src/hg/hgGene/altSplice.c 1.13

Index: src/hg/hgGene/altSplice.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgGene/altSplice.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -b -B -U 1000000 -r1.12 -r1.13
--- src/hg/hgGene/altSplice.c	19 Dec 2008 07:14:02 -0000	1.12
+++ src/hg/hgGene/altSplice.c	19 Aug 2009 23:00:16 -0000	1.13
@@ -1,171 +1,171 @@
 /* altSplice - altSplicing diagram. */
 
 #include "common.h"
 #include "hCommon.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "hdb.h"
 #include "hvGfx.h"
 #include "portable.h"
 #include "altGraphX.h"
 #include "hgGene.h"
 
 static char const rcsid[] = "$Id$";
 
 static int gpBedBasesShared(struct genePred *gp, struct bed *bed)
 /* Return number of bases genePred and bed share. */
 {
 int intersect = 0;
 int i, blockCount = bed->blockCount;
 int s,e;
 for (i=0; i<blockCount; ++i)
     {
     s = bed->chromStart + bed->chromStarts[i];
     e = s + bed->blockSizes[i];
     intersect += gpRangeIntersection(gp, s, e);
     }
 return intersect;
 }
 
 char *altGraphId(struct sqlConnection *conn, struct genePred *gp)
 /* Return altGraphId that overlaps most with genePred. */
 {
 int rowOffset;
 struct sqlResult *sr;
 char **row;
 struct bed *bestBed = NULL;
 int intersect, bestIntersect = 0;
 char extra[64];
 char *ret = NULL;
 
 safef(extra, sizeof(extra), "strand='%s'", gp->strand);
 sr = hRangeQuery(conn, "agxBed", gp->chrom, gp->txStart, gp->txEnd,
 	extra, &rowOffset);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct bed *bed = bedLoad12(row+rowOffset);
     intersect = gpBedBasesShared(gp, bed);
     if (intersect > bestIntersect)
 	{
 	bestIntersect = intersect;
 	bestBed = bed;
 	}
     else
         bedFree(&bed);
     }
 if (bestBed != NULL)
     {
     ret = cloneString(bestBed->name);
     bedFree(&bestBed);
     }
 return ret;
 }
 
 void makeGrayShades(struct hvGfx *hvg, int maxShade, Color shadesOfGray[])
 /* Make eight shades of gray in display. */
 {
 int i;
 for (i=0; i<=maxShade; ++i)
     {
     int level = 255 - (255*i/maxShade);
     if (level < 0) level = 0;
     shadesOfGray[i] = hvGfxFindColorIx(hvg, level, level, level);
     }
 shadesOfGray[maxShade+1] = MG_RED;
 }
 
 char *altGraphXMakeImage(struct altGraphX *ag)
 /* create a drawing of splicing pattern */
 {
 MgFont *font = mgSmallFont();
 int fontHeight = mgFontLineHeight(font);
 struct spaceSaver *ssList = NULL;
 struct hash *heightHash = NULL;
 int rowCount = 0;
 struct tempName gifTn;
 int pixWidth = atoi(cartUsualString(cart, "pix", DEFAULT_PIX_WIDTH ));
 int pixHeight = 0;
 struct hvGfx *hvg;
 int lineHeight = 0;
 double scale = 0;
 Color shadesOfGray[9];
 int maxShade = ArraySize(shadesOfGray)-1;
 
 scale = (double)pixWidth/(ag->tEnd - ag->tStart);
 lineHeight = 2 * fontHeight +1;
 altGraphXLayout(ag, ag->tStart, ag->tEnd, scale, 100, &ssList, &heightHash, &rowCount);
 hashFree(&heightHash);
 pixHeight = rowCount * lineHeight;
 makeTempName(&gifTn, "hgc", ".gif");
-hvg = hvGfxOpenGif(pixWidth, pixHeight, gifTn.forCgi);
+hvg = hvGfxOpenGif(pixWidth, pixHeight, gifTn.forCgi, FALSE);
 makeGrayShades(hvg, maxShade, shadesOfGray);
 hvGfxSetClip(hvg, 0, 0, pixWidth, pixHeight);
 altGraphXDrawPack(ag, ssList, hvg, 0, 0, pixWidth, lineHeight, lineHeight-1,
 		  ag->tStart, ag->tEnd, scale, 
 		  font, MG_BLACK, shadesOfGray, "Dummy", NULL);
 hvGfxUnclip(hvg);
 hvGfxClose(&hvg);
 printf(
        "<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n",
        gifTn.forHtml, pixWidth, pixHeight);
 return cloneString(gifTn.forHtml);
 }
 
 static boolean altSpliceExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if altSplice table exists and has something
  * on this one. */
 {
 char *mark = NULL;
 if (!sqlTableExists(conn, "altGraphX") || !sqlTableExists(conn, "agxBed"))
     return FALSE;
 section->items = altGraphId(conn, curGenePred);
 /* each graph can have different connected components, if there
    is a component take the prefix for matching back to the graph.
    i.e. cut of an '-1' or '-2' */
 if (section->items != NULL)
     if((mark = strrchr((char *)section->items, '-')) != NULL) 
         *mark = '\0';
 return section->items != NULL;
 }
 
 
 static void altSplicePrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out altSplicing info. */
 {
 char *altId = section->items;
 char query[256];
 struct sqlResult *sr;
 char **row;
 struct altGraphX *ag;
 char table[64];
 boolean hasBin;
 
 hFindSplitTable(sqlGetDatabase(conn), curGeneChrom, "altGraphX", table, &hasBin);
 safef(query, sizeof(query), "select * from %s where name='%s'", table, altId);
 sr = sqlGetResult(conn, query);
 if ((row = sqlNextRow(sr)) != NULL)
     {
     ag = altGraphXLoad(row+hasBin);
     hPrintf("<TABLE><TR><TD BGCOLOR=#888888>\n");
     altGraphXMakeImage(ag);
     hPrintf("</TD></TR></TABLE><BR>");
     }
 sqlFreeResult(&sr);
 hPrintf("This graph shows alternative splicing observed in mRNAs and "
         "ESTs that is either conserved in mouse, present in full length "
 	"mRNAs, or observed at least three times in ESTs.");
 }
 
 struct section *altSpliceSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create altSplice section. */
 {
 struct section *section = sectionNew(sectionRa, "altSplice");
 section->exists = altSpliceExists;
 section->print = altSplicePrint;
 return section;
 }