Send array of groups to renderer

diff --git a/src/jalview/gui/RendererI.java b/src/jalview/gui/RendererI.java
index 33c4d76..cc72142 100755 (executable)
--- a/src/jalview/gui/RendererI.java
+++ b/src/jalview/gui/RendererI.java
@@ -10,6 +10,6 @@ public interface RendererI {
 \r
 //    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i);\r
 \r
-    public void drawSequence(Graphics g,SequenceI seq,SequenceGroup sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum);\r
+    public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum);\r
 \r
 }\r

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 6483e8b..69db54d 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -11,7 +11,8 @@ public class SequenceRenderer implements RendererI
   FontMetrics fm;\r
   boolean renderGaps = true;\r
   SequenceGroup currentSequenceGroup = null;\r
-  Color resBoxColour = Color.white;\r
+  SequenceGroup [] allGroups = null;\r
+  Color resBoxColour;\r
   Graphics graphics;\r
 \r
   public SequenceRenderer(AlignViewport av)\r
@@ -33,16 +34,15 @@ public class SequenceRenderer implements RendererI
 \r
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
   {\r
-\r
    if (cs != null)\r
        resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));\r
    else\r
        resBoxColour = Color.white;\r
   }\r
 \r
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)\r
+  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)\r
   {\r
-    currentSequenceGroup = sg;\r
+    allGroups = sg;\r
 \r
     graphics = g;\r
 \r
@@ -60,7 +60,7 @@ public class SequenceRenderer implements RendererI
     int curStart = x1;\r
     int curWidth = width;\r
 \r
-    Color tempColour = Color.red;\r
+    Color tempColour = null;\r
     while (i <= end && i < length)\r
     {\r
       if(inCurrentSequenceGroup(i))\r
@@ -69,7 +69,10 @@ public class SequenceRenderer implements RendererI
              getBoxColour(currentSequenceGroup.cs, seq, i);\r
       }\r
       else if(av.getShowBoxes())\r
-           getBoxColour(av.getGlobalColourScheme(), seq, i);\r
+            getBoxColour(av.getGlobalColourScheme(), seq, i);\r
+      else\r
+        resBoxColour = Color.white;\r
+\r
 \r
       if (resBoxColour != tempColour)\r
       {\r
@@ -112,8 +115,11 @@ public class SequenceRenderer implements RendererI
           if(!currentSequenceGroup.getDisplayText())\r
             continue;\r
 \r
-          if(currentSequenceGroup.getColourText())\r
-            graphics.setColor(resBoxColour.darker());\r
+            if (currentSequenceGroup.getColourText())\r
+            {\r
+              getBoxColour(currentSequenceGroup.cs, seq, i);\r
+              graphics.setColor(resBoxColour.darker());\r
+            }\r
         }\r
         else\r
         {\r
@@ -121,7 +127,10 @@ public class SequenceRenderer implements RendererI
             continue;\r
 \r
           if(av.getColourText())\r
-            graphics.setColor(resBoxColour.darker());\r
+           {\r
+             getBoxColour(av.getGlobalColourScheme(), seq, i);\r
+             graphics.setColor(resBoxColour.darker());\r
+           }\r
         }\r
 \r
       charOffset =  (width - fm.charWidth(s))/2;\r
@@ -133,10 +142,17 @@ public class SequenceRenderer implements RendererI
 \r
   boolean inCurrentSequenceGroup(int res)\r
   {\r
-    if(currentSequenceGroup==null)\r
+    if(allGroups ==null)\r
       return false;\r
 \r
-    return (currentSequenceGroup.getStartRes()<=res && currentSequenceGroup.getEndRes()>=res)?true:false;\r
+    for(int i=0; i<allGroups.length; i++)\r
+      if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)\r
+      {\r
+         currentSequenceGroup = allGroups[i];\r
+         return true;\r
+      }\r
+\r
+    return false;\r
   }\r
 \r
   public void drawHighlightedText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)\r