src/hg/lib/chromInfo.c 1.7

Index: src/hg/lib/chromInfo.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/chromInfo.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/hg/lib/chromInfo.c	26 Nov 2007 22:39:44 -0000	1.6
+++ src/hg/lib/chromInfo.c	24 Mar 2009 15:51:04 -0000	1.7
@@ -1,162 +1,209 @@
 /* chromInfo.c was originally generated by the autoSql program, which also 
  * generated chromInfo.h and chromInfo.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
+#include "hdb.h"
 #include "chromInfo.h"
 
 static char const rcsid[] = "$Id$";
 
 void chromInfoStaticLoad(char **row, struct chromInfo *ret)
 /* Load a row from chromInfo table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->size = sqlUnsigned(row[1]);
 ret->fileName = row[2];
 }
 
 struct chromInfo *chromInfoLoad(char **row)
 /* Load a chromInfo from row fetched with select * from chromInfo
  * from database.  Dispose of this with chromInfoFree(). */
 {
 struct chromInfo *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->size = sqlUnsigned(row[1]);
 ret->fileName = cloneString(row[2]);
 return ret;
 }
 
 struct chromInfo *chromInfoLoadAll(char *fileName) 
 /* Load all chromInfo from a whitespace-separated file.
  * Dispose of this with chromInfoFreeList(). */
 {
 struct chromInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileRow(lf, row))
     {
     el = chromInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct chromInfo *chromInfoLoadAllByChar(char *fileName, char chopper) 
 /* Load all chromInfo from a chopper separated file.
  * Dispose of this with chromInfoFreeList(). */
 {
 struct chromInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = chromInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct chromInfo *chromInfoCommaIn(char **pS, struct chromInfo *ret)
 /* Create a chromInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new chromInfo */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->size = sqlUnsignedComma(&s);
 ret->fileName = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void chromInfoFree(struct chromInfo **pEl)
 /* Free a single dynamically allocated chromInfo such as created
  * with chromInfoLoad(). */
 {
 struct chromInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->fileName);
 freez(pEl);
 }
 
 void chromInfoFreeList(struct chromInfo **pList)
 /* Free a list of dynamically allocated chromInfo's */
 {
 struct chromInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     chromInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void chromInfoOutput(struct chromInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out chromInfo.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->size);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fileName);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 boolean chromSeqFileExists(char *db, char *chrom)
 /* Check whether chromInfo exists for a database, find the path of the */
 /* sequence file for this chromosome and check if the file exists. */
 {
 char seqFile[512];
 struct sqlConnection *conn = sqlConnect(db);
 char query[256];
 char *res = NULL;
 boolean exists = FALSE;
 
 /* if the database exists, check for the chromInfo file */
 if (sqlDatabaseExists(db))
     {
     safef(query, sizeof(query), "select fileName from chromInfo where chrom = '%s'", chrom);
     res = sqlQuickQuery(conn, query, seqFile, 512);
     sqlDisconnect(&conn);
     }
 
 /* if there is not table or no information in the table or if the table */
 /* exists but the file can not be opened return false, otherwise sequence */
 /* file exists and return true */
 if (res != NULL)
     {
     /* chromInfo table exists so check that sequence file can be opened */
     FILE *f = fopen(seqFile, "rb");
     if (f != NULL)
         {
         exists = TRUE;
         fclose(f);
         }
     }
 return exists;
 }
+
+
+struct chromInfo *createChromInfoList(char *name, char *database)
+/* Load up chromosome information for chrom 'name'.
+ * If name is NULL or "all" then load all chroms.
+ * Similar to featureBits.c - could be moved to library */
+{
+struct sqlConnection *conn = hAllocConn(database);
+struct sqlResult *sr = NULL;
+char **row;
+int loaded=0;
+struct chromInfo *ret = NULL;
+unsigned totalSize = 0;
+/* do the query */
+if (!name || sameWord(name, "all"))
+    sr = sqlGetResult(conn, "select * from chromInfo");
+else
+    {
+    char select[256];
+    safef(select, ArraySize(select), "select * from chromInfo where chrom='%s'", name);
+    sr = sqlGetResult(conn, select);
+    }
+/* read the rows and build the chromInfo list */
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    struct chromInfo *el;
+    struct chromInfo *ci;
+    AllocVar(ci);
+    el = chromInfoLoad(row);
+    ci->chrom = cloneString(el->chrom);
+    ci->size = el->size;
+    totalSize += el->size;
+    slAddHead(&ret, ci);
+    ++loaded;
+    }
+if (loaded < 1)
+    errAbort("ERROR: can not find chrom name: '%s'\n", name ? name : "NULL");
+slReverse(&ret);
+if (!name || sameWord(name, "all"))
+    verbose(2, "#\tloaded size info for %d chroms, total size: %u\n",
+        loaded, totalSize);
+sqlFreeResult(&sr);
+hFreeConn(&conn);
+return ret;
+}
+