src/hg/hgTracks/rmskTrack.c 1.13

Index: src/hg/hgTracks/rmskTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/rmskTrack.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -b -B -U 1000000 -r1.12 -r1.13
--- src/hg/hgTracks/rmskTrack.c	3 Sep 2008 19:19:04 -0000	1.12
+++ src/hg/hgTracks/rmskTrack.c	9 Dec 2009 19:53:34 -0000	1.13
@@ -1,181 +1,182 @@
 /* rmskTrack - Handle RepeatMasker track. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hgTracks.h"
 #include "rmskOut.h"
 
 
 /* Repeat items.  Since there are so many of these, to avoid 
  * memory problems we don't query the database and store the results
  * during repeatLoad, but rather query the database during the
  * actual drawing. */
 
 static struct repeatItem *otherRepeatItem = NULL;
 static char *repeatClassNames[] =  {
     "SINE", "LINE", "LTR", "DNA", "Simple", "Low Complexity", "Satellite", "RNA", "Other", "Unknown", 
 };
 static char *repeatClasses[] = {
     "SINE", "LINE", "LTR", "DNA", "Simple_repeat", "Low_complexity", "Satellite", "RNA", "Other", "Unknown", 
 };
 
 static struct repeatItem *makeRepeatItems()
 /* Make the stereotypical repeat masker tracks. */
 {
 struct repeatItem *ri, *riList = NULL;
 int i;
 int numClasses = ArraySize(repeatClasses);
 for (i=0; i<numClasses; ++i)
     {
     AllocVar(ri);
     ri->class = repeatClasses[i];
     ri->className = repeatClassNames[i];
     slAddHead(&riList, ri);
     if (sameString(repeatClassNames[i], "Other"))
         otherRepeatItem = ri;               
     }
 slReverse(&riList);
 return riList;
 }
 
 static void repeatLoad(struct track *tg)
 /* Load up repeat tracks.  (Will query database during drawing for a change.) */
 {
 tg->items = makeRepeatItems();
 }
 
 static void repeatFree(struct track *tg)
 /* Free up repeatMasker items. */
 {
 slFreeList(&tg->items);
 }
 
 static char *repeatName(struct track *tg, void *item)
 /* Return name of repeat item track. */
 {
 struct repeatItem *ri = item;
 return ri->className;
 }
 
 static void repeatDraw(struct track *tg, int seqStart, int seqEnd,
         struct hvGfx *hvg, int xOff, int yOff, int width, 
         MgFont *font, Color color, enum trackVisibility vis)
 {
 int baseWidth = seqEnd - seqStart;
 struct repeatItem *ri;
 int y = yOff;
 int heightPer = tg->heightPer;
 int lineHeight = tg->lineHeight;
 int x1,x2,w;
 boolean isFull = (vis == tvFull);
 Color col;
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr = NULL;
 char **row;
 int rowOffset;
 
 if (isFull)
     {
     /* Do gray scale representation spread out among tracks. */
     struct hash *hash = newHash(6);
     struct rmskOut ro;
     int percId;
     int grayLevel;
     char statusLine[128];
 
     for (ri = tg->items; ri != NULL; ri = ri->next)
         {
 	ri->yOffset = y;
 	y += lineHeight;
 	hashAdd(hash, ri->class, ri);
 	}
     sr = hRangeQuery(conn, tg->mapName, chromName, winStart, winEnd, NULL,
 		     &rowOffset);
     while ((row = sqlNextRow(sr)) != NULL)
         {
 	rmskOutStaticLoad(row+rowOffset, &ro);
 	if (endsWith(ro.repClass, "RNA"))
 	    ri = hashFindVal(hash, "RNA");
 	else
 	    ri = hashFindVal(hash, ro.repClass);
 	if (ri == NULL)
 	   ri = otherRepeatItem;
 	percId = 1000 - ro.milliDiv - ro.milliDel - ro.milliIns;
 	grayLevel = grayInRange(percId, 500, 1000);
 	col = shadesOfGray[grayLevel];
 	x1 = roundingScale(ro.genoStart-winStart, width, baseWidth)+xOff;
 	x2 = roundingScale(ro.genoEnd-winStart, width, baseWidth)+xOff;
 	w = x2-x1;
 	if (w <= 0)
 	    w = 1;
 	hvGfxBox(hvg, x1, ri->yOffset, w, heightPer, col);
 	if (baseWidth <= 100000)
 	    {
 	    if (ri == otherRepeatItem)
 		{
 		sprintf(statusLine, "Repeat %s, family %s, class %s",
 		    ro.repName, ro.repFamily, ro.repClass);
 		}
 	    else
 		{
 		sprintf(statusLine, "Repeat %s, family %s",
 		    ro.repName, ro.repFamily);
 		}
 	    mapBoxHc(hvg, ro.genoStart, ro.genoEnd, x1, ri->yOffset, w, heightPer, tg->mapName,
 	    	ro.repName, statusLine);
 	    }
 	}
     freeHash(&hash);
     }
 else
     {
     char table[64];
     boolean hasBin;
     struct dyString *query = newDyString(1024);
     /* Do black and white on single track.  Fetch less than we need from database. */
     if (hFindSplitTable(database, chromName, tg->mapName, table, &hasBin))
         {
 	dyStringPrintf(query, "select genoStart,genoEnd from %s where ", table);
 	if (hasBin)
 	    hAddBinToQuery(winStart, winEnd, query);
 	dyStringPrintf(query, "genoStart<%u and genoEnd>%u ", winEnd, winStart);
 	/* if we're using a single rmsk table, add genoName to the where clause */
 	if (startsWith("rmsk", table))
 	    dyStringPrintf(query, " and genoName = '%s' ", chromName);
 	sr = sqlGetResult(conn, query->string);
 	while ((row = sqlNextRow(sr)) != NULL)
 	    {
 	    int start = sqlUnsigned(row[0]);
 	    int end = sqlUnsigned(row[1]);
 	    x1 = roundingScale(start-winStart, width, baseWidth)+xOff;
 	    x2 = roundingScale(end-winStart, width, baseWidth)+xOff;
 	    w = x2-x1;
 	    if (w <= 0)
 		w = 1;
 	    hvGfxBox(hvg, x1, yOff, w, heightPer, MG_BLACK);
 	    }
 	}
     dyStringFree(&query);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 void repeatMethods(struct track *tg)
 /* Make track for repeats. */
 {
 tg->loadItems = repeatLoad;
 tg->freeItems = repeatFree;
 tg->drawItems = repeatDraw;
 tg->colorShades = shadesOfGray;
 tg->itemName = repeatName;
 tg->mapItemName = repeatName;
 tg->totalHeight = tgFixedTotalHeightNoOverflow;
 tg->itemHeight = tgFixedItemHeight;
 tg->itemStart = tgItemNoStart;
 tg->itemEnd = tgItemNoEnd;
+tg->mapsSelf = TRUE;
 }