src/hg/hgTracks/netTrack.c 1.24

Index: src/hg/hgTracks/netTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/netTrack.c,v
retrieving revision 1.23
retrieving revision 1.24
diff -b -B -U 4 -r1.23 -r1.24
--- src/hg/hgTracks/netTrack.c	20 Feb 2008 00:42:27 -0000	1.23
+++ src/hg/hgTracks/netTrack.c	17 Mar 2009 04:35:42 -0000	1.24
@@ -8,12 +8,19 @@
 #include "jksql.h"
 #include "hdb.h"
 #include "hgTracks.h"
 #include "chainNet.h"
+#include "chainCart.h"
 #include "chainNetDbLoad.h"
 
 static char const rcsid[] = "$Id$";
 
+struct cartOptions
+    {
+    enum netColorEnum netColor; /*  ChromColors, GrayScale */
+    int levelFilter ; /* filter chains by level 1 thru 6 */
+    };
+
 struct netItem
 /* A net track item. */
     {
     struct netItem *next;
@@ -76,11 +83,27 @@
 {
 netColorLastChrom = "UNKNOWN";
 }
 
-static Color netColor(char *chrom)
+static Color netColor(struct track *tg, char *chrom, int level)
 /* return appropriate color for a chromosome/scaffold */
 {
+struct cartOptions *netCart;
+
+netCart = (struct cartOptions *) tg->extraUiData;
+
+if (netCart->netColor == netColorGrayScale)
+    switch(level)
+	{
+	case 1: return(shadesOfGray[9]); break;
+	case 2: return(shadesOfGray[7]); break;
+	case 3: return(shadesOfGray[6]); break;
+	case 4: return(shadesOfGray[5]); break;
+	case 5: return(shadesOfGray[4]); break;
+	case 6: return(shadesOfGray[3]); break;
+	default: return(shadesOfGray[2]); break;
+	}
+
 static Color color;
 if (!sameString(chrom, netColorLastChrom))
     color = getSeqColor(chrom, rHvg);
 if (0 == color)
@@ -165,9 +188,9 @@
     }
 }
 
 
-static void rNetDraw(struct hvGfx *hvg, struct cnFill *fillList, int level, int y)
+static void rNetDraw(struct track *tg, struct hvGfx *hvg, struct cnFill *fillList, int level, int y)
 /* Recursively draw net. */
 {
 struct cnFill *fill;
 struct cnFill *gap;
@@ -175,9 +198,9 @@
 int orientation;
 
 for (fill = fillList; fill != NULL; fill = fill->next)
     {
-    color = netColor(fill->qName);
+    color = netColor(tg, fill->qName, level);
     invColor = hvGfxContrastingColor(rHvg, color);
     orientation = orientFromChar(fill->qStrand);
     if (fill->children == NULL || fill->tSize * rScale < 2.5)
     /* Draw single solid box if no gaps or no room to draw gaps. */
@@ -204,9 +227,9 @@
     for (gap = fill->children; gap != NULL; gap = gap->next)
         {
 	if (gap->children)
 	    {
-	    rNetDraw(hvg, gap->children, level+2, y + rNextLine);
+	    rNetDraw(tg, hvg, gap->children, level+2, y + rNextLine);
 	    }
 	}
     }
 }
@@ -241,9 +264,9 @@
 	rNextLine = 0;
     rScale = scaleForPixels(width);
 
     /* Recursively do main bit of work. */
-    rNetDraw(hvg, net->fillList, 1, yOff);
+    rNetDraw(tg, hvg, net->fillList, 1, yOff);
     chainNetFree(&net);
     }
 if (vis == tvDense)
     mapBoxToggleVis(hvg, xOff, yOff, width, tg->heightPer, tg);
@@ -251,8 +274,19 @@
 
 void netMethods(struct track *tg)
 /* Make track group for chain/net alignment. */
 {
+struct cartOptions *netCart;
+
+AllocVar(netCart);
+
+netCart->netColor = netColorStringToEnum(
+	trackDbSettingClosestToHomeOrDefault(tg->tdb, NET_COLOR, CHROM_COLORS));
+/* allow cart to override trackDb */
+netCart->netColor = netColorStringToEnum(
+	cartUsualStringClosestToHome(cart, tg->tdb, FALSE, NET_COLOR,
+	netColorEnumToString(netCart->netColor)));
+
 tg->loadItems = netLoad;
 tg->freeItems = netFree;
 tg->drawItems = netDraw;
 tg->itemName = netName;
@@ -261,6 +295,6 @@
 tg->itemHeight = tgFixedItemHeight;
 tg->itemStart = tgItemNoStart;
 tg->itemEnd = tgItemNoEnd;
 tg->mapsSelf = TRUE;
+tg->extraUiData = (void *) netCart;
 }
-