X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=54785ef0e4bbc42237350d9ef5367ecbe4e1147b;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=6483e8b39d7a972f4c3f212a6d309514d7602417;hpb=f59f68c0a389bef51cfc9397dc0c4b645be51c05;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 6483e8b..54785ef 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -11,7 +11,8 @@ public class SequenceRenderer implements RendererI
   FontMetrics fm;
   boolean renderGaps = true;
   SequenceGroup currentSequenceGroup = null;
-  Color resBoxColour = Color.white;
+  SequenceGroup [] allGroups = null;
+  Color resBoxColour;
   Graphics graphics;
 
   public SequenceRenderer(AlignViewport av)
@@ -33,34 +34,33 @@ public class SequenceRenderer implements RendererI
 
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
-
    if (cs != null)
-       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));
+       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
    else
        resBoxColour = Color.white;
   }
 
-  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)
+  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)
   {
-    currentSequenceGroup = sg;
+    allGroups = sg;
 
     graphics = g;
 
-    drawBoxes(seq, start, end, x1, y1, (int) width, height, pid);
+    drawBoxes(seq, start, end, x1, y1, (int) width, height);
 
     fm = g.getFontMetrics();
     drawText(seq,start,end,x1,y1,(int)width,height);
 
   }
 
-  public void drawBoxes(SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {
+  public void drawBoxes(SequenceI seq,int start, int end, int x1, int y1, int width, int height) {
     int i      = start;
     int length = seq.getLength();
 
-    int curStart = x1;
+    int curStart = -1;
     int curWidth = width;
 
-    Color tempColour = Color.red;
+    Color tempColour = null;
     while (i <= end && i < length)
     {
       if(inCurrentSequenceGroup(i))
@@ -69,11 +69,15 @@ public class SequenceRenderer implements RendererI
              getBoxColour(currentSequenceGroup.cs, seq, i);
       }
       else if(av.getShowBoxes())
-           getBoxColour(av.getGlobalColourScheme(), seq, i);
+            getBoxColour(av.getGlobalColourScheme(), seq, i);
+      else
+        resBoxColour = Color.white;
+
 
       if (resBoxColour != tempColour)
       {
-        graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+        if(tempColour!=null)
+          graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
         graphics.setColor(resBoxColour);
 
         curStart = i;
@@ -86,7 +90,9 @@ public class SequenceRenderer implements RendererI
 
       i++;
     }
-    graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+
+
+     graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
   }
 
   public void drawText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
@@ -95,25 +101,30 @@ public class SequenceRenderer implements RendererI
     int charOffset=0;
     char s;
     // Need to find the sequence position here.
+
+    graphics.setColor(Color.black);
+    String sequence  = seq.getSequence();
     for (int i = start; i <= end; i++)
     {
-        if(i<seq.getLength())
-          s = seq.getSequence().charAt(i);
+        if(i<sequence.length())
+          s = sequence.charAt(i);
         else
           s = ' ';
 
         if(!renderGaps && jalview.util.Comparison.isGap(s))
           continue;
 
-        graphics.setColor(Color.black);
 
         if (inCurrentSequenceGroup(i))
         {
           if(!currentSequenceGroup.getDisplayText())
             continue;
 
-          if(currentSequenceGroup.getColourText())
-            graphics.setColor(resBoxColour.darker());
+            if (currentSequenceGroup.getColourText())
+            {
+              getBoxColour(currentSequenceGroup.cs, seq, i);
+              graphics.setColor(resBoxColour.darker());
+            }
         }
         else
         {
@@ -121,22 +132,37 @@ public class SequenceRenderer implements RendererI
             continue;
 
           if(av.getColourText())
-            graphics.setColor(resBoxColour.darker());
+           {
+             getBoxColour(av.getGlobalColourScheme(), seq, i);
+             if(av.getShowBoxes())
+              graphics.setColor(resBoxColour.darker());
+            else
+              graphics.setColor(resBoxColour);
+           }
         }
 
-      charOffset =  (width - fm.charWidth(s))/2;
-      graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
-    }
+          charOffset =  (width - fm.charWidth(s))/2;
+          graphics.drawString(String.valueOf(s),
+                              charOffset + x1 + width * (i - start),
+                              y1 + height - pady);
+        }
 
 
   }
 
   boolean inCurrentSequenceGroup(int res)
   {
-    if(currentSequenceGroup==null)
+    if(allGroups ==null)
       return false;
 
-    return (currentSequenceGroup.getStartRes()<=res && currentSequenceGroup.getEndRes()>=res)?true:false;
+    for(int i=0; i<allGroups.length; i++)
+      if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)
+      {
+         currentSequenceGroup = allGroups[i];
+         return true;
+      }
+
+    return false;
   }
 
   public void drawHighlightedText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
@@ -154,7 +180,7 @@ public class SequenceRenderer implements RendererI
        if(i<seq.getLength())
           s = seq.getSequence().charAt(i);
 
-      charOffset =  (width - fm.charWidth(s))/2;
+     charOffset =  (width - fm.charWidth(s))/2;
       graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
     }
   }