From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 30 Jan 2006 14:45:10 +0000 (+0000)
Subject: Allow features in overview window
X-Git-Tag: Root_VamJalview_2_07b+~213
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=inline;h=bc156d3f5e5184da7d103658603bb3b1a831aee1;p=jalview.git

Allow features in overview window
---

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 4a97e43..048df28 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -24,7 +24,6 @@ import java.awt.*;
 
 import java.util.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -36,7 +35,6 @@ public class FeatureRenderer
     AlignViewport av;
     SequenceGroup currentSequenceGroup = null;
     SequenceGroup[] allGroups = null;
-    Color resBoxColour;
     Graphics graphics;
     float transparency = .4f;
 
@@ -44,6 +42,8 @@ public class FeatureRenderer
     // to be added, in the correct order or rendering
     Vector featuresDisplayed;
 
+    Color currentColour = null;
+
     /**
      * Creates a new FeatureRenderer object.
      *
@@ -59,7 +59,7 @@ public class FeatureRenderer
 
     }
 
-boolean highlightTransparent = true;
+    boolean highlightTransparent = true;
     /**
      * DOCUMENT ME!
      *
@@ -73,7 +73,7 @@ boolean highlightTransparent = true;
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
+    public void drawSequence(Graphics g, SequenceI seq,
         int start, int end, int x1, int y1, int width, int height)
     {
 
@@ -141,7 +141,8 @@ boolean highlightTransparent = true;
 
                 if (fstart == fend)
                 {
-                    g.setColor(getColour(type));
+                    currentColour = getColour(type);
+                    g.setColor(currentColour);
                     g.fillRoundRect((fstart - start) * width, y1, width,
                         height, 4, 4);
                     g.setColor(Color.white);
@@ -164,8 +165,9 @@ boolean highlightTransparent = true;
                         {
                             continue;
                         }
+                        currentColour = getColour(type);
+                        g.setColor(currentColour);
 
-                        g.setColor(getColour(type));
                         g.fillRect((i - start) * width, y1, width, height);
 
                         g.setColor(Color.white);
@@ -187,6 +189,25 @@ boolean highlightTransparent = true;
           }
     }
 
+
+    Image offscreen;
+    Frame nullframe;
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    {
+      currentColour = initialCol;
+      if(offscreen == null)
+      {
+        nullframe = new Frame();
+        nullframe.addNotify();
+        offscreen = nullframe.createImage(1, 1);
+      }
+
+      drawSequence(offscreen.getGraphics(), seq, i, i, 0, 0, 1, 1);
+      return currentColour;
+    }
+
+
+
     public Color getColour(String featureType)
     {
       return (Color)featureColours.get(featureType);
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index c5789fe..9c3e908 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -40,7 +40,7 @@ public class OverviewPanel
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
   SequenceRenderer sr;
-  //FeatureRenderer fr;
+  FeatureRenderer fr;
 
 
   Frame nullFrame;
@@ -57,10 +57,9 @@ public class OverviewPanel
     sr = new SequenceRenderer(av);
     sr.graphics = nullFrame.getGraphics();
     sr.renderGaps( false );
-    //fr = new FeatureRenderer(av);
-    //fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
-    //fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
-
+    fr = new FeatureRenderer(av);
+    fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
+    fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
 
 
     // scale the initial size of overviewpanel to shape of alignment
@@ -245,7 +244,16 @@ public class OverviewPanel
         lastrow = (int)(row*sampleRow);
         lastcol = (int)(col*sampleCol);
 
-        color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);
+        if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)
+        {
+          color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);
+
+          if (av.showSequenceFeatures)
+            color = fr.findFeatureColour(color,
+                                         av.alignment.getSequenceAt(lastrow),
+                                         lastcol);
+        }
+
 
         mg.setColor(color);
         mg.fillRect(col,row,1,1);