Index: src/hg/hgTracks/chromGraphTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/chromGraphTrack.c,v
retrieving revision 1.18
retrieving revision 1.19
diff -b -B -U 1000000 -r1.18 -r1.19
--- src/hg/hgTracks/chromGraphTrack.c	14 Sep 2009 15:23:48 -0000	1.18
+++ src/hg/hgTracks/chromGraphTrack.c	11 Nov 2009 20:41:27 -0000	1.19
@@ -1,337 +1,334 @@
 /* chromGraphTrack - displays track that is just a line
  * connecting certain data points.  This does not handle the
  * data volume that the wiggle track does.  It's meant for
  * things like graphs for gene association studies. */
 #include "common.h"
 #include "hash.h"
 #include "jksql.h"
 #include "trackDb.h"
 #include "hdb.h"
 #include "hgTracks.h"
 #include "hvGfx.h"
 #include "chromGraph.h"
 #include "imageV2.h"
 
 Color colorFromAscii(struct hvGfx *hvg, char *asciiColor)
 /* Get color index for a named color. */
 /* Copy/pasted from hgGenome/mainPage.c ... should be in a library */
 /* somewhere! */
 {
 if (sameWord("red", asciiColor))
     return MG_RED;
 else if (sameWord("blue", asciiColor))
     return MG_BLUE;
 else if (sameWord("yellow", asciiColor))
     return hvGfxFindColorIx(hvg, 220, 220, 0);
 else if (sameWord("purple", asciiColor))
     return hvGfxFindColorIx(hvg, 150, 0, 200);
 else if (sameWord("orange", asciiColor))
     return hvGfxFindColorIx(hvg, 230, 120, 0);
 else if (sameWord("green", asciiColor))
     return hvGfxFindColorIx(hvg, 0, 180, 0);
 else if (sameWord("gray", asciiColor))
     return MG_GRAY;
 else
     return MG_BLACK;
 }
 
 static Color cgColorLikeHgGenome(struct track *tg, struct hvGfx *hvg)
 /* Search the cart variables and use the colors corresponding to the hgGenome */
 /* graph. */
 {
 Color ret;
 struct hashEl *matchingCartSettings = NULL;
 struct hashEl *el;
 char cartGenomeWildStr[256];
 char *graphCartVarName = NULL;
 char *colorCartVarSetting = "black";
 safef(cartGenomeWildStr, sizeof(cartGenomeWildStr), "hgGenome_graph_%s_*", database);
 /* for ex. hgGenome_graph_hg18_1_1 */
 matchingCartSettings = cartFindLike(cart, cartGenomeWildStr);
 for (el = matchingCartSettings; el != NULL; el = el->next)
     {
     char *val = (char *)el->val;
     if (val && sameString(val, tg->mapName))
 	{
 	graphCartVarName = el->name;
 	break;
 	}
     }
 if (graphCartVarName)
     {
     char *colorCartVarName = replaceChars(graphCartVarName, "_graph_", "_graphColor_");
     colorCartVarSetting = cartUsualString(cart, colorCartVarName, "black");
     freeMem(colorCartVarName);
     }
 hashElFreeList(&matchingCartSettings);
 ret = colorFromAscii(hvg, colorCartVarSetting);
 return ret;
 }
 
 static void cgDrawEither(struct track *tg, int seqStart, int seqEnd,
         struct hvGfx *hvg, int xOff, int yOff, int width,
         MgFont *font, Color color, enum trackVisibility vis,
 	char *binFileName)
 /* Draw chromosome graph - either built in or not. */
 {
 struct chromGraphSettings *cgs = tg->customPt;
 int x,y,lastX=0,lastY=0, llastX = 0, llastY = 0;
 int height = tg->height;
 int maxGapToFill = cgs->maxGapToFill;
 int lastPos = -maxGapToFill-1;
 double minVal = cgs->minVal;
 double yScale = (height-1)/(cgs->maxVal - minVal);
 double xScale = scaleForPixels(width);
 Color myColor = cgColorLikeHgGenome(tg, hvg);
 
 /* Draw background lines in full mode. */
 if (vis == tvFull && cgs->linesAtCount != 0)
     {
     int i;
     Color lightBlue = hvGfxFindRgb(hvg, &guidelineColor);
     for (i=0; i<cgs->linesAtCount; ++i)
         {
 	y = height - 1 - (cgs->linesAt[i] - minVal)*yScale + yOff;
 	hvGfxBox(hvg, xOff, y, width, 1, lightBlue);
 	}
     }
 
 if (binFileName)
     {
     struct chromGraphBin *cgb = chromGraphBinOpen(binFileName);
     if (chromGraphBinSeekToChrom(cgb, chromName))
 	{
 	int seqStartMinus = seqStart - cgs->maxGapToFill;
 	while (chromGraphBinNextVal(cgb))
 	    {
 	    int pos = cgb->chromStart;
 	    if (pos >= seqStartMinus)
 		{
 		double val = cgb->val;
 		x = (pos - seqStart)*xScale + xOff;
 		y = height - 1 - (val - minVal)*yScale + yOff;
 		if (x >= xOff)
 		    {
 		    if (pos - lastPos <= maxGapToFill)
 			{
 			if (llastX != lastX || llastY != lastY || lastX != x || lastY != y)
 			    hvGfxLine(hvg, lastX, lastY, x, y, myColor);
 			}
 		    else
 			hvGfxDot(hvg, x, y, myColor);
 		    }
 		llastX = lastX;
 		llastY = lastY;
 		lastX = x;
 		lastY = y;
 		lastPos = pos;
 		if (pos >= seqEnd)
 		    break;
 		}
 	    }
 	}
     }
 else
     {
     struct sqlConnection *conn = hAllocConn(database);
     char query[512];
     struct sqlResult *sr;
     char **row;
     /* Construct query.  Set up a little more than window so that
      * we can draw connecting lines. */
     safef(query, sizeof(query),
 	"select chromStart,val from %s "
 	"where chrom='%s' and chromStart>=%d and chromStart<%d",
 	tg->mapName, chromName,
 	seqStart - cgs->maxGapToFill, seqEnd + cgs->maxGapToFill);
     sr = sqlGetResult(conn, query);
 
     /* Loop through drawing lines from one point to another unless
      * the points are too far apart. */
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	int pos = sqlUnsigned(row[0]);
 	double val = atof(row[1]);
 	x = (pos - seqStart)*xScale + xOff;
 	y = height - 1 - (val - minVal)*yScale + yOff;
 	if (x >= xOff)
 	    {
 	    if (pos - lastPos <= maxGapToFill)
 		{
 		if (llastX != lastX || llastY != lastY || lastX != x || lastY != y)
 		    hvGfxLine(hvg, lastX, lastY, x, y, myColor);
 		}
 	    else
 		hvGfxDot(hvg, x, y, myColor);
 	    }
 	llastX = lastX;
 	llastY = lastY;
 	lastX = x;
 	lastY = y;
 	lastPos = pos;
 	if (pos >= seqEnd)
 	    break;
 	}
     sqlFreeResult(&sr);
     hFreeConn(&conn);
     }
 
 /* Do map box */
 xOff = hvGfxAdjXW(hvg, xOff, width);
 
 char *encodedTrack = cgiEncode(tg->mapName);
-#ifdef IMAGEv2_UI
-if(theImgBox && curMap)
+if(theImgBox && curImgTrack)
     {
     char link[512];     // FIXME: winStart/winEnd are not right when using a portal
     safef(link,sizeof(link),"%s&o=%d&t=%d&g=%s", hgcNameAndSettings(),
         winStart, winEnd, encodedTrack);
     #ifdef IMAGEv2_SHORT_MAPITEMS
         if(xOff < insideX && xOff+width > insideX)
             warn("cgDrawEither(%s) map item spanning slices. LX:%d TY:%d RX:%d BY:%d  link:[%s]",encodedTrack,xOff, yOff, xOff+width, yOff+height, link);
     #endif//def IMAGEv2_SHORT_MAPITEMS
     imgTrackAddMapItem(curImgTrack,link,NULL,xOff,yOff,xOff+width,yOff+height);
-    //mapSetItemAdd(curMap,link,NULL,xOff,yOff,xOff+width,yOff+height);
     }
 else
-#endif//def IMAGEv2_UI
     {
     hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", xOff, yOff, xOff+width,
         yOff+height);
     hPrintf("HREF=\"%s&o=%d&t=%d&g=%s&c=%s&l=%d&r=%d&db=%s&pix=%d\">\n",
             hgcNameAndSettings(), winStart, winEnd, encodedTrack, chromName, winStart, winEnd,
             database, tl.picWidth);
     }
 }
 
 static void cgDrawItems(struct track *tg, int seqStart, int seqEnd,
         struct hvGfx *hvg, int xOff, int yOff, int width,
         MgFont *font, Color color, enum trackVisibility vis)
 /* Draw chromosome graph for built-in track. */
 {
 cgDrawEither(tg, seqStart, seqEnd, hvg, xOff, yOff, width,
 	font, color, vis, NULL);
 }
 
 static void cgDrawItemsCt(struct track *tg, int seqStart, int seqEnd,
         struct hvGfx *hvg, int xOff, int yOff, int width,
         MgFont *font, Color color, enum trackVisibility vis)
 /* Draw chromosome graph for customTrack. */
 {
 cgDrawEither(tg, seqStart, seqEnd, hvg, xOff, yOff, width,
 	font, color, vis, trackDbRequiredSetting(tg->tdb, "binaryFile"));
 }
 
 
 int cgTotalHeight(struct track *tg, enum trackVisibility vis)
 /* Most fixed height track groups will use this to figure out the height
  * they use. */
 {
 struct chromGraphSettings *cgs = tg->customPt;
 switch (vis)
     {
     case tvFull:
     case tvPack:
         tg->height = cgs->pixels;
 	break;
     case tvDense:
     default:
         tg->height = tl.fontHeight;
 	break;
     }
 return tg->height;
 }
 
 void wrapTextAndCenter(struct hvGfx *hvg, int xOff, int yOff, int width,
 	int height,  MgFont *font, Color color, char *text)
 /* Try and word-wrap text into box more or less. */
 {
 struct slName *word, *wordList = slNameListFromString(text, ' ');
 int wordCount = slCount(wordList);
 int fontHeight = tl.fontHeight;
 int lineCount = height / fontHeight;
 int yUsed, y;
 if (lineCount > wordCount) lineCount = wordCount;
 yUsed = lineCount * fontHeight;
 y = (height - yUsed)/2 + yOff;
 for (word = wordList; word != NULL; word = word->next)
     {
     hvGfxText(hvg, xOff, y, color, font, word->name);
     y += fontHeight;
     }
 }
 
 void cgLeftLabels(struct track *tg, int seqStart, int seqEnd,
 	struct hvGfx *hvg, int xOff, int yOff, int width, int height,
 	boolean withCenterLabels, MgFont *font, Color color,
 	enum trackVisibility vis)
 /* Draw labels to the left. */
 {
 struct chromGraphSettings *cgs = tg->customPt;
 if (vis == tvDense || cgs->linesAtCount == 0)
     {
     hvGfxTextRight(hvg, xOff, yOff, width - 1, height,
 	color, font, tg->shortLabel);
     }
 else
     {
     int i;
     int realHeight = height;
     int realYoff = yOff;
     double minVal = cgs->minVal;
     double yScale;
     int tickSize = tl.nWidth;
     int numPos = tickSize * 1.25;
 
     if (withCenterLabels)
         {
 	int centerLabelHeight = tl.fontHeight;
 	realHeight -= centerLabelHeight;
 	realYoff += centerLabelHeight;
 	}
     yScale = (realHeight-1)/(cgs->maxVal - minVal);
     for (i=0; i<cgs->linesAtCount; ++i)
         {
 	double val = cgs->linesAt[i];
 	int y = realHeight - 1 - (val - minVal)*yScale + realYoff;
 	char numText[16];
 	hvGfxBox(hvg, xOff + width - tickSize, y, tickSize, 1, color);
 	safef(numText, sizeof(numText), "%g", val);
 	hvGfxTextRight(hvg, xOff, y - tl.fontHeight+2,
 		width - numPos, tl.fontHeight,
 		color, font, numText);
 	}
     wrapTextAndCenter(hvg, xOff+1, yOff, width*5*tl.nWidth, height,
     	font, color, tg->shortLabel);
     }
 }
 
 static void chromGraphMethodsCommon(struct track *tg)
 /* Get chromGraph methods common to built in and custom tracks. */
 {
 tg->loadItems = tgLoadNothing;
 tg->totalHeight = cgTotalHeight;
 tg->freeItems = tgFreeNothing;
 tg->drawLeftLabels = cgLeftLabels;
 tg->mapsSelf = TRUE;
 }
 
 void chromGraphMethods(struct track *tg)
 /* Fill in chromGraph methods for built in track. */
 {
 chromGraphMethodsCommon(tg);
 tg->drawItems = cgDrawItems;
 struct sqlConnection *conn = hAllocConn(database);
 tg->customPt = chromGraphSettingsGet(tg->mapName, conn,
 	tg->tdb, cart);
 hFreeConn(&conn);
 }
 
 void chromGraphMethodsCt(struct track *tg)
 /* Fill in chromGraph methods for custom track. */
 {
 tg->drawItems = cgDrawItemsCt;
 chromGraphMethodsCommon(tg);
 tg->customPt = chromGraphSettingsGet(tg->mapName, NULL, tg->tdb, cart);
 }
 

