a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/hg/lib/ggDump.c src/hg/lib/ggDump.c
index ca6b601..f9d7729 100644
--- src/hg/lib/ggDump.c
+++ src/hg/lib/ggDump.c
@@ -1,153 +1,152 @@
 /*****************************************************************************
  * Copyright (C) 2000 Jim Kent.  This source code may be freely used         *
  * for personal, academic, and non-profit purposes.  Commercial use          *
  * permitted only by explicit agreement with Jim Kent (jim_kent@pacbell.net) *
  *****************************************************************************/
 /* ggDump - Dump out geneGraph structures. */
 #include "common.h"
 #include "ggMrnaAli.h"
 #include "ggPrivate.h"
 
-static char const rcsid[] = "$Id: ggDump.c,v 1.6 2005/04/13 06:25:53 markd Exp $";
 
 static char charForType(int type)
 /* Return character corresponding to edge. */
 {
 char c = 0;
 switch (type)
     {
     case ggSoftStart:
 	c = '{';
 	break;
     case ggSoftEnd:
 	c = '}';
 	break;
     case ggHardStart:
 	c = '[';
 	break;
     case ggHardEnd:
 	c = ']';
 	break;
     case ggUnused:
         c = 'x';
 	break;
     default:
 	errAbort("Unknown vertex type %d", type);
 	break;
     }
 return c;
 }
 
 void asciiArtDumpDa(struct ggAliInfo *da, int start, int end)
 /* Display list of dense Alis in artistic ascii format. */
 {
 enum { screenWidth = 80};
 static char line[screenWidth+1];
 int ggiWidth = end - start;
 double scaler = (double)(screenWidth-1)/ggiWidth;
 struct ggVertex *v;
 int pos;
 int i;
 
 memset(line, ' ', screenWidth);
 v = da->vertices;
 for (i=0; i<da->vertexCount; ++i,++v)
     {
     char c = charForType(v->type);
     pos = round((v->position-start) * scaler);
     assert(pos >= 0 && pos < screenWidth);
     line[pos] = c;
     }
 printf("%s\n", line);
 }
 
 void dumpGgAliInfo(struct ggAliInfo *da, int start, int end)
 /* Display list of dense Alis. */
 {
 struct ggVertex *v;
 int i;
 
 v = da->vertices;
 for (i=0; i<da->vertexCount; ++i,++v)
     {
     char c = charForType(v->type);
     if (v->type == ggSoftStart || v->type == ggHardStart)
 	printf("%c%d ", c, v->position);
     else
 	printf("%d%c   ", v->position, c);
     }
 printf("\n");
 }
 
 void dumpMc(struct ggMrnaCluster *mc)
 /* Display mc on the screen. */
 {
 struct ggAliInfo *da;
 struct maRef *ref;
 
 printf("refs -");
 for (ref = mc->refList; ref != NULL; ref = ref->next)
     printf(" %s", ref->ma->tName);
 printf("\n");
 for (da = mc->mrnaList; da != NULL; da = da->next)
     dumpGgAliInfo(da, mc->tStart, mc->tEnd);
 }
 
 void dumpGg(struct geneGraph *gg)
 /* Print out a gene graph. */
 {
 int i,j;
 int vertexCount = gg->vertexCount;
 
 printf("geneGraph has %d vertices\n", vertexCount);
 for (i=0; i<vertexCount; ++i)
     {
     struct ggVertex *v = &gg->vertices[i];
     bool *arcsOut = gg->edgeMatrix[i];
     printf("  %d %5d %c   ", i, v->position, charForType(v->type));
     for (j=0; j<vertexCount; ++j)
 	{
 	if (arcsOut[j])
 	    printf(" %d", j);
 	}
     printf("\n");
     }
 }
 
 void freeGgMrnaAli(struct ggMrnaAli **pMa)
 /* Free up a single ggMrnaAli. */
 {
 struct ggMrnaAli *ma;
 if ((ma = *pMa) != NULL)
     {
     freeMem(ma->tName);
     freeMem(ma->blocks);
     freez(pMa);
     }
 }
 
 void freeGgMrnaAliList(struct ggMrnaAli **pMaList)
 /* Free up ggMrnaAli list */
 {
 struct ggMrnaAli *ma,*next;
 for (ma = *pMaList; ma != NULL; ma = next)
     {
     next = ma->next;
     freeGgMrnaAli(&ma);
     }
 *pMaList = NULL;
 }
 
 void freeGgMrnaInput(struct ggMrnaInput **pCi)
 /* Free up a ggMrnaInput. */
 {
 struct ggMrnaInput *ci;
 if ((ci = *pCi) != NULL)
     {
     ggMrnaAliFreeList(&ci->maList);
     freeDnaSeq(&ci->genoSeq);
     freez(pCi);
     }
 }