src/hg/hgTables/bigBed.c 1.1

Index: src/hg/hgTables/bigBed.c
===================================================================
RCS file: src/hg/hgTables/bigBed.c
diff -N src/hg/hgTables/bigBed.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/hgTables/bigBed.c	16 Mar 2009 05:08:48 -0000	1.1
@@ -0,0 +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));
+
+
+/* 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);
+}