From 1f705a7597d9558cbb6962826bfdc2f0ac2c6a50 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:16:21 +0000
Subject: [PATCH] Fastest implementation so far

---
 src/jalview/appletgui/OverviewPanel.java |   47 ++++++++++++++++++++++--------
 1 file changed, 35 insertions(+), 12 deletions(-)

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 48f075e..e8f9f9f 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -59,7 +59,6 @@ public class OverviewPanel
     sr.renderGaps( false );
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
-    fr.drawText = false;
     fr.overview = true;
 
 
@@ -192,7 +191,6 @@ public class OverviewPanel
      fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
    }
 
-
     resizing = true;
 
     if ( (getSize().width > 0) && (getSize().height > 0))
@@ -218,6 +216,14 @@ public class OverviewPanel
     int alwidth = av.alignment.getWidth();
     int alheight = av.alignment.getHeight();
 
+    if (av.showSequenceFeatures)
+    {
+      fr.renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
+      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+      fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
+    }
+
     if (getSize().width > 0 && getSize().height > 0)
     {
       width = getSize().width;
@@ -238,27 +244,34 @@ public class OverviewPanel
     float sampleCol = (float) alwidth / (float) width;
     float sampleRow = (float) alheight / (float) sequencesHeight;
 
-    int lastcol=-1, lastrow=0;
+    int lastcol=0, lastseq=0;
+    int xstart=0, ystart=0;
     Color color = Color.yellow;
-    int row, col;
+    int col, sameRow = 0, sameCol = 0;
     jalview.datamodel.SequenceI sequence;
-    for (row = 0; row < sequencesHeight; row++)
+
+    for (int row = 0; row <= sequencesHeight; row++)
     {
-      sequence = av.getAlignment().getSequenceAt(lastrow);
+      if((int)(row*sampleRow)==lastseq)
+      {
+        sameRow ++;
+        continue;
+      }
+
+      sequence = av.getAlignment().getSequenceAt(lastseq);
+
       for (col = 0; col < width; col++)
       {
-        if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
+        if((int)(col*sampleCol) == lastcol)
         {
-          mg.drawLine(col, row, col, row);
+          sameCol ++;
           continue;
         }
 
-        lastrow = (int)(row*sampleRow);
         lastcol = (int)(col*sampleCol);
 
-        if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)
+        if(sequence.getLength()>lastcol)
         {
-
           color = sr.findSequenceColour(sequence, lastcol);
 
           if (av.showSequenceFeatures)
@@ -270,9 +283,19 @@ public class OverviewPanel
           color = color.white;
 
         mg.setColor(color);
-        mg.drawLine(col,row,col,row);
+        if (sameCol == 1 && sameRow == 1)
+          mg.drawLine(xstart, ystart, xstart, ystart);
+        else
+          mg.fillRect(xstart, ystart, sameCol, sameRow);
 
+        xstart = col;
+        sameCol = 1;
       }
+
+
+      lastseq = (int)(row*sampleRow);
+      ystart = row;
+      sameRow = 1;
     }
 
     if (av.conservation != null)
-- 
1.7.10.2