else if (aParentName != NULL && sameString(aParentName, b->name))
     return 1;
 else if (aParentName != NULL && bParentName != NULL && sameString(aParentName, bParentName))
     return strcmp(getAttributeVal(a, "var_type"), getAttributeVal(b, "var_type"));
 else
     {
     const struct bed8Attrs *bedCmpA = a, *bedCmpB = b;
     if (aParentName != NULL)
 	bedCmpA = hashFindVal(nameHash, aParentName);
     if (bParentName != NULL)
 	bedCmpB = hashFindVal(nameHash, bParentName);
     // no need to compare chrom here
     int diff = ((bedCmpB->chromEnd - bedCmpB->chromStart) -
 		(bedCmpA->chromEnd - bedCmpA->chromStart));
     if (diff == 0)
 	{
 	diff = bedCmpA->chromStart - bedCmpB->chromStart;
 	if (diff == 0)
 	    diff = strcmp(bedCmpA->name, bedCmpB->name);
 	}
     return diff;
     }
 }
 
 static void gvfLoad(struct track *tg)
 /* Load GVF items from a bed8Attrs database table. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 int rowOffset;
 struct sqlResult *sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
 char **row;
 struct bed8Attrs *list = NULL;
 // if we someday get dense GVF tracks, might consider upping the default hash size:
 if (nameHash == NULL)
     nameHash= hashNew(0);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct bed8Attrs *gvf = bed8AttrsLoad(row+rowOffset);
     slAddHead(&list, gvf);
     hashAdd(nameHash, gvf->name, gvf);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 slSort(&list, gvfHierCmp);
 tg->items = list;
 }
 
 void gvfMethods(struct track *tg)
 /* Load GVF variant data. */
 {
 bedMethods(tg);
 tg->canPack = TRUE;
 tg->loadItems = gvfLoad;
 tg->itemColor = gvfColor;
 }