ecd4f71ea1c566e01e66eb050657f0270f5dc278
angie
  Tue Dec 6 08:58:41 2011 -0800
Feature #3711 (VCF haplo-sorting display): David requested that non-leafbranches always appear as rectangles.  Now the triangular vs. rectangular
option applies only to leaf clusters.

diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c
index 3772c3c..10b37e7 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -172,41 +172,41 @@
 					     VCF_HAP_COLORBY_VAR, VCF_DEFAULT_HAP_COLORBY);
 char varName[1024];
 safef(varName, sizeof(varName), "%s." VCF_HAP_COLORBY_VAR, name);
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_ALTONLY, sameString(colorBy, VCF_HAP_COLORBY_ALTONLY));
 printf("reference alleles invisible, alternate alleles in black<BR>\n");
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_REFALT, sameString(colorBy, VCF_HAP_COLORBY_REFALT));
 printf("reference alleles in blue, alternate alleles in red<BR>\n");
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_BASE, sameString(colorBy, VCF_HAP_COLORBY_BASE));
 printf("first base of allele (A = red, C = blue, G = green, T = magenta)<BR>\n");
 }
 
 static void vcfCfgHapClusterTreeAngle(struct cart *cart, struct trackDb *tdb, char *name,
 				   boolean compositeLevel)
 /* Let the user choose branch shape. */
 {
-printf("<B>Haplotype clustering tree branch shape:</B><BR>\n");
+printf("<B>Haplotype clustering tree leaf shape:</B><BR>\n");
 char *treeAngle = cartUsualStringClosestToHome(cart, tdb, compositeLevel,
 					     VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE);
 char varName[1024];
 safef(varName, sizeof(varName), "%s." VCF_HAP_TREEANGLE_VAR, name);
 cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_TRIANGLE,
 		   sameString(treeAngle, VCF_HAP_TREEANGLE_TRIANGLE));
-printf("triangular<BR>\n");
+printf("draw leaf clusters as &lt;<BR>\n");
 cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_RECTANGLE,
 		   sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE));
-printf("rectangular<BR>\n");
+printf("draw leaf clusters as [<BR>\n");
 }
 
 static void vcfCfgHapClusterHeight(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
 				   char *name, boolean compositeLevel)
 /* Let the user specify a height for the track. */
 {
 if (vcff != NULL && vcff->genotypeCount > 1)
     {
     printf("<B>Haplotype sorting display height:</B> \n");
     int cartHeight = cartUsualIntClosestToHome(cart, tdb, compositeLevel,
 					       VCF_HAP_HEIGHT_VAR, VCF_DEFAULT_HAP_HEIGHT);
     char varName[1024];
     safef(varName, sizeof(varName), "%s." VCF_HAP_HEIGHT_VAR, name);
     cgiMakeIntVarInRange(varName, cartHeight, "Height (in pixels) of track", 5, "4", "2500");
     puts("<BR>");