src/hg/hgTables/bigBed.c 1.2

Index: src/hg/hgTables/bigBed.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTables/bigBed.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/hgTables/bigBed.c	16 Mar 2009 05:08:48 -0000	1.1
+++ src/hg/hgTables/bigBed.c	16 Mar 2009 18:23:06 -0000	1.2
@@ -1,127 +1,127 @@
 /* bigBed - stuff to handle bigBed in the Table Browser. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "localmem.h"
 #include "jksql.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "web.h"
 #include "bed.h"
 #include "hdb.h"
 #include "trackDb.h"
 #include "customTrack.h"
 #include "hmmstats.h"
 #include "correlate.h"
 #include "asParse.h"
 #include "bbiFile.h"
 #include "bigBed.h"
 #include "hgTables.h"
 
 static char const rcsid[] = "$Id$";
 
 boolean isBigBed(char *table)
 /* Return TRUE if table corresponds to a bigBed file. */
 {
 return trackIsType(table, "bigBed");
 }
 
 char *bigBedFileName(char *table, struct sqlConnection *conn)
 /* Return file name associated with bigBed.  This handles differences whether it's
  * a custom or built-in track.  Do a freeMem on returned string when done. */
 {
 /* Implementation is same as bigWig. */
 return bigWigFileName(table, conn);
 }
 
 void bigBedDescribeFields(char *table, struct sqlConnection *conn)
 /* Print out an HTML table showing table fields and types for bigBed file. */
 {
 }
 
 void showSchemaBigBed(char *table)
 /* Show schema on bigBed. */
 {
 /* Figure out bigBed file name and open it.  Get contents for first chromosome as an example. */
 struct sqlConnection *conn = hAllocConn(database);
 char *fileName = bigBedFileName(table, conn);
 struct bbiFile *bbi = bigBedFileOpen(fileName);
 struct bbiChromInfo *chromList = bbiChromList(bbi);
 struct lm *lm = lmInit(0);
 struct bigBedInterval *ivList = bigBedIntervalQuery(bbi, chromList->name, 0, chromList->size, 10, lm);
 
 /* Get description of columns, making it up from BED records if need be. */
 struct asObject *as = bigBedAs(bbi);
 if (as == NULL)
-    as = asParseText(bedAsDef(bbi->definedFieldCount));
+    as = asParseText(bedAsDef(bbi->definedFieldCount, bbi->fieldCount));
 
 
 /* Put up table that describes fields. */
 hTableStart();
 hPrintf("<TR><TH>field</TH>");
 hPrintf("<TH>example</TH>");
 hPrintf("<TH>description</TH> ");
 puts("</TR>\n");
 struct asColumn *col;
 int colCount = 0;
 char *row[bbi->fieldCount];
 char startBuf[16], endBuf[16];
 char *dupeRest = lmCloneString(lm, ivList->rest);	/* Manage rest-stomping side-effect */
 bigBedIntervalToRow(ivList, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
 ivList->rest = dupeRest;
 for (col = as->columnList; col != NULL; col = col->next)
     {
     hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
     hPrintf("<TD>%s</TD>", row[colCount]);
     hPrintf("<TD>%s</TD></TR>", col->comment);
     ++colCount;
     }
 
 /* If more fields than descriptions put up minimally helpful info (at least has example). */
 for ( ; colCount < bbi->fieldCount; ++colCount)
     {
     hPrintf("<TR><TD><TT>column%d</TT></TD>", colCount+1);
     hPrintf("<TD>%s</TD>", row[colCount]);
     hPrintf("<TD>n/a</TD></TR>\n");
     }
 hTableEnd();
 
 
 /* Put up another section with sample rows. */
 webNewSection("Sample Rows");
 hTableStart();
 
 /* Print field names as column headers for example */
 hPrintf("<TR>");
 int colIx = 0;
 for (col = as->columnList; col != NULL; col = col->next)
     {
     hPrintf("<TH>%s</TH>", col->name);
     ++colIx;
     }
 for (; colIx < colCount; ++colIx)
     hPrintf("<TH>column%d</TH>", colIx+1);
 hPrintf("</TR>\n");
 
 /* Print sample lines. */
 struct bigBedInterval *iv;
 for (iv=ivList; iv != NULL; iv = iv->next)
     {
     bigBedIntervalToRow(iv, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
     hPrintf("<TR>");
     for (colIx=0; colIx<colCount; ++colIx)
         {
 	writeHtmlCell(row[colIx]);
 	}
     hPrintf("</TR>\n");
     }
 hTableEnd();
 
 /* Clean up and go home. */
 lmCleanup(&lm);
 bbiFileClose(&bbi);
 freeMem(fileName);
 hFreeConn(&conn);
 }