src/hg/instinct/hgBamBam/hgAnnotations.c 1.4

Index: src/hg/instinct/hgBamBam/hgAnnotations.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/hgBamBam/hgAnnotations.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/instinct/hgBamBam/hgAnnotations.c	31 May 2010 00:02:34 -0000	1.3
+++ src/hg/instinct/hgBamBam/hgAnnotations.c	31 May 2010 00:55:19 -0000	1.4
@@ -1183,8 +1183,9 @@
 
 struct chromLay *cl;
 vgSetClip(vg, settings->dataOffsetX, 0, settings->dataWidth, settings->height);
 
+int yOff = CYTO_HEIGHT;
 boolean singleChrom = FALSE;
 if (slCount(settings->layoutList) == 1)
     singleChrom = TRUE;
 
@@ -1199,34 +1200,34 @@
     int rightX = leftX + chromWidth;
     if (rightX > width - 1)
         rightX = width - 1;
 
-    vgBox(vg, leftX, 0, 1, labelHeight, MG_GRAY);
-    vgBox(vg, rightX, 0, 1, labelHeight, MG_GRAY);
+    vgBox(vg, leftX, yOff, 1, labelHeight, MG_GRAY);
+    vgBox(vg, rightX, yOff, 1, labelHeight, MG_GRAY);
 
     int strWidth;
     if (!singleChrom)
         {
         char *pt = cl->chrom;
         strWidth = mgFontStringWidth(settings->font, pt);
         if (strWidth < chromWidth)
-            vgTextCentered(vg, cl->pxStart, 0, chromWidth, labelHeight,
+            vgTextCentered(vg, cl->pxStart, yOff, chromWidth, labelHeight,
                            MG_BLACK, settings->font, pt);
         else
             {
             pt = cl->chrom + 3;
             strWidth = mgFontStringWidth(settings->font, pt);
             if (strWidth < chromWidth)
-		vgTextCentered(vg, cl->pxStart, 0, chromWidth, labelHeight,
+		vgTextCentered(vg, cl->pxStart, yOff, chromWidth, labelHeight,
 			       MG_BLACK, settings->font, pt);
             } 
         }
     else
         {
         char str[128]; 
         unsigned long x;
 
-        int y = labelHeight/2 - settings->fontHeight/4;
+        int y = labelHeight/2 - settings->fontHeight/4 + yOff;
         vgText(vg, cl->pxStart + 3, y, MG_BLACK, settings->font, cl->chrom);
         int minX = cl->pxStart + mgFontStringWidth(settings->font, cl->chrom);
 
         double numBases = cl->baseEnd - cl->baseStart;
@@ -1253,9 +1254,9 @@
 
             if (tickX <= minX || tickX > rightX)
                 continue;
 
-            int tickY = labelHeight/2 - settings->fontHeight/2 - 1;
+            int tickY = labelHeight/2 - settings->fontHeight/2 - 1 + yOff;
             vgBox(vg, tickX, tickY, 1, settings->fontHeight+1, MG_BLACK);
             safef(str, sizeof(str), "%lu", x);
 
             strWidth = mgFontStringWidth(settings->font, str);
@@ -1294,9 +1295,9 @@
     prepareImage(vg->vg, settings);
 
     drawChromLabels(vg->vg, settings, settings->layoutList);
 
-    drawIdeogram(vg, settings, settings->layoutList, DEFAULT_LABEL_HEIGHT);
+    drawIdeogram(vg, settings, settings->layoutList, 0);
 
     hvGfxClose(&vg);
     }
 
@@ -1361,9 +1362,9 @@
 
 int midY = height / 2;
 int buffer = 3;
 int scaleWidth = round(((double) width) * scaleBases / numBases);
-int startX = round((double)width / 2.0) - scaleWidth / 2;
+int startX = round((double)width / 2.0) - scaleWidth / 2 + settings->dataOffsetX;
 
 int dashTop = (height - settings->fontHeight)/2;
 /* draw line on left/right side */
 vgBox(vg, startX, dashTop, 1, settings->fontHeight, MG_BLACK);