src/hg/hgTracks/cytoBandTrack.c 1.12

Index: src/hg/hgTracks/cytoBandTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/cytoBandTrack.c,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 1000000 -r1.11 -r1.12
--- src/hg/hgTracks/cytoBandTrack.c	24 Sep 2009 22:13:13 -0000	1.11
+++ src/hg/hgTracks/cytoBandTrack.c	9 Dec 2009 03:28:58 -0000	1.12
@@ -1,260 +1,262 @@
 /* cytoBandTrack - also known as chromosome band track. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hgTracks.h"
 #include "hCommon.h"
 #include "cytoBand.h"
 #include "hCytoBand.h"
 
 static Color cytoBandItemColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* Figure out color of band. */
 {
 return hCytoBandColor(item, hvg, hCytoBandDbIsDmel(database),
 	tg->ixColor, tg->ixAltColor, shadesOfGray, maxShade);
 }
 
 static char *cytoBandItemName(struct track *tg, void *item)
 /* Return name of cytoBand track item. */
 {
 return hCytoBandName(item, hCytoBandDbIsDmel(database));
 }
 
 int cytoBandStart(struct track *tg, void *item)
 /* Return the start position of a cytoBand. */
 {
 return ((struct cytoBand *)item)->chromStart;
 }
 
 int cytoBandEnd(struct track *tg, void *item)
 /* Return the end position of a cytoBand. */
 {
 return ((struct cytoBand *)item)->chromEnd;
 }
 
 int cytoBandIdeoStart(struct track *tg, void *item)
 /* Return the start position of a cytoBand. */
 {
 return ((struct cytoBand *)item)->chromStart + winStart;
 }
 
 int cytoBandIdeoEnd(struct track *tg, void *item)
 /* Return the end position of a cytoBand. */
 {
 return ((struct cytoBand *)item)->chromEnd + winStart;
 }
 
 static void cytoBandDrawAt(struct track *tg, void *item,
 	struct hvGfx *hvg, int xOff, int y, double scale,
 	MgFont *font, Color color, enum trackVisibility vis)
 /* Draw cytoBand items. */
 {
 struct cytoBand *band = item;
 int heightPer = tg->heightPer;
 int x1,x2,w;
 
 x1 = round((double)((int)tg->itemStart(tg,band) - winStart)*scale) + xOff;
 x2 = round((double)((int)tg->itemEnd(tg,band) - winStart)*scale) + xOff;
 /* Clip here so that text will tend to be more visible... */
 if (x1 < xOff)
     x1 = xOff;
 if (x2 > insideX + insideWidth)
     x2 = insideX + insideWidth;
 w = x2-x1;
 if (w < 1)
     w = 1;
 
 hCytoBandDrawAt(band, hvg, x1, y, w, heightPer, hCytoBandDbIsDmel(database), font,
 	mgFontPixelHeight(font), tg->ixColor, tg->ixAltColor,
 	shadesOfGray, maxShade);
 
 if(tg->mapsSelf)
     tg->mapItem(tg, hvg, band, band->name, band->name, band->chromStart, band->chromEnd,
 		x1, y, w, heightPer);
 else
     mapBoxHc(hvg, band->chromStart, band->chromEnd, x1,y,w,heightPer, tg->mapName,
 	     band->name, band->name);
 }
 
 
 static void loadCytoBands(struct track *tg)
 /* Load up simpleRepeats from database table to track items. */
 {
 bedLoadItem(tg, "cytoBand", (ItemLoader)cytoBandLoad);
 }
 
 static void loadCytoBandsIdeo(struct track *tg)
 /* Load up cytoBandIdeo from database table to track items. */
 {
 char query[256];
 safef(query, sizeof(query),
       "select * from cytoBandIdeo where chrom like '%s'", chromName);
 if(hTableExists(database, "cytoBandIdeo"))
     bedLoadItemByQuery(tg, "cytoBandIdeo", query, (ItemLoader)cytoBandLoad);
 if(slCount(tg->items) == 0)
     {
     tg->limitedVisSet = TRUE;
     tg->limitedVis = tvHide;
     }
 }
 
 static void freeCytoBands(struct track *tg)
 /* Free up isochore items. */
 {
 cytoBandFreeList((struct cytoBand**)&tg->items);
 }
 
 void cytoBandIdeoDraw(struct track *tg,
 		      int seqStart, int seqEnd,
 		      struct hvGfx *hvg, int xOff, int yOff, int width,
 		      MgFont *font, Color color, enum trackVisibility vis)
 /* Draw the entire chromosome with a little red box around our
    current position. */
 {
 double scale = 0;
 int xBorder = 4;
 int lineHeight = 0;
 int heightPer = 0;
 int x1, x2;
 int yBorder = 0;
 int chromSize = hChromSize(database, chromName);
 struct cytoBand *cbList = NULL, *cb = NULL;
 scale = (double) (width - (2 * xBorder)) / chromSize;
 
 /* Subtrack 10 for the 5 pixels buffer on either side. */
 tg->heightPer -= 11;
 tg->lineHeight -= 11;
 lineHeight = tg->lineHeight;
 heightPer = tg->heightPer;
 yOff = yOff;
 
 /* Time to draw the bands. */
 hvGfxSetClip(hvg, xOff, yOff, insideWidth, tg->height);
 genericDrawItems(tg, 0, chromSize, hvg, xOff+xBorder, yOff+5, width-(2*xBorder), font, color, tvDense);
 
 x1 = round((winStart)*scale) + xOff + xBorder -1;
 x2 = round((winEnd)*scale) + xOff + xBorder -1;
 if(x1 >= x2)
     x2 = x1+1;
 yBorder = tg->heightPer + 7 + 1;
 
 
 /* Draw an outline around chromosome for visualization purposes. Helps
  to make the chromosome look better. */
 hvGfxLine(hvg, xOff+xBorder, yOff+4, xOff+width-xBorder, yOff+4, MG_BLACK);
 hvGfxLine(hvg, xOff+xBorder, yOff+yBorder-3, xOff+width-xBorder, yOff+yBorder-3, MG_BLACK);
 hvGfxLine(hvg, xOff+xBorder, yOff+4, xOff+xBorder, yOff+yBorder-3, MG_BLACK);
 hvGfxLine(hvg, xOff+width-xBorder, yOff+4, xOff+width-xBorder, yOff+yBorder-3, MG_BLACK);
 
 /* Find and draw the centromere which is defined as the
  two bands with gieStain "acen" */
 cbList = tg->items;
 for(cb = cbList; cb != NULL; cb = cb->next)
     {
     /* If centromere do some drawing. */
     if(sameString(cb->gieStain, "acen"))
 	{
 	int cenLeft, cenRight, cenTop, cenBottom;
 
 	/* Get the coordinates of the edges of the centromere. */
 	cenLeft = round((cb->chromStart)*scale) + xOff + xBorder;
 	cenRight = round((cb->next->chromEnd)*scale) + xOff + xBorder;
 	cenTop = yOff+4;
 	cenBottom = yOff + yBorder - 3;
 
 	/* Draw centromere itself. */
 	hCytoBandDrawCentromere(hvg, cenLeft, cenTop, cenRight - cenLeft,
 	     cenBottom-cenTop+1, MG_WHITE, hCytoBandCentromereColor(hvg));
 	break;
 	}
     }
 
 /* Draw a red box around position in current browser window.  double
  thick so two lines each. */
 hvGfxBox(hvg, x1, yOff+1, x2-x1, 2, MG_RED);
 hvGfxBox(hvg, x1, yOff + yBorder - 1, x2-x1, 2, MG_RED);
 hvGfxBox(hvg, x1, yOff+1, 2, yBorder, MG_RED);
 hvGfxBox(hvg, x2, yOff+1, 2, yBorder, MG_RED);
 hvGfxUnclip(hvg);
 
 /* Put back the lineHeight for the track
    now that we are done spoofing tgDrawItems(). */
 tg->heightPer += 11;
 tg->lineHeight += 11;
 }
 
 void cytoBandIdeoMapItem(struct track *tg, struct hvGfx *hvg, void *item,
 			    char *itemName, char *mapItemName, int start, int end,
 			    int x, int y, int width, int height)
 /* Print out a box to jump to band in browser window .*/
 {
 struct cytoBand *cb = item;
-//#define CHROM_MAP_OF_OLD
-#ifndef CHROM_MAP_OF_OLD
-x = hvGfxAdjXW(hvg, x, width);
+if(advancedJavascriptFeaturesEnabled(cart))
+    {
+    x = hvGfxAdjXW(hvg, x, width);
 
     hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x, y, x+width, y+height);
     hPrintf("onclick='return false;' ");
     hPrintf("HREF=\"#\" class='cytoBand'");
     mapStatusMessage("%s %s:%d-%d", (cb->name==NULL?"":cb->name),cb->chrom, cb->chromStart+1, cb->chromEnd);
     hPrintf(">\n");
-#else//ifdef CHROM_MAP_OF_OLD
-mapBoxJumpTo(hvg, x, y, width, height, cb->chrom, cb->chromStart, cb->chromEnd, cb->name);
-#endif//def CHROM_MAP_OF_OLD
+    }
+else
+    {
+    mapBoxJumpTo(hvg, x, y, width, height, cb->chrom, cb->chromStart, cb->chromEnd, cb->name);
+    }
 }
 
 int cytoBandIdeoTotalHeight(struct track *tg, enum trackVisibility vis)
 /* Return the (nonstandard) height of the cytoBandIdeo track. */
 {
 tg->heightPer = tl.fontHeight + 11;
 tg->lineHeight = tl.fontHeight + 11;
 tg->limitedVisSet = TRUE;
 if(vis != tvHide && slCount(tg->items) > 0)
     {
     tg->limitedVis = tvDense;
     tg->height = tg->lineHeight;
     }
 else
     {
     tg->limitedVis = tvHide;
     tg->height = 0;
     }
 return tg->height;
 }
 
 void cytoBandIdeoMethods(struct track *tg)
 /* Make track for simple repeats. */
 {
 tg->totalHeight = cytoBandIdeoTotalHeight;
 tg->mapItem = cytoBandIdeoMapItem;
 tg->mapsSelf = TRUE;
 tg->itemStart = cytoBandIdeoStart;
 tg->itemEnd = cytoBandIdeoEnd;
 tg->loadItems = loadCytoBandsIdeo;
 tg->freeItems = freeCytoBands;
 tg->drawItems = cytoBandIdeoDraw;
 tg->drawItemAt = cytoBandDrawAt;
 tg->itemColor = cytoBandItemColor;
 tg->itemName = cytoBandItemName;
 tg->drawName = TRUE;
 }
 
 void cytoBandMethods(struct track *tg)
 /* Make track for simple repeats. */
 {
 tg->itemStart = cytoBandStart;
 tg->itemEnd = cytoBandEnd;
 tg->loadItems = loadCytoBands;
 tg->freeItems = freeCytoBands;
 tg->drawItems = genericDrawItems;
 tg->drawItemAt = cytoBandDrawAt;
 tg->itemColor = cytoBandItemColor;
 tg->itemName = cytoBandItemName;
 tg->drawName = TRUE;
 }