9723799cf6f1a8fb714ae1493b224b8e91aebf09
tdreszer
  Mon Jul 30 12:17:38 2012 -0700
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
diff --git src/hg/hgc/mafClick.c src/hg/hgc/mafClick.c
index 822a5e6..40254cf 100644
--- src/hg/hgc/mafClick.c
+++ src/hg/hgc/mafClick.c
@@ -191,32 +191,31 @@
                        s, cgiEncode(chrom),
                        chrom, s, e, dbOnly, revComp);
                     }
                 else
                     fprintf(f, "  ");
                 }
             else
                 {
                 fprintf(f, "    ");
                 }
 
             dyStringClear(dy);
             dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size);
             fprintf(f, "<A TITLE=\"%s\"> %*s </A> ", dy->string, srcChars, org);
 
-            updateSummaryLine(summaryLine, referenceText + lineStart,
-                                    mc->text + lineStart, size);
+            updateSummaryLine(summaryLine, referenceText + lineStart, mc->text + lineStart, size);
             blueCapWrite(f, mc->text + lineStart, size,
 			 (onlyDiff && mc != maf->components) ? referenceText + lineStart : NULL);
 	    fprintf(f, "\n");
 	    }
 	else
 	    {
 	    if (((mc->leftStatus == MAF_CONTIG_STATUS) && (mc->rightStatus == MAF_CONTIG_STATUS) )
 	    || ((mc->leftStatus == MAF_TANDEM_STATUS) && (mc->rightStatus == MAF_TANDEM_STATUS) )
 	    || ((mc->leftStatus == MAF_INSERT_STATUS) && (mc->rightStatus == MAF_INSERT_STATUS) )
 	    || ((mc->leftStatus == MAF_MISSING_STATUS) && (mc->rightStatus == MAF_MISSING_STATUS) ))
 		{
                 if (lineStart == 0)
 		    {
 		    int s = mc->start;
 		    int e = s + mc->rightLen;
@@ -430,60 +429,58 @@
 }
 
 static void capMafOnTrack(struct mafAli *maf, char *track, boolean onlyCds)
 /* Capitalize parts of maf that correspond to exons according
  * to given gene prediction track.  */
 {
 char dbOnly[64];
 char *chrom;
 struct mafComp *mc = maf->components;
 strncpy(dbOnly, mc->src, sizeof(dbOnly));
 chrom = chopPrefix(dbOnly);
 capAliTextOnTrack(maf, dbOnly, chrom, track, onlyCds);
 }
 #endif
 
-static struct mafAli *mafOrAxtLoadInRegion2(struct sqlConnection *conn,
-        struct sqlConnection *conn2, struct trackDb *tdb,
-        char *chrom, int start, int end, char *axtOtherDb, char *file)
+static struct mafAli *mafOrAxtLoadInRegion2(struct sqlConnection *conn,struct sqlConnection *conn2,
+                                            struct trackDb *tdb, char *chrom, int start, int end,
+                                            char *axtOtherDb, char *file)
 {
 if (axtOtherDb != NULL)
     {
     struct hash *qSizeHash = hChromSizeHash(axtOtherDb);
     struct mafAli *mafList = axtLoadAsMafInRegion(conn, tdb->table,
-        chrom, start, end,
-	database, axtOtherDb, hChromSize(database, chrom), qSizeHash);
+            chrom, start, end, database, axtOtherDb, hChromSize(database, chrom), qSizeHash);
     hashFree(&qSizeHash);
     return mafList;
     }
 else
     return mafLoadInRegion2(conn, conn2, tdb->table, chrom,
 	start, end, file);
 }
 
 /* Load mafs from region, either from maf or axt file. */
 static struct mafAli *mafOrAxtLoadInRegion(struct sqlConnection *conn,
 	struct trackDb *tdb, char *chrom, int start, int end,
 	char *axtOtherDb)
 /* Load mafs from region, either from maf or axt file. */
 {
 if (axtOtherDb != NULL)
     {
     struct hash *qSizeHash = hChromSizeHash(axtOtherDb);
     struct mafAli *mafList = axtLoadAsMafInRegion(conn, tdb->table,
-        chrom, start, end,
-        database, axtOtherDb, hChromSize(database, chrom), qSizeHash);
+            chrom, start, end, database, axtOtherDb, hChromSize(database, chrom), qSizeHash);
     hashFree(&qSizeHash);
     return mafList;
     }
 else
     return mafLoadInRegion(conn, tdb->table, chrom, start, end);
 }
 
 #ifdef ADDEXONCAPITAL
 static char *codeAll[] = {
 	"coding",
 	"all",
 };
 #endif
 
 static char *showAll[] = {
@@ -754,32 +751,32 @@
             puts("<B>Components not displayed:</B> ");
             while ((species = hashNextName(&hc)) != NULL)
                 printf("%s ", species);
             puts("<BR>");
             }
 
 
 	for (maf = subList; maf != NULL; maf = maf->next)
 	    {
 	    mafLowerCase(maf);
 #ifdef ADDEXONCAPITAL
 	    if (capTrack != NULL)
                 capMafOnTrack(maf, capTrack, onlyCds);
 #endif
             printf("<B>Alignment block %d of %d in window, %d - %d, %d bps </B>\n",
-                ++aliIx,realCount,maf->components->start + 1,maf->components->start + maf->components->size,
-                maf->components->size);
+                   ++aliIx,realCount,maf->components->start + 1,
+                   maf->components->start + maf->components->size, maf->components->size);
             mafPrettyOut(stdout, maf, 70,onlyDiff, aliIx);
             }
 	mafAliFreeList(&subList);
 	}
     else
 	{
         printf("No multiple alignment in browser window");
 	}
     printf("</PRE></TT>");
     }
 }
 
 static void mafOrAxtClick(struct sqlConnection *conn, struct trackDb *tdb, char *axtOtherDb)
 {
 struct sqlConnection *conn2 = hAllocConn(database);
@@ -935,31 +932,32 @@
 	if (mc->strand == '-')
 	    reverseIntRange(&s, &e, mc->srcSize);
 
 
 	if (mc->text != NULL)
 	    {
 	    fprintf(f, "    ");
 
             dyStringClear(dy);
             dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size);
             fprintf(f, "<A TITLE=\"%s\"> %*s </A> ", dy->string, srcChars, org);
 
             updateSummaryLine(summaryLine, referenceText + lineStart,
                                     mc->text + lineStart, size);
             blueCapWriteGsid(f, mc->text + lineStart, size,
-                (onlyDiff && mc != maf->components) ? referenceText + lineStart : NULL, isProtein,
+                             (onlyDiff && mc != maf->components) ? referenceText + lineStart
+                                                                 : NULL, isProtein,
                  mc->start-mafOrig);
             fprintf(f, "\n");
             }
 	else
 	    {
 	    if (((mc->leftStatus == MAF_CONTIG_STATUS) && (mc->rightStatus == MAF_CONTIG_STATUS) )
 	    || ((mc->leftStatus == MAF_TANDEM_STATUS) && (mc->rightStatus == MAF_TANDEM_STATUS) )
 	    || ((mc->leftStatus == MAF_INSERT_STATUS) && (mc->rightStatus == MAF_INSERT_STATUS) )
 	    || ((mc->leftStatus == MAF_MISSING_STATUS) && (mc->rightStatus == MAF_MISSING_STATUS) ))
 		{
                 if (lineStart == 0)
 		    {
 		    int s = mc->start;
 		    int e = s + mc->rightLen;
 		    //struct dyString *dy = newDyString(512);
@@ -1254,32 +1252,32 @@
             while ((species = hashNextName(&hc)) != NULL)
                 {
 		/* print a break every 6 items */
 		if (((itemPrinted % 6) == 0) && (itemPrinted >0))
 		    printf("<br>");
 		printf("%s ", species);
 		itemPrinted++;
 		}
             puts("<BR>");
             }
 
 	for (maf = subList; maf != NULL; maf = maf->next)
             {
             mafLowerCase(maf);
             printf("<B>Alignment block %d of %d in window, %d - %d, %d bps </B>\n",
-                ++aliIx,realCount,maf->components->start + 1,maf->components->start + maf->components->size,
-                maf->components->size);
+                   ++aliIx,realCount,maf->components->start + 1,
+                   maf->components->start + maf->components->size, maf->components->size);
             if (strstr(tdb->type, "wigMafProt"))
                 {
 		mafPrettyOutGsid(stdout, maf,210,onlyDiff, aliIx, 1, mafOrig);
 		}
 	    else
 		{
 	        mafPrettyOutGsid(stdout, maf, 70,onlyDiff, aliIx, 0, mafOrig);
 		}
 	    }
 	mafAliFreeList(&subList);
 	}
     else
 	{
         printf("No multiple alignment in browser window");
 	}