src/hg/hgTables/bigBed.c 1.4

Index: src/hg/hgTables/bigBed.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTables/bigBed.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/hgTables/bigBed.c	16 Mar 2009 18:35:13 -0000	1.3
+++ src/hg/hgTables/bigBed.c	17 Mar 2009 04:28:38 -0000	1.4
@@ -1,132 +1,185 @@
 /* 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 "obscure.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. */
+struct hash *asColumnHash(struct asObject *as)
+/* Return a hash full of the object's columns, keyed by colum name */
 {
+struct hash *hash = hashNew(6);
+struct asColumn *col;
+for (col = as->columnList; col != NULL; col = col->next)
+    hashAdd(hash, col->name, col);
+return hash;
+}
+
+static void fillField(struct hash *colHash, char *key, char output[HDB_MAX_FIELD_STRING])
+/* If key is in colHash, then copy key to output. */
+{
+if (hashLookup(colHash, key))
+    strncpy(output, key, HDB_MAX_FIELD_STRING-1);
 }
 
+struct hTableInfo *bigBedToHti(char *table, struct sqlConnection *conn)
+/* Get fields of bigBed into hti structure. */
+{
+char *fileName = bigBedFileName(table, conn);
+/* Get columns in asObject format, from file or failing that as bed-standard. */
+struct bbiFile *bbi = bigBedFileOpen(fileName);
+struct asObject *as = bigBedAs(bbi);
+if (as == NULL) 
+    as = asParseText(bedAsDef(bbi->definedFieldCount, bbi->fieldCount));
+
+/* Allocate hTableInfo structure and fill in info about bed fields. */
+struct hash *colHash = asColumnHash(as);
+struct hTableInfo *hti;
+AllocVar(hti);
+hti->rootName = cloneString(table);
+hti->isPos= TRUE;
+fillField(colHash, "chrom", hti->chromField);
+fillField(colHash, "chromStart", hti->startField);
+fillField(colHash, "chromEnd", hti->endField);
+fillField(colHash, "name", hti->nameField);
+fillField(colHash, "score", hti->scoreField);
+fillField(colHash, "strand", hti->strandField);
+fillField(colHash, "thickStart", hti->cdsStartField);
+fillField(colHash, "thickEnd", hti->cdsEndField);
+fillField(colHash, "blockCount", hti->countField);
+fillField(colHash, "chromStarts", hti->startsField);
+fillField(colHash, "blockSizes", hti->endsSizesField);
+hti->hasCDS = (bbi->definedFieldCount >= 8);
+hti->hasBlocks = (bbi->definedFieldCount >= 12);
+char type[256];
+safef(type, sizeof(type), "bed %d %c", bbi->definedFieldCount,
+	(bbi->definedFieldCount == bbi->fieldCount ? '.' : '+'));
+hti->type = cloneString(type);
+
+hashFree(&colHash);
+bbiFileClose(&bbi);
+return hti;
+}
+
+
 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);
+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, bbi->fieldCount));
 
 hPrintf("<B>Big Bed File:</B> %s", fileName);
-hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;<B>Row Count:</B> ");
+hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;<B>Item Count:</B> ");
 printLongWithCommas(stdout, bigBedItemCount(bbi));
 hPrintf("<BR>\n");
 hPrintf("<B>Format description:</B> %s<BR>", as->comment);
 
 /* 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);
 }