src/hg/hgTracks/rnaFoldTrack.c 1.7

Index: src/hg/hgTracks/rnaFoldTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/rnaFoldTrack.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/hg/hgTracks/rnaFoldTrack.c	3 Sep 2008 19:19:04 -0000	1.6
+++ src/hg/hgTracks/rnaFoldTrack.c	3 Mar 2009 19:38:52 -0000	1.7
@@ -1,228 +1,230 @@
 /* rnaStructure - stuff to handle loading and coloring of rna
    secondary structure predictions.
 */
 
 #include "common.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hgTracks.h"
 #include "bed.h"
 #include "rnaSecStr.h"
 #include "rnautil.h"
 
 static char const rcsid[] = "$Id$";
 
 
 void bedLoadItemBySqlResult(struct track *tg, struct sqlResult *sr, int rowOffset, ItemLoader loader)
 /* Generic tg->item loader. */
 {
 char **row = NULL;
 struct slList *itemList = NULL, *item = NULL;
 
 if (NULL == sr)
     errAbort("While loading track %s, bedLoadItemSqlResult was given empty sqlResult", tg->mapName);
 
 while ((row = sqlNextRow(sr)) != NULL)
     {
     item = loader(row + rowOffset);
     slAddHead(&itemList, item);
     }
 slSort(&itemList, bedCmp);
 tg->items = itemList;
 }
 
 
 void scoreFilterSqlClause(struct track *tg, char *extraWhere, size_t size, int defaultFilterScore)
 /* Make a 'where' clause for the sql query if the scoreFilter has been set. */
 {
 char option[128]; /* Option -  score filter */
 char *optionScoreVal;
 int  optionScore = defaultFilterScore;
 
 safef(option, sizeof(option), "%s.scoreFilter", tg->mapName);
 optionScoreVal = trackDbSetting(tg->tdb, "scoreFilter");
 if (optionScoreVal != NULL)
     optionScore = atoi(optionScoreVal);
 optionScore = cartUsualInt(cart, option, optionScore);
 
 safef(extraWhere, size, "score >= %d",optionScore);
 }			   		   
 
 
 void loadRnaSecStr(struct track *tg)
 /* Load up rnaSecStr from database table to track items. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 int rowOffset = 0;
 struct sqlResult *sr = NULL;
 char extraWhere[128];
 
 scoreFilterSqlClause(tg, extraWhere, sizeof(extraWhere), 0);
 sr = hRangeQuery(conn, tg->mapName, chromName, winStart, winEnd, extraWhere, &rowOffset);
 bedLoadItemBySqlResult(tg, sr, rowOffset, (ItemLoader)rnaSecStrLoad);
 
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 void freeRnaSecStr(struct track *tg)
 /* Free up rnaSecStr items. */
 {
 rnaSecStrFreeList((struct rnaSecStr**)&tg->items);
 }
 
 void spreadAndColorString(struct hvGfx *hvg, int x, int y, int width, int height,
 			  Color *colorIxs, int maxShade, MgFont *font, char *text, int count, 
 			  double *scores, double minScore, double maxScore)
 /* Draw evenly spaced letters in string. The scores array contains a
  * score for each letter in the text string. The score will determine
  * which color in the colorIxs will be used for a given
  * letter. ColorIxs is an array of size maxShade+1. The count param is
  * the number of bases to print, not length of the input line
  * (text) */
 {
 char c[2] = "";
 int i;
 int x1, x2;
 Color clr;
 
 for (i=0; i<count; i++, text++, scores++)
     {
     x1         = i * width / count;
     x2         = (i+1) * width/count;
     clr        = colorIxs[assignBin(*scores, minScore, maxScore, maxShade+1)];
     c[0]       = *text;
     hvGfxTextCentered(hvg, x1+x, y, x2-x1, height, clr, font, c);
     }
 }
 
 void spreadAndGrayShadeString(struct hvGfx *hvg, int x, int y, int width, int height,
 			  MgFont *font, char *text, int count, double *scores, double minScore, double maxScore)
 /* Draw evenly spaced letters in string and gray shade letters according to scores. */
 {
 spreadAndColorString(hvg, x, y, width, height, shadesOfGray+2, maxShade-2, font, text, count, scores, minScore, maxScore);
 }
 
 void spreadRnaFoldAnno(struct hvGfx *hvg, int x, int y, int width, int height, Color color, MgFont *font, struct rnaSecStr *item)
 /* Draw parenthesis structure which defines rna secondary structure. */
 {
 char *fold     = cloneString(item->secStr);
 double *scores = CloneArray(item->conf, item->size);
 if (*item->strand == '-')
 {
     reverseFold(fold);
     reverseDoubles(scores, item->size);
 }
 spreadAndGrayShadeString(hvg, x, y, width, height, font, fold, item->size, scores, 0.0, 1.0);
 freeMem(fold);
 freeMem(scores);
 }
 
 
 void drawCharBox(struct hvGfx *hvg, int x, int y, int width, int height, Color color, char *s, char c)
 /* s defines a string which spans width. Draw a box in intervals
  * corresponding to positions where s has letter c */
 {
 double charWidth = ((double)width)/strlen(s);
 int i = 0, begin = 0, length = 0;
 
 for (;*s;s++,i++)
     {
     if (*s == c)
 	{
 	if (!length)
 	    begin = i;
 	length++;
 	}
     /* Draw box if at end of interval or at end of string */
     if (*s != c || !*(s+1) )
 	if (length)
 	    {
 	    int x1 = x + (int) begin *charWidth;
 	    int w  = (int) length*charWidth;
 	    hvGfxBox(hvg, x1, y, w, height, color);
 	    length = 0;
 	    }
     }
 }
 
 
 void colorSingleStranded(struct hvGfx *hvg, int x, int y, int width, int height, Color color, struct rnaSecStr *item)
 {
 char *fold = cloneString(item->secStr);
 if (*item->strand == '-')
     reverseFold(fold);
 drawCharBox(hvg, x, y, width, height, color, fold, '.');
 freeMem(fold);
 }
 
 
 void rnaSecStrDrawAt(struct track *tg, void *item, 
 		     struct hvGfx *hvg, int xOff, int y, 
 		     double scale, MgFont *font, Color color, enum trackVisibility vis)
 /* Draw a single simple rnaSecStr item at position. */
 {
 struct rnaSecStr *rnaSecStr = item;
 int heightPer = tg->heightPer;
 int x1 = round((double)((int)rnaSecStr->chromStart-winStart)*scale) + xOff;
 int x2 = round((double)((int)rnaSecStr->chromEnd-winStart)*scale) + xOff;
 int w;
 struct trackDb *tdb = tg->tdb;
-int scoreMin = atoi(trackDbSettingOrDefault(tdb, "scoreMin", "0"));
-int scoreMax = atoi(trackDbSettingOrDefault(tdb, "scoreMax", "1000"));
+int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0"));
+int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000"));
+scoreMin = cartUsualIntClosestToHome(cart,tdb, FALSE, "scoreMin", scoreMin);
+scoreMax = cartUsualIntClosestToHome(cart,tdb, FALSE, "scoreMax", scoreMax);
 
 if (tg->itemColor != NULL)
     color = tg->itemColor(tg, rnaSecStr, hvg);
 else
     {
     if (tg->colorShades)
 	color = tg->colorShades[grayInRange(rnaSecStr->score, scoreMin, scoreMax)];
     }
 w = x2-x1;
 if (w < 1)
     w = 1;
 if (color)
     {
     if (zoomedToBaseLevel)
 	spreadRnaFoldAnno(hvg, x1, y, w, heightPer, color, font, rnaSecStr);
     else {
     hvGfxBox(hvg, x1, y, w, heightPer, color);
     colorSingleStranded(hvg, x1, y, w, heightPer, lighterColor(hvg, color), rnaSecStr);
     if (tg->subType == lfWithBarbs || tg->exonArrows)
 	{
 	int dir = 0;
 	if (rnaSecStr->strand[0] == '+')
 	    dir = 1;
 	else if(rnaSecStr->strand[0] == '-') 
 	    dir = -1;
 	if (dir != 0 && w > 2)
 	    {
 	    int midY = y + (heightPer>>1);
 	    Color textColor = hvGfxContrastingColor(hvg, color);
 	    clippedBarbs(hvg, x1, midY, w, 2, 5, dir, textColor, TRUE);
 	    }
 	}
     }
     if (tg->drawName && vis != tvSquish)
 	{
 	char *s = tg->itemName(tg, rnaSecStr);
 	w = x2-x1;
 	if (w > mgFontStringWidth(font, s))
 	    {
 	    Color textColor = hvGfxContrastingColor(hvg, color);
 	    hvGfxTextCentered(hvg, x1, y, w, heightPer, textColor, font, s);
 	    }
 	mapBoxHc(hvg, rnaSecStr->chromStart, rnaSecStr->chromEnd, x1, y, x2 - x1, heightPer,
 		 tg->mapName, tg->mapItemName(tg, rnaSecStr), NULL);
 	}
     }
 }
 
 void rnaSecStrMethods(struct track *tg)
 /* Make track which visualizes RNA secondary structure annotation. */
 {
 tg->loadItems  = loadRnaSecStr;
 tg->freeItems  = freeRnaSecStr;
 tg->drawItemAt = rnaSecStrDrawAt;
 }