6172ee24c819e779de63549b5a0db2f0742465f5
chinhli
  Tue Jan 29 16:12:24 2013 -0800
Track #8533 NumtS tracks: Add logic to numtsClick.c to handle the shortened name in 'numtSMitochondrion' table. For example, old NumtS data for or hg18, hg19 and mm9 have name like Mms_NumtS_096_b1, and all new species like dog and cow now have a shorten name like 'SS_NumtS_246')
diff --git src/hg/hgc/numtsClick.c src/hg/hgc/numtsClick.c
index 24a12c4..b4fa72a 100644
--- src/hg/hgc/numtsClick.c
+++ src/hg/hgc/numtsClick.c
@@ -1,128 +1,135 @@
 /* numtsClick - hgc code to display Numts track item detail page */
 #include "common.h"
 #include "hgc.h"
 #include "numtsClick.h"
 
 void doNumtS(struct trackDb *tdb, char *itemName)
 /* Put up page for NumtS. */
 {
 char *table = tdb->table;
 struct sqlConnection *conn = hAllocConn(database);
 struct bed *bed;
 char query[512];
 struct sqlResult *sr;
 char **row;
 boolean firstTime = TRUE;
 int start = cartInt(cart, "o");
 int num = 6;
 char itemNameDash[64]; /* itenName appended with a "_" */
 char itemNameTrimmed[64]; /* itemName trimed at last "_" */
 int sDiff = 30; /* acceptable difference of genomics size */
 /* message strings */
 char *clickMsg = NULL;
 char *openMsg1 = "Click 'browser' link below to open Genome Browser at genomic position where";
 char *openMsg2 = "maps\n";
 char *openMsgM = "Click 'browser' link below to open Genome Browser at mitochondrial position where";
 
 
 genericHeader(tdb, itemName);
 genericBedClick(conn, tdb, itemName, start, num);
 
 safecpy(itemNameDash, sizeof(itemNameDash),itemName);
 safecat(itemNameDash,64,"_");
 safecpy(itemNameTrimmed, sizeof(itemNameTrimmed),itemName);
 chopSuffixAt(itemNameTrimmed, '_');
 
 safef(query, sizeof(query), "select chrom, chromStart, chromEnd, name, score, strand from %s where name='%s'",
       table, itemName);
 sr = sqlGetResult(conn, query);
 int sSize=0;
 while ((row = sqlNextRow(sr)) != NULL)
     {
         bed = bedLoad6(row);
         sSize = bed->chromEnd - bed->chromStart;
         /* printf("sSize is: %5d <BR>", sSize); */
     }
 
 
 if (sameString("hg18", database))
 {
   if (sameString("numtS", table) || sameString("numtSAssembled", table))
       {
       safef(query, sizeof(query),
           "select  chrom, chromStart, chromEnd, name, score, strand "
           "from numtSMitochondrionChrPlacement where ( "
           "(name = '%s') OR (((name REGEXP '^%s') OR (name='%s')) AND "
           " (ABS((chromEnd - chromStart)-%d) <= %d ))) ",
       itemName, itemNameDash, itemNameTrimmed, sSize, sDiff);
       clickMsg = openMsgM;
       }
     else if (sameString("numtSMitochondrion", table))
       {
       safef(query, sizeof(query),
           "select  chrom, chromStart, chromEnd, name, score, strand "
           "from numtS where ( "
           "(name = '%s') OR (((name REGEXP '^%s') OR (name='%s')) AND "
           " (ABS((chromEnd - chromStart)-%d) <= %d ))) ",
       itemName, itemNameDash, itemNameTrimmed, sSize, sDiff);
       clickMsg = openMsg1;
         }
     else if (sameString("numtSMitochondrionChrPlacement", table))
       {
       safef(query, sizeof(query),
           "select  chrom, chromStart, chromEnd, name, score, strand "
           "from numtS where ( "
           "(name = '%s') OR (((name REGEXP '^%s') OR (name='%s')) AND "
           " (ABS((chromEnd - chromStart)-%d) <= %d ))) ",
       itemName, itemNameDash, itemNameTrimmed, sSize, sDiff);
       clickMsg = openMsg1;
       }
 } else {
   if (sameString("numtS", table) || sameString("numtSAssembled", table))
      {
+      if (sameString("hg19", database) || sameString("mm9", database))
+      {  
      safef(query, sizeof(query),
          "select  chrom, chromStart, chromEnd, name, score, strand "
          "from numtSMitochondrion where name = '%s'  ", itemName);
+      } else {
+          safef(query, sizeof(query),
+              "select  chrom, chromStart, chromEnd, name, score, strand "
+            "from numtSMitochondrion where name = '%s'  ", itemNameTrimmed);
+      }  
      clickMsg = openMsgM;
      }
   else if (sameString("numtSMitochondrion", table))
      {
       safef(query, sizeof(query),
           "select  chrom, chromStart, chromEnd, name, score, strand "
-          "from numtS where name = '%s'", itemName);
+          "from numtS where name like '%s%%'", itemName);
       clickMsg = openMsg1;
      }
 }
 
     sr = sqlGetResult(conn, query);
     firstTime = TRUE;
 
     while ((row = sqlNextRow(sr)) != NULL)
         {
         printf("<PRE><TT>");
         if (firstTime)
             {
             firstTime = FALSE;
         printf("<BR><H3>%s item '%s' %s</H3><BR>", clickMsg, itemName, openMsg2);
 
             printf("BROWSER | NAME                CHROMOSOME      START        END     SIZE    SCORE  STRAND \n");
             printf("--------|--------------------------------------------------------------------------------------------\n");
 
             }
         bed = bedLoad6(row);
         printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">browser</A> | ",
                hgTracksPathAndSettings(), database,
                bed->chrom, bed->chromStart+1, bed->chromEnd);
 
         printf("%-20s %-10s %9d  %9d    %5d    %5d    %1s",
             bed->name, bed->chrom, bed->chromStart+1, bed->chromEnd,
             (bed->chromEnd - bed->chromStart),bed->score, bed->strand);
 
         printf("</TT></PRE>");
         }
 
  printf("<BR>");
  printTrackHtml(tdb);
  hFreeConn(&conn);
 }