0950c73d715f02c493129eedff225843b7c3da98
angie
  Wed Nov 30 14:34:35 2011 -0800
Feature #3710 (vcfTabix UI options): added section headers forhaplo-sorting display and filters; added some explanatory text at
the beginning of the haplo-sorting section.

diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c
index 0a3394b..8f27f8a 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -143,82 +143,80 @@
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     if (isNotEmpty(errCatch->message->string))
 	warn("unable to open %s: %s", fileOrUrl, errCatch->message->string);
     }
 errCatchFree(&errCatch);
 return vcff;
 }
 
 static void vcfCfgHapClusterEnable(struct cart *cart, struct trackDb *tdb, char *name,
 				   boolean compositeLevel)
 /* Let the user enable/disable haplotype sorting display. */
 {
-printf("<B>Enable Haplotype sorting display: </B>");
 boolean hapClustEnabled = cartUsualBooleanClosestToHome(cart, tdb, compositeLevel,
 							VCF_HAP_ENABLED_VAR, TRUE);
 char cartVar[1024];
 safef(cartVar, sizeof(cartVar), "%s." VCF_HAP_ENABLED_VAR, name);
 cgiMakeCheckBox(cartVar, hapClustEnabled);
-printf("<BR>\n");
+printf("<B>Enable Haplotype sorting display</B><BR>\n");
 }
 
 static void vcfCfgHapClusterColor(struct cart *cart, struct trackDb *tdb, char *name,
 				   boolean compositeLevel)
 /* Let the user choose how to color the sorted haplotypes. */
 {
-printf("<B>Color sorted haplotypes by:</B>\n");
+printf("<B>Haplotype coloring scheme:</B><BR>\n");
 char *colorBy = cartUsualStringClosestToHome(cart, tdb, compositeLevel,
 					     VCF_HAP_COLORBY_VAR, VCF_HAP_COLORBY_REFALT);
 boolean colorByRefAlt = sameString(colorBy, VCF_HAP_COLORBY_REFALT);
 char varName[1024];
 safef(varName, sizeof(varName), "%s." VCF_HAP_COLORBY_VAR, name);
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_REFALT, colorByRefAlt);
-printf("reference/alternate alleles (reference = blue, alternate = red)\n");
+printf("reference/alternate alleles (reference = blue, alternate = red)<BR>\n");
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_BASE, !colorByRefAlt);
 printf("first base of allele (A = red, C = blue, G = green, T = magenta)<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>");
     }
 }
 
 static void vcfCfgHapCluster(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
 			     char *name, boolean compositeLevel)
 /* Show controls for haplotype-sorting display, which only makes sense to do when
  * the VCF file describes multiple genotypes. */
 {
 vcfCfgHapClusterEnable(cart, tdb, name, compositeLevel);
 vcfCfgHaplotypeCenter(cart, tdb, name, compositeLevel, vcff, NULL, NULL, 0, "mainForm");
 vcfCfgHapClusterColor(cart, tdb, name, compositeLevel);
 vcfCfgHapClusterHeight(cart, tdb, vcff, name, compositeLevel);
-//      thicken lines?
-//      outline center variant?
+puts("<BR>");
 }
 
 static void vcfCfgMinQual(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
 			  char *name, boolean compositeLevel)
 /* If checkbox is checked, apply minimum value filter to QUAL column. */
 {
 char cartVar[1024];
 safef(cartVar, sizeof(cartVar), "%s." VCF_APPLY_MIN_QUAL_VAR, name);
 boolean applyFilter = cartUsualBooleanClosestToHome(cart, tdb, compositeLevel,
 					VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL);
 cgiMakeCheckBox(cartVar, applyFilter);
 printf("<B>Exclude items with QUAL score less than &nbsp;</B>\n");
 double minQual = cartUsualDoubleClosestToHome(cart, tdb, compositeLevel, VCF_MIN_QUAL_VAR,
 					      VCF_DEFAULT_MIN_QUAL);
 safef(cartVar, sizeof(cartVar), "%s." VCF_MIN_QUAL_VAR, name);
@@ -271,31 +269,41 @@
 cgiMakeDoubleVarInRange(varName, cartMinFreq, "minor allele frequency between 0.0 and 0.5", 5,
 			"0.0", "0.5");
 puts("<BR>");
 }
 
 void vcfCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed)
 /* VCF: Variant Call Format.  redmine #3710 */
 {
 boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
 printf("<TABLE%s><TR><TD>", boxed ? " width='100%'" : "");
 struct vcfFile *vcff = vcfHopefullyOpenHeader(cart, tdb);
 if (vcff != NULL)
     {
     boolean compositeLevel = isNameAtCompositeLevel(tdb, name);
     if (vcff->genotypeCount > 1)
+	{
+	puts("<H3>Haplotype sorting display</H3>");
+	puts("<P>When this display mode is enabled and genotypes are phased or homozygous, "
+	     "each genotype is split into two independent haplotypes. "
+	     "These local haplotypes are clustered by similarity around a central variant. "
+	     "Haplotypes are reordered for display using the clustering tree, which is "
+	     "drawn in the left label area. "
+	     "Local haplotype blocks can often be identified using this display.</P>");
 	vcfCfgHapCluster(cart, tdb, vcff, name, compositeLevel);
+	}
+    puts("<H3>Filters</H3>");
     vcfCfgMinQual(cart, tdb, vcff, name, compositeLevel);
     vcfCfgFilterColumn(cart, tdb, vcff, name, compositeLevel);
     vcfCfgMinAlleleFreq(cart, tdb, vcff, name, compositeLevel);
     }
 else
     {
     printf("Sorry, couldn't access VCF file.<BR>\n");
     }
 
 puts("</TD>");
 if (boxed && fileExists(hHelpFile("hgVcfTrackHelp")))
     printf("<TD style='text-align:right'><A HREF=\"../goldenPath/help/hgVcfTrackHelp.html\" "
            "TARGET=_BLANK>VCF configuration help</A></TD>");
 
 printf("</TR></TABLE>");