Index: src/hg/hgTracks/cgapSageTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/cgapSageTrack.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 1000000 -r1.13 -r1.14
--- src/hg/hgTracks/cgapSageTrack.c	3 Sep 2008 19:19:01 -0000	1.13
+++ src/hg/hgTracks/cgapSageTrack.c	21 Dec 2009 22:43:32 -0000	1.14
@@ -1,307 +1,309 @@
 /* cgapSageTrack - module for CGAP SAGE track. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hgTracks.h"
 #include "hCommon.h"
 #include "cgapSage/cgapSage.h"
 #include "cgapSage/cgapSageLib.h"
 
 static int grayIxForCgap(double tpm)
 /* Return a grayIx based on the score. */
 {
 int val = (int)ceil(tpm);
 return grayInRange(val, 0, 150);
 }
 
 static struct hash *libTissueHash(struct sqlConnection *conn)
 /* Read two columns of a table and hash em up. */
 {
 struct hash *ret = newHash(9);
 struct sqlResult *sr = NULL;
 char query[40] = "select libId,tissue from cgapSageLib";
 char **row;
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     hashAdd(ret, row[0], cloneString(row[1]));
 sqlFreeResult(&sr);
 return ret;
 }
 
 struct cgapSageTpmHashEl 
 /* A convenience struct for computing means. */
     {
     double total;
     long freqTotal;
     long libTotals;
     int count;
     };
 
 static boolean keepThisLib(char *tissue, char *libId)
 /* Tissue filtering code checks cart. */
 {
 char *tissueHl = cartUsualString(cart, "cgapSage.tissueHl", "All");
 if (!tissue)
     errAbort("NULL tissue or libId passed into keepThisLib()");
 if (sameString(tissueHl, "All") || sameString(tissue, tissueHl))
     return TRUE;
 return FALSE;
 }
 
 static struct hash *combineCgapSages(struct cgapSage *tag, struct hash *libHash, struct hash *libTotHash)
 /* Go through the each lib for a tag and combine it's score using a hash for */
 /* repeated tissues. */
 {
 struct hash *tpmHash = newHash(5);
 int i;
 for (i = 0; i < tag->numLibs; i++)
     {
     char libId[16];
     char *libName;
     int libTotTags = 0;
     struct cgapSageTpmHashEl *tpm;
     safef(libId, sizeof(libId), "%d", tag->libIds[i]);
     libName = hashMustFindVal(libHash, libId);
     tpm = hashFindVal(tpmHash, libName);
     libTotTags = hashIntVal(libTotHash, libId);
     if (keepThisLib(libName, libId))
 	{
 	if (tpm)
 	    {
 	    tpm->count++;
 	    tpm->freqTotal += tag->freqs[i];
 	    tpm->total += tag->tagTpms[i];
 	    tpm->libTotals += libTotTags;
 	    }
 	else
 	    {
 	    AllocVar(tpm);
 	    tpm->count = 1;
 	    tpm->total = tag->tagTpms[i];
 	    tpm->freqTotal = tag->freqs[i];
 	    tpm->libTotals = libTotTags;
 	    hashAdd(tpmHash, libName, tpm);
 	    }
 	}
     }
 return tpmHash;
 }
 
 static struct linkedFeatures *skeletonLf(struct cgapSage *tag)
 /* Fill in everything except the name and score. */
 {
 struct linkedFeatures *lf;
 struct simpleFeature *sf;
 AllocVar(lf);
 AllocVar(sf);
 lf->start = sf->start = tag->chromStart;
 lf->end = sf->end = tag->chromEnd;
 lf->tallStart = tag->thickStart;
 lf->tallEnd = tag->thickEnd;
 lf->orientation = orientFromChar(tag->strand[0]);
 lf->components = sf;
 return lf;
 }
 
 static void addSimpleFeature(struct linkedFeatures *lf)
 /* Make a dumb simpleFeature out of a single linkedFeatures. */
 {
 struct simpleFeature *sf;
 AllocVar(sf);
 sf->start = lf->start;
 sf->end = lf->end;
 sf->grayIx = lf->grayIx;
 lf->components = sf;
 }
 
 static char *cgapSageMapItemName(struct track *tg, void *item)
 /* Use what's in the ->extra for the name. */
 {
 struct linkedFeatures *lf = item;
 return (char *)lf->extra;
 }
 
 static void cgapSageMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end,
 			    int x, int y, int width, int height)
 {
 struct linkedFeatures *lf = item;
 mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height, 
                   tg->mapName, itemName, NULL, NULL, TRUE,
                   (char *)lf->extra);
 }
 
 int cgapLinkedFeaturesCmp(const void *va, const void *vb)
 /* Compare to sort based on chrom,chromStart. */
 {
 const struct linkedFeatures *a = *((struct linkedFeatures **)va);
 const struct linkedFeatures *b = *((struct linkedFeatures **)vb);
 return (int)b->score - (int)a->score;
 }
 
 static struct linkedFeatures *cgapSageToLinkedFeatures(struct cgapSage *tag, 
                   struct hash *libHash, struct hash *libTotHash, enum trackVisibility vis)
 /* Convert a single CGAP tag to a list of linkedFeatures. */
 {
 struct linkedFeatures *libList = NULL;
 struct linkedFeatures *skel = skeletonLf(tag);
 int i;
 if (vis == tvDense)
     /* Just use the skeleton one. */
     {
     int tagTotal = 0;
     int freqTotal = 0;
     int libsUsed = 0;
     for (i = 0; i < tag->numLibs; i++)
 	{
 	char libId[16];
 	char *libName;
 	safef(libId, sizeof(libId), "%d", tag->libIds[i]);
 	libName = hashMustFindVal(libHash, libId);
 	if (keepThisLib(libName, libId))
 	    {
 	    int libTotal = hashIntVal(libTotHash, libId);
 	    tagTotal += libTotal;
 	    freqTotal += tag->freqs[i];
 	    libsUsed++;
 	    }
 	}
     if (libsUsed > 0)
 	{
-	safef(skel->name, sizeof(skel->name), "whatever");
+	skel->name = cloneString("whatever");
 	skel->score = (float)((double)freqTotal * (1000000/tagTotal));
 	skel->grayIx = grayIxForCgap(skel->score);
 	addSimpleFeature(skel);
 	libList = skel;
 	}
     }
 else if (vis == tvPack)
     {
     /* If it's pack mode, average tissues into one linkedFeature. */
     struct hash *tpmHash = combineCgapSages(tag, libHash, libTotHash);
     struct hashEl *tpmList = hashElListHash(tpmHash);
     struct hashEl *tpmEl;
     slSort(&tpmList, slNameCmp);
     for (tpmEl = tpmList; tpmEl != NULL; tpmEl = tpmEl->next)
 	{
 	struct linkedFeatures *tiss = CloneVar(skel);
 	struct cgapSageTpmHashEl *tpm = (struct cgapSageTpmHashEl *)tpmEl->val;
 	char link[256];
 	char *encTissName = NULL;
 	double score = 0;
-	safef(tiss->name, sizeof(tiss->name), "%s (%d)", tpmEl->name, tpm->count);
+        int len = strlen(tpmEl->name) + 32;
+        tiss->name = needMem(len);
+	safef(tiss->name, len, "%s (%d)", tpmEl->name, tpm->count);
 	encTissName = cgiEncode(tpmEl->name);
 	safef(link, sizeof(link), "i=%s&tiss=%s", tag->name, encTissName);
 	score = (double)tpm->freqTotal*(1000000/(double)tpm->libTotals);
 	tiss->score = (float)score;
 	tiss->grayIx = grayIxForCgap(score);
 	tiss->extra = cloneString(link);
 	freeMem(encTissName);
 	addSimpleFeature(tiss);
 	slAddHead(&libList, tiss);
 	}
     hashElFreeList(&tpmList);
     freeHashAndVals(&tpmHash);
     }
 else 
     /* full mode */
     {
     for (i = 0; i < tag->numLibs; i++)
 	{
 	char libId[16];
 	char *libName;
 	char link[256];
 	struct linkedFeatures *lf;
 	safef(libId, sizeof(libId), "%d", tag->libIds[i]);
 	libName = hashMustFindVal(libHash, libId);
 	if (keepThisLib(libName, libId))
 	    {	    
 	    lf = CloneVar(skel);
-	    safef(lf->name, sizeof(lf->name), "%s", libName);
+	    lf->name = cloneString(libName);
 	    safef(link, sizeof(link), "i=%s&lib=%s", tag->name, libId);
 	    lf->score = (float)tag->tagTpms[i];
 	    lf->grayIx = grayIxForCgap(tag->tagTpms[i]);
 	    lf->extra = cloneString(link);
 	    addSimpleFeature(lf);	
 	    slAddHead(&libList, lf);
 	    }
 	}
     }
 slSort(&libList, cgapLinkedFeaturesCmp);
 slReverse(&libList);
 return libList;
 }
 
 struct hash *getTotTagsHashFromTable(struct sqlConnection *conn)
 /* Load the cgapSageLib table for the db then call getTotTagsHash. */
 {
 struct cgapSageLib *libs = cgapSageLibLoadByQuery(conn, "select * from cgapSageLib");
 struct hash *libTotHash = getTotTagsHash(libs);
 cgapSageLibFreeList(&libs);
 return libTotHash;
 }
 
 void cgapSageLoadItems(struct track *tg)
 /* This function loads the beds in the current window into a linkedFeatures list. */
 /* Each bed entry may turn into multiple linkedFeatures because one is made for */
 /* each library at a given tag (bed). */
 {
 struct linkedFeatures *itemList = NULL;
 struct sqlConnection *conn = hAllocConn(database);
 struct hash *libHash = libTissueHash(conn);
 struct hash *libTotHash = getTotTagsHashFromTable(conn);
 struct sqlResult *sr = NULL;
 char **row;
 int rowOffset;
 sr = hOrderedRangeQuery(conn, tg->mapName, chromName, winStart, winEnd,
 			NULL, &rowOffset);
 if ((winEnd - winStart) > CGAP_SAGE_DENSE_GOVERNOR)
     tg->visibility = tvDense;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct cgapSage *tag = cgapSageLoad(row+rowOffset);
     struct linkedFeatures *oneLfList = cgapSageToLinkedFeatures(tag, libHash, libTotHash, tg->visibility);
     itemList = slCat(oneLfList, itemList);
     }
 slReverse(&itemList);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 tg->items = itemList;
 }
 
 /***** All the drawing/color-related stuff. ******/
 
 static Color cgapShadesOfRed[10+1];
 /* This will go from white to darker red. */
 
 static Color cgapSageItemColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* Return color to draw CGAP SAGE item */
 {
 struct linkedFeatures *thisItem = item;
 return cgapShadesOfRed[thisItem->grayIx];
 }
 
 void cgapSageDrawItems(struct track *tg, 
         int seqStart, int seqEnd,
         struct hvGfx *hvg, int xOff, int yOff, int width, 
         MgFont *font, Color color, enum trackVisibility vis)
 /* Initialize the colors, then do the normal drawing. */
 {
 static struct rgbColor lowerColor = {205, 191, 191};
 static struct rgbColor cgapRed = {205, 0, 0};
 hvGfxMakeColorGradient(hvg, &lowerColor, &cgapRed, 10, cgapShadesOfRed);
 genericDrawItems(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis);
 }
 
 void cgapSageMethods(struct track *tg)
 /* Make track for simple repeats. */
 {
 linkedFeaturesMethods(tg);
 tg->loadItems = cgapSageLoadItems;
 tg->itemColor = cgapSageItemColor;
 tg->drawItems = cgapSageDrawItems;
 tg->mapItemName = cgapSageMapItemName;
 tg->mapItem = cgapSageMapItem;
 }

