From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 24 Feb 2006 11:41:26 +0000 (+0000)
Subject: Features now array for speed of rendering
X-Git-Tag: Root_VamJalview_2_07b+~100
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=391968dd70ca76090306df9b5852bbef10ab4ede;p=jalview.git

Features now array for speed of rendering
---

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 22789a1..405fe98 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -24,8 +24,6 @@ import java.awt.*;
 
 import java.util.*;
 
-import java.awt.image.*;
-
 
 /**
  * DOCUMENT ME!
@@ -40,17 +38,19 @@ public class FeatureRenderer
     float transparency = 1.0f;
     FontMetrics fm;
     int charOffset;
-    boolean drawText = true;
-
-    // The following vector holds the features which are
-    // to be added, in the correct order or rendering
-    Vector featuresDisplayed = null;
 
     // A higher level for grouping features of a
    // particular type
     Hashtable featureGroups = null;
 
 
+    // This is actually an Integer held in the hashtable,
+    // Retrieved using the key feature type
+    Object currentColour;
+
+    String [] renderOrder;
+
+
     /**
      * Creates a new FeatureRenderer object.
      *
@@ -62,27 +62,67 @@ public class FeatureRenderer
         initColours();
     }
 
+
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    {
+      if(!av.showSequenceFeatures)
+        return initialCol;
+
+        lastSequence = seq;
+        sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();
+        if(sequenceFeatures==null)
+          return initialCol;
+
+        sfSize = sequenceFeatures.length;
+
+      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
+        return Color.white;
+
+      currentColour = null;
+
+      drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);
+
+      if(currentColour==null)
+        return initialCol;
+
+      return new Color( ((Integer)currentColour).intValue() );
+    }
     /**
      * This is used by the Molecule Viewer to get the accurate colour
      * of the rendered sequence
      */
-    BufferedImage bi;
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+
+    boolean overview = false;
+
+    int white = Color.white.getRGB();
+    public int findFeatureColour(int initialCol, int seqIndex, int column)
     {
       if(!av.showSequenceFeatures)
         return initialCol;
 
-      if (bi == null)
-        bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
+      if(seqIndex!=lastSequenceIndex)
+      {
+        lastSequence = av.alignment.getSequenceAt(seqIndex);
+        lastSequenceIndex = seqIndex;
+        sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();
+        if(sequenceFeatures==null)
+          return initialCol;
 
-      bi.setRGB(0,0, initialCol.getRGB());
+        sfSize = sequenceFeatures.length;
+      }
 
-      drawText = false;
 
-      drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);
-      drawText = true;
+      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+        return Color.white.getRGB();
+
+      currentColour = null;
+
+      drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);
+
+      if(currentColour==null)
+        return initialCol;
 
-      return new Color(bi.getRGB(0, 0));
+      return  ((Integer)currentColour).intValue();
     }
 
 
@@ -99,18 +139,41 @@ public class FeatureRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
+   // String type;
+   // SequenceFeature sf;
+    int lastSequenceIndex=-1;
+    SequenceI lastSequence;
+    SequenceFeature [] sequenceFeatures;
+    int sfSize, sfindex, spos, epos;
+
     public void drawSequence(Graphics g, SequenceI seq,
-                             int start, int end, int x1, int y1, int width, int height)
+                             int start, int end, int y1, int width, int height)
     {
-
-        //System.out.println(start+" "+end+" "+x1+" "+y1);
-      if (seq.getDatasetSequence().getSequenceFeatures() == null
-          || seq.getDatasetSequence().getSequenceFeatures().size()==0)
+      if (   seq.getDatasetSequence().getSequenceFeatures() == null
+          || seq.getDatasetSequence().getSequenceFeatures().length==0)
         return;
 
-      fm = g.getFontMetrics();
 
-      if (transparency != 1)
+      if(g!=null)
+        fm = g.getFontMetrics();
+
+
+      if (av.featuresDisplayed == null || renderOrder==null)
+       {
+         findAllFeatures();
+         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+         sfSize = sequenceFeatures.length;
+       }
+
+       if(lastSequence==null || seq!=lastSequence)
+      {
+        lastSequence = seq;
+        sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+        sfSize = sequenceFeatures.length;
+      }
+
+
+      if (transparency != 1 && g!=null)
       {
         Graphics2D g2 = (Graphics2D) g;
         g2.setComposite(
@@ -118,61 +181,80 @@ public class FeatureRenderer
                 AlphaComposite.SRC_OVER, transparency));
       }
 
-      String type;
-      SequenceFeature sf;
-      if (featuresDisplayed == null)
-        findAllFeatures();
-
-      Enumeration e = featuresDisplayed.elements(), e2;
-
-      // Loop through each visible feature
-      while (e.hasMoreElements())
+      if(!overview)
       {
+        spos = lastSequence.findPosition(start);
+        epos = lastSequence.findPosition(end);
+      }
+
+      String type;
+      for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
+       {
+        type =  renderOrder[renderIndex];
 
-        type = e.nextElement().toString();
-        e2 = seq.getDatasetSequence().getSequenceFeatures().elements();
         // loop through all features in sequence to find
         // current feature to render
-          while (e2.hasMoreElements())
+        for (sfindex = 0; sfindex < sfSize; sfindex++)
         {
-
-          sf = (SequenceFeature) e2.nextElement();
-          if (!type.equals(sf.getType()))
+          if (!sequenceFeatures[sfindex].type.equals(type))
             continue;
 
-          if(featureGroups!=null
-             && sf.getFeatureGroup()!=null
-             && featureGroups.containsKey(sf.getFeatureGroup())
-             && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue())
+          if (featureGroups != null
+              && sequenceFeatures[sfindex].featureGroup != null
+              &&
+              featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+              &&
+              ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
+              booleanValue())
           {
             continue;
           }
 
-          if (sf.getBegin() > seq.getEnd())
+          if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
+                            || sequenceFeatures[sfindex].getEnd() < spos))
             continue;
 
-          if (type.equals("disulfide bond"))
+          if (overview)
+          {
+
+            if (sequenceFeatures[sfindex].begin - 1 <= start &&
+                sequenceFeatures[sfindex].end + 1 >= start)
+            {
+              currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                  type);
+            }
+
+          }
+          else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
           {
 
             renderFeature(g, seq,
-                          seq.findIndex(sf.getBegin()) - 1,
-                          seq.findIndex(sf.getBegin()) - 1,
-                          type, start, end, x1, y1, width, height);
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          new Color( ( (Integer) av.featuresDisplayed.get(
+                sequenceFeatures[sfindex].type)).intValue()),
+                          start, end, y1, width, height);
             renderFeature(g, seq,
-                          seq.findIndex(sf.getEnd()) - 1,
-                          seq.findIndex(sf.getEnd()) - 1,
-                          type, start, end, x1, y1, width, height);
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          new Color( ( (Integer) av.featuresDisplayed.get(
+                sequenceFeatures[sfindex].type)).intValue()),
+                          start, end, y1, width, height);
 
           }
           else
             renderFeature(g, seq,
-                          seq.findIndex(sf.getBegin()) - 1,
-                          seq.findIndex(sf.getEnd()) - 1,
-                          type, start, end, x1, y1, width, height);
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          getColour(sequenceFeatures[sfindex].type),
+                          start, end, y1, width, height);
+
+
         }
+
       }
 
-        if(transparency!=1.0f)
+        if(transparency!=1.0f && g!=null)
         {
           Graphics2D g2 = (Graphics2D) g;
           g2.setComposite(
@@ -182,69 +264,78 @@ public class FeatureRenderer
     }
 
 
+    char s;
+    int i;
     void renderFeature(Graphics g, SequenceI seq,
-                       int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)
+                       int fstart, int fend, Color featureColour, int start, int end,  int y1, int width, int height)
     {
 
       if (((fstart <= end) && (fend >= start)))
       {
-          if (fstart < start)
-          { // fix for if the feature we have starts before the sequence start,
-              fstart = start; // but the feature end is still valid!!
-          }
+        if (fstart < start)
+        { // fix for if the feature we have starts before the sequence start,
+          fstart = start; // but the feature end is still valid!!
+        }
 
-          if (fend >= end)
-          {
-            fend = end;
-          }
-          for (int i = fstart; i <= fend; i++)
+        if (fend >= end)
+        {
+          fend = end;
+        }
+
+          for (i = fstart; i <= fend; i++)
           {
-            char s = seq.getSequence().charAt(i);
+            s = seq.getSequence().charAt(i);
 
             if (jalview.util.Comparison.isGap(s))
             {
               continue;
             }
 
-            g.setColor(getColour(type));
+            g.setColor(featureColour);
 
             g.fillRect( (i - start) * width, y1, width, height);
 
-            if(drawText)
-           {
-             g.setColor(Color.white);
-             charOffset = (width - fm.charWidth(s)) / 2;
-             g.drawString(String.valueOf(s),
-                          charOffset + x1 + (width * (i - start)),
-                          (y1 + height) - height / 5); //pady = height / 5;
-           }
+            g.setColor(Color.white);
+            charOffset = (width - fm.charWidth(s)) / 2;
+            g.drawString(String.valueOf(s),
+                         charOffset + (width * (i - start)),
+                         (y1 + height) - height / 5); //pady = height / 5;
+
           }
-        }
+      }
     }
 
     void findAllFeatures()
     {
-      Vector features = new Vector();
-      SequenceFeature sf;
-      featuresDisplayed = new Vector();
-      Enumeration e;
+      av.featuresDisplayed = new Hashtable();
       for (int i = 0; i < av.alignment.getHeight(); i++)
       {
-        features = av.alignment.getSequenceAt(i).getDatasetSequence().
+        SequenceFeature [] features = av.alignment.getSequenceAt(i).getDatasetSequence().
             getSequenceFeatures();
+
         if (features == null)
           continue;
 
-        e = features.elements();
-        while (e.hasMoreElements())
+        int index = 0;
+        while (index < features.length)
         {
-          sf = (SequenceFeature) e.nextElement();
-          if (!featuresDisplayed.contains(sf.getType()))
+          if (!av.featuresDisplayed.containsKey(features[index].getType()))
           {
-            featuresDisplayed.addElement(sf.getType());
+            av.featuresDisplayed.put(features[index].getType(),
+                                  new Integer( getColour(features[index].getType()).getRGB()) );
           }
+          index++;
         }
       }
+
+      renderOrder = new String[av.featuresDisplayed.size()];
+      Enumeration en = av.featuresDisplayed.keys();
+      int i = 0;
+      while(en.hasMoreElements())
+      {
+        renderOrder[i] = en.nextElement().toString();
+        i++;
+      }
     }
 
     public Color getColour(String featureType)
@@ -254,10 +345,13 @@ public class FeatureRenderer
 
     public void addNewFeature(String name, Color col)
     {
+
       setColour(name, col);
-      if(featuresDisplayed==null)
-        featuresDisplayed = new Vector();
-      featuresDisplayed.insertElementAt(name, 0);
+      if(av.featuresDisplayed==null)
+        av.featuresDisplayed = new Hashtable();
+
+
+      av.featuresDisplayed.put(name, "NOGROUP");
     }
 
     public void setColour(String featureType, Color col)
@@ -280,14 +374,22 @@ public class FeatureRenderer
       // The feature table will display high priority
       // features at the top, but theses are the ones
       // we need to render last, so invert the data
-      featuresDisplayed.clear();
+      av.featuresDisplayed.clear();
+
+      renderOrder = new String[data.length];
+
+      if(data.length>0)
       for(int i=data.length-1; i>-1; i--)
       {
        String type = data[i][0].toString();
        setColour(type, (Color)data[i][1]);
        if( ((Boolean)data[i][2]).booleanValue() )
-         featuresDisplayed.addElement(type);
+       {
+         av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+       }
+       renderOrder[i] = type;
       }
+
     }
 
     Hashtable featureColours = new Hashtable();
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index eb74454..3979ebe 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -35,6 +35,7 @@ public class FeatureSettings extends JPanel
   final FeatureRenderer fr;
   final AlignmentPanel ap;
   final AlignViewport av;
+  Hashtable allFeatures;
   Object [][] originalData;
   final JInternalFrame frame;
   JScrollPane scrollPane = new JScrollPane();
@@ -124,8 +125,12 @@ public class FeatureSettings extends JPanel
     bigPanel.add(transPanel, BorderLayout.SOUTH);
     bigPanel.add(scrollPane, BorderLayout.CENTER);
     if(groupPanel!=null)
+    {
+      groupPanel.setLayout(
+          new GridLayout(groupPanel.getComponentCount()/3, 4));
+      groupPanel.validate();
       bigPanel.add(groupPanel, BorderLayout.NORTH);
-
+    }
     add(bigPanel, BorderLayout.CENTER);
     add(buttonPanel, BorderLayout.SOUTH);
 
@@ -139,30 +144,28 @@ public class FeatureSettings extends JPanel
     else
       fr.featureGroups.clear();
 
-    Vector allFeatures = new Vector();
-    Vector features;
-    Enumeration e;
-    SequenceFeature sf;
+    allFeatures = new Hashtable();
+    SequenceFeature[] features;
 
   for (int i = 0; i < av.alignment.getHeight(); i++)
   {
     features = av.alignment.getSequenceAt(i).getDatasetSequence().
         getSequenceFeatures();
+
     if (features == null)
       continue;
 
-    e = features.elements();
-    while (e.hasMoreElements())
+    int index = 0;
+    while (index < features.length)
     {
-      sf = (SequenceFeature) e.nextElement();
-      if(sf.getFeatureGroup()!=null
-          && !fr.featureGroups.containsKey(sf.getFeatureGroup()))
+      if(features[index].getFeatureGroup()!=null
+          && !fr.featureGroups.containsKey(features[index].getFeatureGroup()))
        {
-         fr.featureGroups.put(sf.getFeatureGroup(), new Boolean(true));
+         fr.featureGroups.put(features[index].getFeatureGroup(), new Boolean(true));
          if(groupPanel==null)
             groupPanel = new JPanel();
 
-          final JCheckBox check = new JCheckBox(sf.getFeatureGroup(), true);
+          final JCheckBox check = new JCheckBox(features[index].getFeatureGroup(), true);
           check.setFont(new Font("Serif", Font.BOLD, 12));
           check.addItemListener(new ItemListener()
               {
@@ -176,15 +179,19 @@ public class FeatureSettings extends JPanel
                     if (ap.overviewPanel != null)
                       ap.overviewPanel.updateOverviewImage();
                   }
-
+                  resetTable();
                 }
               });
           groupPanel.add(check);
        }
-      if (!allFeatures.contains(sf.getType()))
+      if (!allFeatures.contains(features[index].getType()))
       {
-        allFeatures.addElement(sf.getType());
+        if(features[index].featureGroup!=null)
+          allFeatures.put(features[index].getType(), features[index].featureGroup);
+        else
+          allFeatures.put(features[index].getType(), "NOGROUP");
       }
+      index++;
     }
   }
     if(allFeatures.size()<1)
@@ -200,87 +207,111 @@ public class FeatureSettings extends JPanel
        return;
      }
 
+     resetTable();
+  }
+
+  void resetTable()
+  {
     int fSize = allFeatures.size();
 
     String type;
     boolean originalExists = false;
-    if(originalData!=null)
+    if (originalData != null)
       originalExists = true;
     else
       originalData = new Object[fSize][3];
 
-    Object [][] data = new Object[fSize][3];
-    for(int i=0; i<fSize; i++)
+    Object[][] tmp = new Object[fSize][3];
+    int tmpIndex = 0;
+
+    Enumeration en = allFeatures.keys();
+    int i=0;
+    while(en.hasMoreElements())
     {
-      type = allFeatures.elementAt(i).toString();
+      type = en.nextElement().toString();
       Color col = fr.getColour(type);
-      data[i][0]=type;
-      data[i][1]=col;
-      if(fr.featuresDisplayed!=null)
-         data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));
-      else
-        data[i][2] = new Boolean(true);
-
-      if(!originalExists)
+
+
+      //This will ignore any features which are in groups not shown
+     if(fr.featureGroups==null
+           ||   ((Boolean)fr.featureGroups.get(allFeatures.get(type))).booleanValue())
+      {
+        tmp[tmpIndex][0] = type;
+        tmp[tmpIndex][1] = col;
+        if (av.featuresDisplayed != null)
+          tmp[tmpIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));
+        else
+          tmp[tmpIndex][2] = new Boolean(true);
+
+        tmpIndex++;
+      }
+
+
+      if (!originalExists)
       {
         originalData[i][0] = type;
         originalData[i][1] = col;
-        if (fr.featuresDisplayed != null)
-          originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));
+        if (av.featuresDisplayed != null)
+          originalData[i][2] = new Boolean(av.featuresDisplayed.contains(type));
         else
           originalData[i][2] = new Boolean(true);
       }
+      i++;
     }
-    ////////////////////////////////////
-        //Now build the table
-        table = new JTable(new FeatureTableModel(data));
-        scrollPane.setViewportView(table);
-        table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
-        table.setFont(new Font("Verdana", Font.PLAIN, 12));
-        table.setDefaultRenderer(Color.class,
-                             new ColorRenderer());
 
-        table.setDefaultEditor(Color.class,
-                          new ColorEditor());
+    Object [][]data = new Object[tmpIndex][3];
+    System.arraycopy(tmp, 0, data,0, tmpIndex);
 
-        table.getColumnModel().getColumn(0).setPreferredWidth(200);
+    table = new JTable(new FeatureTableModel(data));
+    scrollPane.setViewportView(table);
+    table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
+    table.setFont(new Font("Verdana", Font.PLAIN, 12));
+    table.setDefaultRenderer(Color.class,
+                         new ColorRenderer());
 
-        table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+    table.setDefaultEditor(Color.class,
+                      new ColorEditor());
 
-        table.addMouseListener(new MouseAdapter()
-            {
-              public void mousePressed(MouseEvent evt)
-              {
-                selectedRow = table.rowAtPoint(evt.getPoint());
-              }
-            });
+    table.getColumnModel().getColumn(0).setPreferredWidth(200);
+
+    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 
-        table.addMouseMotionListener(new MouseMotionAdapter()
+    table.addMouseListener(new MouseAdapter()
+        {
+          public void mousePressed(MouseEvent evt)
+          {
+            selectedRow = table.rowAtPoint(evt.getPoint());
+          }
+        });
+
+    table.addMouseMotionListener(new MouseMotionAdapter()
+        {
+          public void mouseDragged(MouseEvent evt)
+          {
+            int newRow = table.rowAtPoint(evt.getPoint());
+            if(newRow!=selectedRow
+               && selectedRow!=-1
+               && newRow!=-1)
             {
-              public void mouseDragged(MouseEvent evt)
-              {
-                int newRow = table.rowAtPoint(evt.getPoint());
-                if(newRow!=selectedRow
-                   && selectedRow!=-1
-                   && newRow!=-1)
-                {
-                  Object[] temp = new Object[3];
-                  temp[0] = table.getValueAt(selectedRow, 0);
-                  temp[1] = table.getValueAt(selectedRow, 1);
-                  temp[2] = table.getValueAt(selectedRow, 2);
+              Object[] temp = new Object[3];
+              temp[0] = table.getValueAt(selectedRow, 0);
+              temp[1] = table.getValueAt(selectedRow, 1);
+              temp[2] = table.getValueAt(selectedRow, 2);
 
-                  table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
-                  table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
-                  table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
+              table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
+              table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
+              table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
 
-                  table.setValueAt(temp[0], newRow, 0);
-                  table.setValueAt(temp[1], newRow, 1);
-                  table.setValueAt(temp[2], newRow, 2);
+              table.setValueAt(temp[0], newRow, 0);
+              table.setValueAt(temp[1], newRow, 1);
+              table.setValueAt(temp[2], newRow, 2);
 
-                  selectedRow = newRow;
-                }
-              }
-        });
+              selectedRow = newRow;
+            }
+          }
+    });
+
+    updateFeatureRenderer(data);
 
   }
 
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index c690490..a1e8ea0 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -65,7 +65,9 @@ public class OverviewPanel extends JPanel implements Runnable
 
         sr = new SequenceRenderer(av);
         sr.renderGaps( false );
+        sr.forOverview = true;
         fr = new FeatureRenderer(av);
+        fr.overview = true;
 
 
         // scale the initial size of overviewpanel to shape of alignment
@@ -245,11 +247,10 @@ public class OverviewPanel extends JPanel implements Runnable
 
        if (av.showSequenceFeatures)
        {
-         fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().
-             featuresDisplayed;
          fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
          fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
          fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
+         fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
        }
 
         int alwidth = av.alignment.getWidth();
@@ -275,14 +276,15 @@ public class OverviewPanel extends JPanel implements Runnable
         float sampleRow = (float) alheight / (float) sequencesHeight;
 
         int lastcol=-1, lastrow=-1;
-        Color color = Color.white;
-        for (int col = 0; col < width; col++)
+        int color = Color.white.getRGB();
+        int row, col;
+        for (row = 0; row < sequencesHeight; row++)
         {
-          for (int row = 0; row < sequencesHeight; row++)
-          {
+            for (col = 0; col < width; col++)
+            {
             if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
             {
-              miniMe.setRGB(col,row,color.getRGB());
+              miniMe.setRGB(col,row,color);
               continue;
             }
 
@@ -292,17 +294,24 @@ public class OverviewPanel extends JPanel implements Runnable
             if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)
             {
              color = sr.getResidueBoxColour(
-                av.alignment.getSequenceAt(lastrow), lastcol);
+                av.alignment.getSequenceAt(lastrow), lastcol).getRGB();
 
              if(av.showSequenceFeatures)
-                 color = fr.findFeatureColour(color,  av.alignment.getSequenceAt(lastrow),
-                                             lastcol);
+                 color = fr.findFeatureColour(color,  lastrow, lastcol);
 
             }
 
-            miniMe.setRGB(col,row,color.getRGB());
+            miniMe.setRGB(col,row,color);
+
 
-            if (av.conservation != null)
+          }
+        }
+
+        if (av.conservation != null)
+        {
+          for (col = 0; col < width; col++)
+          {
+            lastcol = (int) (col * sampleCol);
             {
               mg.translate(col, sequencesHeight);
               ap.annotationPanel.drawGraph(mg, av.conservation,
@@ -310,11 +319,10 @@ public class OverviewPanel extends JPanel implements Runnable
                                            graphHeight,
                                            (int) (col * sampleCol),
                                            (int) (col * sampleCol) + 1);
-              mg.translate(-col, -sequencesHeight);
+              mg.translate( -col, -sequencesHeight);
             }
           }
         }
-
         System.gc();
 
         resizing = false;