src/hg/hgSuggest/hgSuggest.c 1.2

Index: src/hg/hgSuggest/hgSuggest.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgSuggest/hgSuggest.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/hgSuggest/hgSuggest.c	9 Feb 2010 08:41:02 -0000	1.1
+++ src/hg/hgSuggest/hgSuggest.c	10 Feb 2010 06:23:00 -0000	1.2
@@ -16,44 +16,56 @@
 }
 
 int main(int argc, char *argv[])
 {
-    char *prefix = cgiOptionalString("prefix");
-    char *database = cgiOptionalString("db");
-    struct sqlConnection *conn;
-    char query[2048];
-    char **row;
-    struct sqlResult *sr;
-    int count = 0;
-    boolean hasKnownCanonical;
-    boolean hasRefSeq;
-    struct dyString *str = newDyString(1000);
-    char previous[256];
+char *prefix = sqlEscapeString(cgiOptionalString("prefix"));
+char *database = sqlEscapeString(cgiOptionalString("db"));
+int exact = cgiOptionalInt("exact", 0);
+struct sqlConnection *conn;
+char query[2048];
+char **row;
+struct sqlResult *sr;
+int count = 0;
+boolean hasKnownCanonical;
+boolean hasRefSeq;
+struct dyString *str = newDyString(10000);
+char previous[256];
 
-    if(prefix == NULL || database == NULL)
+if(prefix == NULL || database == NULL)
         fail("Missing prefix or database parameter");
 
-    conn = hAllocConn(database);
+conn = hAllocConn(database);
 
-    hasKnownCanonical = sqlTableExists(conn, "knownCanonical");
-    hasRefSeq = sqlTableExists(conn, "refGene");
-    if(!hasKnownCanonical && !hasRefSeq)
+hasKnownCanonical = sqlTableExists(conn, "knownCanonical");
+hasRefSeq = sqlTableExists(conn, "refGene");
+if(!hasKnownCanonical && !hasRefSeq)
         fail("gene autosuggest is not supported for this assembly because it does not have a knownCanonical or a refGene table");
 
-    puts("Content-Type:text/plain");
-    puts("\n");
+puts("Content-Type:text/plain");
+puts("\n");
 
-    dyStringPrintf(str, "[\n");
+dyStringPrintf(str, "[\n");
+if(exact)
+    {
+    if(hasKnownCanonical)
+        safef(query, sizeof(query), "select x.geneSymbol, k.chrom, k2.txStart, k2.txEnd from knownCanonical k, knownGene k2, kgXref x where k.transcript = x.kgID and k.transcript = k2.name and x.geneSymbol = '%s' order by x.geneSymbol, k2.txEnd - k2.txStart desc", prefix);
+    else
+        safef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd from refGene r where r.name2 = '%s' order by r.name2, r.txEnd - r.txStart desc", prefix);
+    }
+else
+    {
     // We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
     // Also note that we take advantage of the fact that searches are case-insensitive in mysql.
     // Some tables have duplicates (e.g. 2 TTn's in mm9 knownCanonical); currently the larger one wins.
     if(hasKnownCanonical)
         safef(query, sizeof(query), "select x.geneSymbol, k.chrom, k2.txStart, k2.txEnd from knownCanonical k, knownGene k2, kgXref x where k.transcript = x.kgID and k.transcript = k2.name and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k2.txEnd - k2.txStart desc", prefix);
     else
         // arbitrarily prefer the longest isoform
         safef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd from refGene r where r.name2 LIKE '%s%%' order by r.name2, r.txEnd - r.txStart desc", prefix);
-    sr = sqlGetResult(conn, query);
-    while ((row = sqlNextRow(sr)) != NULL)
+    }
+sr = sqlGetResult(conn, query);
+previous[0] = 0;
+while ((row = sqlNextRow(sr)) != NULL)
         {
         if(!previous[0] || !sameString(previous, row[0]))
             {
             count++;
@@ -61,8 +73,8 @@
                            row[0], row[1], atoi(row[2])+1, row[3]);
             safef(previous, sizeof(previous), row[0]);
             }
         }
-    dyStringPrintf(str, "\n]\n");
-    puts(dyStringContents(str));
-    return 0;
+dyStringPrintf(str, "\n]\n");
+puts(dyStringContents(str));
+return 0;
 }