830bf78503682a5aead5d8833bffc9367c3f29c4
larrym
  Thu Jun 14 12:00:06 2012 -0700
remove odd/even classes for view menu
diff --git src/hg/hgTracks/menu.c src/hg/hgTracks/menu.c
index 8665c3b..fc78d44 100644
--- src/hg/hgTracks/menu.c
+++ src/hg/hgTracks/menu.c
@@ -1,361 +1,363 @@
 // Code to create hgTracks menu bar
 
 #include "common.h"
 #include "dystring.h"
 #include "ensFace.h"
 #include "agpFrag.h"
 #include "ctgPos.h"
 #include "hCommon.h"
 #include "htmshell.h"
 #include "hash.h"
 #include "liftOver.h"
 #include "wikiLink.h"
 #include "web.h"
 #include "hgTracks.h"
 
 /* list of links to display in a menu */
 struct hotLink
     {
     struct hotLink *next;
     char *name;
     char *url;
     char *id;
     boolean external;
     };
 
 static void appendLink(struct hotLink **links, char *url, char *name, char *id, boolean external)
 {
 // append to list of links for later printing and/or communication with javascript client
 struct hotLink *link;
 AllocVar(link);
 link->name = cloneString(name);
 link->url = cloneString(url);
 link->id = cloneString(id);
 link->external = external;
 slAddTail(links, link);
 }
 
 static void printEnsemblAnchor(char *database, char* archive,
                                char *chrName, int start, int end, struct hotLink **links)
 /* Print anchor to Ensembl display on same window. */
 {
 char *scientificName = hScientificName(database);
 char *dir = ensOrgNameFromScientificName(scientificName);
 struct dyString *ensUrl;
 char *name;
 int localStart, localEnd;
 
 name = chrName;
 
 if (sameWord(scientificName, "Takifugu rubripes"))
     {
     /* for Fugu, must give scaffold, not chr coordinates */
     /* Also, must give "chrom" as "scaffold_N", name below. */
     if (differentWord(chromName,"chrM") &&
     !hScaffoldPos(database, chromName, winStart, winEnd,
                         &name, &localStart, &localEnd))
         /* position doesn't appear on Ensembl browser.
          * Ensembl doesn't show scaffolds < 2K */
         return;
     }
 else if (sameWord(scientificName, "Gasterosteus aculeatus"))
     {
     if (differentWord("chrM", chrName))
     {
     char *fixupName = replaceChars(chrName, "chr", "group");
     name = fixupName;
     }
     }
 else if (sameWord(scientificName, "Ciona intestinalis"))
     {
     if (stringIn("chr0", chrName))
 	{
 	char *fixupName = replaceChars(chrName, "chr0", "chr");
 	name = fixupName;
 	}
     }
 else if (sameWord(scientificName, "Saccharomyces cerevisiae"))
     {
     if (stringIn("2micron", chrName))
 	{
 	char *fixupName = replaceChars(chrName, "2micron", "2-micron");
 	name = fixupName;
 	}
     }
 
 if (sameWord(chrName, "chrM"))
     name = "chrMt";
 ensUrl = ensContigViewUrl(database, dir, name, seqBaseCount, start+1, end, archive);
 appendLink(links, ensUrl->string, "Ensembl", "ensemblLink", TRUE);
 /* NOTE: you can not freeMem(dir) because sometimes it is a literal
  * constant */
 freeMem(scientificName);
 dyStringFree(&ensUrl);
 }
 
 static void fr2ScaffoldEnsemblLink(char *archive, struct hotLink **links)
 /* print out Ensembl link to appropriate scaffold there */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr = NULL;
 char **row = NULL;
 char query[256];
 safef(query, sizeof(query),
 "select * from chrUn_gold where chrom = '%s' and chromStart<%u and chromEnd>%u",
 chromName, winEnd, winStart);
 sr = sqlGetResult(conn, query);
 
 int itemCount = 0;
 struct agpFrag *agpItem = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     agpFragFree(&agpItem);  // if there is a second one
     agpItem = agpFragLoad(row+1);
     ++itemCount;
     if (itemCount > 1)
 	break;
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 if (1 == itemCount)
     {   // verify *entirely* within single contig
     if ((winEnd <= agpItem->chromEnd) &&
 	(winStart >= agpItem->chromStart))
 	{
 	int agpStart = winStart - agpItem->chromStart;
 	int agpEnd = agpStart + winEnd - winStart;
 	printEnsemblAnchor(database, archive, agpItem->frag,
                            agpStart, agpEnd, links);
 	}
     }
 agpFragFree(&agpItem);  // the one we maybe used
 }
 
 void printMenuBar()
 /* Put up the menu bar. */
 {
 struct hotLink *link, *links = NULL;
 int i, len;
 char *menuStr, buf[4096], uiVars[1024];
 safef(uiVars, sizeof(uiVars), "%s=%u", cartSessionVarName(), cartSessionId(cart));
 
 menuStr = menuBar(cart);
 
 // Create top items in view menu
 safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.psOutput=on", uiVars);
 appendLink(&links, buf, "PDF/PS", "pdfLink", FALSE);
 safef(buf, sizeof(buf), "%s&o=%d&g=getDna&i=mixed&c=%s&l=%d&r=%d&db=%s&%s",
       hgcNameAndSettings(), winStart, chromName, winStart, winEnd, database, uiVars);
 appendLink(&links, buf, "DNA", "dnaLink", FALSE);
 safef(buf, sizeof(buf), "../cgi-bin/hgConvert?hgsid=%d&db=%s", cartSessionId(cart), database);
 appendLink(&links, buf, "In other genomes", "convertMenuLink", FALSE);
 
 // Add link-outs to other dbs as appropriate for this assembly
 if (differentWord(database,"susScr2"))
     {
     /* Print Ensembl anchor for latest assembly of organisms we have
      * supported by Ensembl == if versionString from trackVersion exists */
     char ensVersionString[256], ensDateReference[256];
     ensGeneTrackVersion(database, ensVersionString, ensDateReference, sizeof(ensVersionString));
 
     if (sameWord(database,"hg19"))
         {
         printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links);
         }
     else if (sameWord(database,"hg18"))
         {
         printEnsemblAnchor(database, "ncbi36", chromName, winStart, winEnd, &links);
         }
     else if (sameWord(database,"oryCun2") || sameWord(database,"anoCar2") || sameWord(database,"calJac3"))
         {
         printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links);
         }
     else if (ensVersionString[0])
         {
         char *archive = NULL;
         if (ensDateReference[0] && differentWord("current", ensDateReference))
             archive = cloneString(ensDateReference);
         /*  Can we perhaps map from a UCSC random chrom to an Ensembl contig ? */
         if (isUnknownChrom(database, chromName))
             {
             //	which table to check
             char *ctgPos = "ctgPos";
 
             if (sameWord(database,"fr2"))
                 fr2ScaffoldEnsemblLink(archive, &links);
             else if (hTableExists(database, UCSC_TO_ENSEMBL))
                 printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links);
             else if (hTableExists(database, ctgPos))
                 /* see if we are entirely within a single contig */
                 {
                 struct sqlConnection *conn = hAllocConn(database);
                 struct sqlResult *sr = NULL;
                 char **row = NULL;
                 char query[256];
                 safef(query, sizeof(query),
                       "select * from %s where chrom = '%s' and chromStart<%u and chromEnd>%u",
                       ctgPos, chromName, winEnd, winStart);
                 sr = sqlGetResult(conn, query);
 
                 int itemCount = 0;
                 struct ctgPos *ctgItem = NULL;
                 while ((row = sqlNextRow(sr)) != NULL)
                     {
                     ctgPosFree(&ctgItem);   // if there is a second one
                     ctgItem = ctgPosLoad(row);
                     ++itemCount;
                     if (itemCount > 1)
                         break;
                     }
                 sqlFreeResult(&sr);
                 hFreeConn(&conn);
                 if (1 == itemCount)
                     {   // verify *entirely* within single contig
                     if ((winEnd <= ctgItem->chromEnd) &&
                         (winStart >= ctgItem->chromStart))
                         {
                         int ctgStart = winStart - ctgItem->chromStart;
                         int ctgEnd = ctgStart + winEnd - winStart;
                         printEnsemblAnchor(database, archive, ctgItem->contig,
                                            ctgStart, ctgEnd, &links);
                         }
                     }
                 ctgPosFree(&ctgItem);   // the one we maybe used
                 }
             }
         else
             {
             printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links);
             }
         }
     }
 
 if (sameString(database, "hg18"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&build=previous&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "hg19"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "mm8"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "danRer2"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7955&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "galGal3"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9031&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "canFam2"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9615&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "rheMac2"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9544&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "panTro2"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9598&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "anoGam1"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7165&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "bosTau6"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9913&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (startsWith("oryLat", database))
     {
     safef(buf, sizeof(buf), "http://medaka.utgenome.org/browser_ens_jump.php?revision=version1.0&chr=chromosome%s&start=%d&end=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "UTGB", "medakaLink", TRUE);
     }
 else if (sameString(database, "cb3"))
     {
     safef(buf, sizeof(buf), "http://www.wormbase.org/db/seq/gbrowse/briggsae?name=%s:%d-%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
     }
 else if (sameString(database, "cb4"))
     {
     safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_briggsae?name=%s:%d-%d",
           chromName, winStart+1, winEnd);
     appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
     }
 else if (sameString(database, "ce10"))
     {
     safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_elegans?name=%s:%d-%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
     }
 else if (sameString(database, "ce4"))
     {
     safef(buf, sizeof(buf), "http://ws170.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
     }
 else if (sameString(database, "ce2"))
     {
     safef(buf, sizeof(buf), "http://ws120.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
     }
 
 // finish View menu
 safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgTracksConfigPage=configure", uiVars);
 appendLink(&links, buf, "Configure Browser", "configureMenuLink", FALSE);
 safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.reset=on", uiVars);
 appendLink(&links, buf, "Default Tracks", "defaultTracksMenuLink", FALSE);
 safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.defaultImgOrder=on", uiVars);
 appendLink(&links, buf, "Default Track Order", "defaultTrackOrderMenuLink", FALSE);
 appendLink(&links, "../cgi-bin/cartReset", "Reset all user settings", "cartResetMenuLink", FALSE);
 
 struct dyString *viewMenu = dyStringCreate("<li class='menuparent'><span>View</span>\n<ul style='display: none; visibility: hidden;'>\n");
 len = slCount(links);
 for(i = 0, link = links; link != NULL; i++, link = link->next)
     {
     char class[100];
     if(i == 0)
         safef(class, sizeof(class), "first ");
     else if (i + 1 == len)
         safef(class, sizeof(class), "last ");
     else
         class[0] = 0;
-    safecat(class, sizeof(class), i % 2 ? "odd" : "even");
     char *encodedName = htmlEncode(link->name);
-    dyStringPrintf(viewMenu, "<li class='%s'><a href='%s' id='%s'%s>%s</a></li>\n", class, link->url, link->id, 
+    dyStringAppend(viewMenu, "<li");
+    if(*class)
+        dyStringPrintf(viewMenu, " class='%s'", class);
+    dyStringPrintf(viewMenu, "><a href='%s' id='%s'%s>%s</a></li>\n", link->url, link->id,
                    link->external ? " TARGET='_blank'" : "", encodedName);
     freez(&encodedName);
     }
 dyStringAppend(viewMenu, "</ul>\n</li>\n");
 
 menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", dyStringCannibalize(&viewMenu));
 hPuts(menuStr);
 freez(&menuStr);
 }