4cab7f311cadce7428c1d7e1c4dfdcb0d3a43033
angie
  Wed Jul 27 10:32:19 2011 -0700
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting.  Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.

diff --git src/hg/lib/hui.c src/hg/lib/hui.c
index 1364274..134c590 100644
--- src/hg/lib/hui.c
+++ src/hg/lib/hui.c
@@ -16,30 +16,31 @@
 #include "chainDb.h"
 #include "netCart.h"
 #include "obscure.h"
 #include "wiggle.h"
 #include "phyloTree.h"
 #include "hgMaf.h"
 #include "udc.h"
 #include "customTrack.h"
 #include "encode/encodePeak.h"
 #include "mdb.h"
 #include "web.h"
 #include "hPrint.h"
 #include "fileUi.h"
 #include "bigBed.h"
 #include "bigWig.h"
+#include "vcfUi.h"
 
 static char const rcsid[] = "$Id: hui.c,v 1.297 2010/06/02 19:27:51 tdreszer Exp $";
 
 #define SMALLBUF 128
 #define MAX_SUBGROUP 9
 #define ADD_BUTTON_LABEL        "add"
 #define CLEAR_BUTTON_LABEL      "clear"
 #define JBUFSIZE 2048
 
 //#define PM_BUTTON "<A NAME=\"%s\"></A><A HREF=\"#%s\"><IMG height=18 width=18 onclick=\"return (setCheckBoxesThatContain('%s',%s,true,'%s','','%s') == false);\" id=\"btn_%s\" src=\"../images/%s\" alt=\"%s\"></A>\n"
 //#define DEF_BUTTON "<A NAME=\"%s\"></A><A HREF=\"#%s\"><IMG onclick=\"setCheckBoxesThatContain('%s',true,false,'%s','','%s'); return (setCheckBoxesThatContain('%s',false,false,'%s','_defOff','%s') == false);\" id=\"btn_%s\" src=\"../images/%s\" alt=\"%s\"></A>\n"
 //#define DEFAULT_BUTTON(nameOrId,anc,beg,contains) printf(DEF_BUTTON,(anc),(anc),(nameOrId),        (beg),(contains),(nameOrId),(beg),(contains),(anc),"defaults_sm.png","default")
 //#define    PLUS_BUTTON(nameOrId,anc,beg,contains) printf(PM_BUTTON, (anc),(anc),(nameOrId),"true", (beg),(contains),(anc),"add_sm.gif",   "+")
 //#define   MINUS_BUTTON(nameOrId,anc,beg,contains) printf(PM_BUTTON, (anc),(anc),(nameOrId),"false",(beg),(contains),(anc),"remove_sm.gif","-")
 #define PM_BUTTON  "<IMG height=18 width=18 onclick=\"setCheckBoxesThatContain('%s',%s,true,'%s','','%s');\" id=\"btn_%s\" src=\"../images/%s\" alt=\"%s\">\n"
@@ -3718,30 +3719,32 @@
                         break;
     case cfgWigMaf:     wigMafCfgUi(cart,tdb,prefix,title,boxed, db);
                         break;
     case cfgGenePred:   genePredCfgUi(cart,tdb,prefix,title,boxed);
                         break;
     case cfgChain:      chainCfgUi(db,cart,tdb,prefix,title,boxed, NULL);
                         break;
     case cfgNetAlign:	netAlignCfgUi(db,cart,tdb,prefix,title,boxed);
                         break;
     case cfgBedFilt:    bedUi(tdb,cart,title, boxed);
                  	break;
 #ifdef USE_BAM
     case cfgBam:        bamCfgUi(cart, tdb, prefix, title, boxed);
 			break;
 #endif
+    case cfgVcf:	vcfCfgUi(cart, tdb, prefix, title, boxed);
+			break;
     case cfgPsl:	pslCfgUi(db,cart,tdb,prefix,title,boxed);
                         break;
     default:            warn("Track type is not known to multi-view composites. type is: %d ", cType);
                         break;
     }
 }
 
 char *encodeRestrictionDateDisplay(char *db,struct trackDb *trackDb)
 /* Create a string for ENCODE restriction date of this track
    if return is not null, then free it after use */
 {
 if (!trackDb)
     return NULL;
 
 boolean addMonths = FALSE;
@@ -4248,57 +4251,57 @@
 /* safef into javascript a sequence of commands that will force a refresh
  * of this same form, updating the values of whatever variables are necessary
  * to say what we want to do. */
 {
 safef(javascript, JBUFSIZE*sizeof(char),
       "document.%s.action = '%s'; document.%s.%s.value='%s'; "
       "document.%s.submit();",
       formName, cgiScriptName(), formName, buttonVar, label,
       formName);
 }
 
 #define MANY_SUBTRACKS  8
 
 #define WIGGLE_HELP_PAGE  "../goldenPath/help/hgWiggleTrackHelp.html"
 
-static boolean cfgBeginBoxAndTitle(struct trackDb *tdb, boolean boxed, char *title)
+boolean cfgBeginBoxAndTitle(struct trackDb *tdb, boolean boxed, char *title)
 /* Handle start of box and title for individual track type settings */
 {
 if(!boxed)
     {
     boxed = trackDbSettingOn(tdb,"boxedCfg");
     if(boxed)
         printf("<BR>");
     }
 if (boxed)
     {
     printf("<TABLE class='blueBox");
     char *view = tdbGetViewName(tdb);
     if(view != NULL)
         printf(" %s",view);
     printf("' style='background-color:%s;'><TR><TD>", COLOR_BG_ALTDEFAULT);
     if (title)
         printf("<CENTER><B>%s Configuration</B></CENTER>\n", title);
     }
 else if (title)
     printf("<p><B>%s &nbsp;</b>", title );
 else
     printf("<p>");
 return boxed;
 }
 
-static void cfgEndBox(boolean boxed)
+void cfgEndBox(boolean boxed)
 /* Handle end of box and title for individual track type settings */
 {
 if (boxed)
     puts("</td></tr></table>");
 }
 
 void wigCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed)
 /* UI for the wiggle track */
 {
 char *typeLine = NULL;  /*  to parse the trackDb type line  */
 char *words[8];     /*  to parse the trackDb type line  */
 int wordCount = 0;  /*  to parse the trackDb type line  */
 char option[256];
 double minY;        /*  from trackDb or cart    */
 double maxY;        /*  from trackDb or cart    */