src/hg/near/hgNear/knownGene.c 1.34

Index: src/hg/near/hgNear/knownGene.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/near/hgNear/knownGene.c,v
retrieving revision 1.33
retrieving revision 1.34
diff -b -B -U 1000000 -r1.33 -r1.34
--- src/hg/near/hgNear/knownGene.c	3 Sep 2008 19:20:42 -0000	1.33
+++ src/hg/near/hgNear/knownGene.c	7 May 2010 03:37:42 -0000	1.34
@@ -1,348 +1,348 @@
 /* colKnownGene - columns having to do with knownGene and closely tables. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "obscure.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "hdb.h"
 #include "hCommon.h"
 #include "hgNear.h"
 #include "kgAlias.h"
 #include "findKGAlias.h"
 
 static char const rcsid[] = "$Id$";
 
 static char *posFromRow3(char **row)
 /* Convert chrom/start/end row to position. */
 {
 char buf[128];
 char *chrom;
 int start,end;
 
 chrom = row[0];
 start = sqlUnsigned(row[1]);
 end = sqlUnsigned(row[2]);
 safef(buf, sizeof(buf), "%s:%d-%d", chrom, start+1, end);
 return cloneString(buf);
 }
 
 
 static char *genePredPosFromTable(char *table, struct genePos *gp, 
 	struct sqlConnection *conn)
 /* Get genePred position from table.  Well, actually just get it from gp. */
 {
 if (gp->chrom != NULL)
     {
     char pos[256];
     safef(pos, sizeof(pos), "%s:%d-%d", gp->chrom, gp->start+1, gp->end);
     return cloneString(pos);
     }
 else
     {
     char query[256];
     struct sqlResult *sr;
     char *pos = NULL;
     char **row;
 
     safef(query, sizeof(query), 
     	"select chrom,txStart,txEnd from %s where name = '%s'",
 	table, gp->name);
     sr = sqlGetResult(conn, query);
     if ((row = sqlNextRow(sr)) != NULL)
         pos = posFromRow3(row);
     sqlFreeResult(&sr);
     return pos;
     }
 }
 
 static char *genePredPosVal(struct column *col, struct genePos *gp, 
 	struct sqlConnection *conn)
 /* Get genome position of genePred type table. */
 {
 return genePredPosFromTable(col->table, gp, conn);
 }
 
 static void genePredPosPrint(struct column *col, struct genePos *gp, 
 	struct sqlConnection *conn)
 /* Print genome position with hyperlink to browser. */
 {
 char *pos = col->cellVal(col, gp, conn);
 char *chrom;
 int start, end;
 
 hPrintf("<TD>");
 if (pos == NULL)
     hPrintf("n/a");
 else
     {
     char numBuf[32];
     hgParseChromRange(database, pos, &chrom, &start, &end);
     sprintLongWithCommas(numBuf, (start+end+1)/2);
     hPrintf("<A HREF=\"%s?db=%s&position=%s&%s&%s=full\">",
 	    hgTracksName(), database, pos, cartSidUrlString(cart), genomeSetting("geneTable"));
     hPrintf("%s&nbsp;%s</A>", chrom, numBuf);
     freeMem(pos);
     }
 hPrintf("</TD>");
 }
 
 static void genePredPosFilterControls(struct column *col, struct sqlConnection *conn)
 /* Print out controls for advanced filter. */
 {
 hPrintf("chromosome: ");
 advFilterRemakeTextVar(col, "chr", 8);
 hPrintf(" start: ");
 advFilterRemakeTextVar(col, "start", 8);
 hPrintf(" end: ");
 advFilterRemakeTextVar(col, "end", 8);
 }
 
 static struct genePos *genePredPosAdvFilter(struct column *col, 
 	struct sqlConnection *conn, struct genePos *list)
 /* Do advanced filter on position. */
 {
 char *chrom = advFilterVal(col, "chr");
 char *startString = advFilterVal(col, "start");
 char *endString = advFilterVal(col, "end");
 if (chrom != NULL)
     {
     struct genePos *newList = NULL, *gp, *next;
     for (gp = list; gp != NULL; gp = next)
 	{
 	next = gp->next;
 	if (sameWord(chrom, gp->chrom))
 	    {
 	    slAddHead(&newList, gp);
 	    }
 	}
     slReverse(&newList);
     list = newList;
     }
 if (startString != NULL)
     {
     int start = atoi(startString)-1;
     struct genePos *newList = NULL, *gp, *next;
     for (gp = list; gp != NULL; gp = next)
 	{
 	next = gp->next;
 	if (gp->end > start)
 	    {
 	    slAddHead(&newList, gp);
 	    }
 	}
     slReverse(&newList);
     list = newList;
     }
 if (endString != NULL)
     {
     int end = atoi(endString);
     struct genePos *newList = NULL, *gp, *next;
     for (gp = list; gp != NULL; gp = next)
 	{
 	next = gp->next;
 	if (gp->start < end)
 	    {
 	    slAddHead(&newList, gp);
 	    }
 	}
     slReverse(&newList);
     list = newList;
     }
 return list;
 }
 
 static void genePredPosMethods(struct column *col, char *table)
 /* Put in methods for genePred based positions. */
 {
 col->table = table;
 col->exists = simpleTableExists;
 col->cellVal = genePredPosVal;
 col->cellPrint = genePredPosPrint;
 col->filterControls = genePredPosFilterControls;
 col->advFilter = genePredPosAdvFilter;
 }
 
 static char *knownPosCellVal(struct column *col, struct genePos *gp, 
 	struct sqlConnection *conn)
 /* Get genome position of knownPos table.  Ok to have col NULL. */
 {
 char *pos = genePredPosFromTable("knownGene", gp, conn);
 if (pos == NULL)
     {
     /* As a backup plan, try to find accession in all_mrna table. */
     char query[256];
     struct sqlResult *sr;
     char **row;
     safef(query, sizeof(query), "select tName, tStart, tEnd from %s where qName = '%s'",
 	"all_mrna", gp->name);
     sr = sqlGetResult(conn, query);
     if ((row = sqlNextRow(sr)) != NULL)
 	pos = posFromRow3(row);
     sqlFreeResult(&sr);
     }
 return pos;
 }
 
 static struct genePos *genePosFromQuery(struct sqlConnection *conn, char *query, boolean oneOnly)
 /* Get all positions from a query that returns 5 columns. */
 {
 struct sqlResult *sr;
 char **row;
 struct genePos *gpList = NULL, *gp;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     AllocVar(gp);
     genePosFillFrom5(gp, row);
     slAddHead(&gpList, gp);
     if (oneOnly)
         break;
     }
 sqlFreeResult(&sr);
 return gpList;
 }
 
 struct genePos *knownPosAll(struct sqlConnection *conn)
 /* Get all positions in knownGene table. */
 {
 if (showOnlyCanonical())
     return genePosFromQuery(conn, genomeSetting("allGeneQuery"), FALSE);
 else
     return genePosFromQuery(conn, genomeSetting("allTranscriptQuery"), FALSE);
 }
 
 struct genePos *knownPosOne(struct sqlConnection *conn, char *name)
 /* Get all positions of named gene. */
 {
 char query[1024];
 safef(query, sizeof(query), genomeSetting("oneGeneQuery"), name);
 return genePosFromQuery(conn, query, FALSE);
 }
 
 struct genePos *knownPosFirst(struct sqlConnection *conn)
 /* Get first gene in known gene table. */
 {
 char *query = genomeSetting("allGeneQuery");
 struct genePos *gp = genePosFromQuery(conn, query, TRUE);
 return gp;
 }
 
 void setupColumnKnownPos(struct column *col, char *parameters)
 /* Set up column that links to genome browser based on known gene
  * position. */
 {
 genePredPosMethods(col, genomeSetting("geneTable"));
 col->cellVal = knownPosCellVal;
 }
 
 static void linkToDetailsCellPrint(struct column *col, struct genePos *gp, 
 	struct sqlConnection *conn)
 /* Print a link to known genes details page. */
 {
 char *s = col->cellVal(col, gp, conn);
 fillInKnownPos(gp, conn);
 hPrintf("<TD>");
 hPrintf("<A HREF=\"../cgi-bin/hgGene?%s&%s=%s&%s=%s&%s=%s&%s=%d&%s=%d\">", 
 	cartSidUrlString(cart), 
 	"db", database,
 	"hgg_gene", gp->name,
 	"hgg_chrom", gp->chrom,
 	"hgg_start", gp->start,
 	"hgg_end", gp->end);
 if (s == NULL) 
     {
     hPrintf("n/a");
     }
 else
     {
-    hPrintNonBreak(s);
+    hPrintEncodedNonBreak(s);
     freeMem(s);
     }
 hPrintf("</A></TD>");
 }
 
 void fillInKnownPos(struct genePos *gp, struct sqlConnection *conn)
 /* If gp->chrom is not filled in go look it up. */
 {
 if (gp->chrom == NULL)
     {
     char *pos = knownPosCellVal(NULL, gp, conn);
     char *chrom;
     hgParseChromRange(database, pos, &chrom, &gp->start, &gp->end);
     gp->chrom = cloneString(chrom);
     }
 }
 
 struct searchResult *knownGeneSearchResult(struct sqlConnection *conn, 
 	char *kgID, char *alias)
 /* Return a searchResult for a known gene. */
 {
 struct searchResult *sr;
 struct dyString *dy = dyStringNew(1024);
 char description[512];
 char query[256];
 char name[64];
 
 /* Allocate and fill in with geneID. */
 AllocVar(sr);
 sr->gp.name = cloneString(kgID);
 
 /* Get gene symbol into short label if possible. */
 safef(query, sizeof(query),
 	"select geneSymbol from kgXref where kgID = '%s'", kgID);
 if (sqlQuickQuery(conn, query, name, sizeof(name)))
     sr->shortLabel = cloneString(name);
 else
     sr->shortLabel = cloneString(kgID);
 
 /* Add alias to long label if need be */
 if (alias != NULL && !sameWord(name, alias))
     dyStringPrintf(dy, "(aka %s) ", alias);
 
 /* Add description to long label. */
 safef(query, sizeof(query), 
     "select description from kgXref where kgID = '%s'", kgID);
 if (sqlQuickQuery(conn, query, description, sizeof(description)))
     dyStringAppend(dy, description);
 sr->longLabel = cloneString(dy->string);
 
 /* Cleanup and go home. */
 dyStringFree(&dy);
 return sr;
 }
 
 static struct searchResult *knownNameSimpleSearch(struct column *col, 
     struct sqlConnection *conn, char *search)
 /* Look for matches to known genes. */
 {
 struct kgAlias *ka, *kaList;
 struct searchResult *srList = NULL, *sr;
 kaList = findKGAlias(database, search, "F");
 for (ka = kaList; ka != NULL; ka = ka->next)
     {
     sr = knownGeneSearchResult(conn, ka->kgID, ka->alias);
     slAddHead(&srList, sr);
     }
 return srList;
 }
 
 void setupColumnKnownDetails(struct column *col, char *parameters)
 /* Set up a column that links to details page for known genes. */
 {
 setupColumnLookup(col, parameters);
 col->cellPrint = linkToDetailsCellPrint;
 }
 
 void setupColumnKnownName(struct column *col, char *parameters)
 /* Set up a column that looks up name to display, and selects on a click. */
 {
 setupColumnLookup(col, parameters);
 col->cellPrint = cellSelfLinkPrint;
 col->simpleSearch = knownNameSimpleSearch;
 }