a6266677d433cec482c6c28b0787d84bff1e01a8
hiram
  Tue Sep 6 10:30:23 2011 -0700
rearrange static function definitions to avoid compiler problems on Suse linux
diff --git src/lib/oldGff.c src/lib/oldGff.c
index 307fd90..3b84229 100644
--- src/lib/oldGff.c
+++ src/lib/oldGff.c
@@ -28,31 +28,57 @@
     char score[62];	/* A number between 0 and 1 */
     char strand[4];	/* + or - */
     char frame[4];     /* 0, 1, 2, or . */
     char group[128];  /* Name of gene  cosmid.number. */
     };
 
 static int gffSegLineScan(struct gff* gff, struct gffSegLine *seg)
 {
     int scanned = sscanf(gff->buf, "%s %s %s %ld %ld %s %1s %s %s",
 	seg->seqname, seg->source, seg->feature,
 	&seg->start, &seg->end,
 	seg->score, seg->strand, seg->frame, seg->group);
     return scanned;
 }
 
-static boolean _gffSeekDoubleSharpLine();
+static boolean _gffGetLine(struct gff *gff)
+/* Get the next line into a gff file.  (private)
+ * return FALSE at EOF or if problem. */
+{
+char *s;
+s = fgets(gff->buf, gff->bufSize, gff->file);
+if (s == NULL)
+    {
+    return FALSE;
+    }
+gff->bytesInBuf = strlen(gff->buf);
+gff->readIx = 0;
+gff->lineNumber += 1;
+return TRUE;
+}
+
+static boolean _gffSeekDoubleSharpLine(struct gff *gff)
+/* Go find next line that begins with ## */
+{
+for (;;)
+    {
+    if (!_gffGetLine(gff)) return FALSE;
+    if (gff->bytesInBuf >= 2)
+	if (gff->buf[0] == '#' && gff->buf[1] == '#') 
+		return TRUE;
+    }
+}
 
 boolean gffOpen(struct gff *gff, char *fileName)
 /* Initialize gff structure and open file for it. */
 {
     dnaUtilOpen();
 
     /* Initialize structure and open file. */
     zeroBytes(gff, sizeof(*gff));
     gff->memPool = lmInit(16*1024);
     gff->fileSize = fileSize(fileName);
     if (gff->fileSize < 0 ||
        (gff->file = fopen(fileName, "rb")) == NULL)
 	    {
             warn("Couldn't find the file named %s\n", fileName);
 	    return FALSE;
@@ -69,79 +95,51 @@
 	}
 
     return TRUE;
 }
 
 void gffClose(struct gff *gff)
 /* Close down gff structure. */
 {
 if (gff->file != NULL)
     fclose(gff->file);
 freeMem(gff->dna);
 lmCleanup(&gff->memPool);
 zeroBytes(gff, sizeof(*gff));
 }
 
-static boolean _gffGetLine(struct gff *gff)
-/* Get the next line into a gff file.  (private)
- * return FALSE at EOF or if problem. */
-{
-char *s;
-s = fgets(gff->buf, gff->bufSize, gff->file);
-if (s == NULL)
-    {
-    return FALSE;
-    }
-gff->bytesInBuf = strlen(gff->buf);
-gff->readIx = 0;
-gff->lineNumber += 1;
-return TRUE;
-}
-
 #if 0 /* unused */
 static boolean _gffAtEof(struct gff *gff)
 /* Returns TRUE if at the end of gff file. */
 {
 return gff->file == NULL;
 }
 #endif	
 
 #if 0 /* unused */
 static char _getGffChar(struct gff *gff)
 /* Return next byte (not next base) in gff file. Return zero
  * if at end of file. */
 {
 if (gff->readIx >= gff->bytesInBuf)
 	{
 	if (!_gffGetLine(gff)) return 0;
 	}
 return gff->buf[gff->readIx++];
 }
 #endif
 
-static boolean _gffSeekDoubleSharpLine(struct gff *gff)
-/* Go find next line that begins with ## */
-{
-for (;;)
-    {
-    if (!_gffGetLine(gff)) return FALSE;
-    if (gff->bytesInBuf >= 2)
-	if (gff->buf[0] == '#' && gff->buf[1] == '#') 
-		return TRUE;
-    }
-}
-
 static boolean _gffSeekDna(struct gff *gff)
 /* Skip through file until you get the DNA */ 
 {
 static char dnaIdent[] = "##DNA";
 
 rewind(gff->file);
 for (;;)
     {
     if (!_gffGetLine(gff)) return FALSE;
     if (strncmp(gff->buf, dnaIdent, strlen(dnaIdent)) == 0)
 	{
 	sscanf(gff->buf, "##DNA %s", gff->dnaName);
 	gff->bytesInBuf = 0; /* We're done with gff line. */
 	return TRUE;
 	}