X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=72654893e7efe75edce5d3967a32daa468fff902;hb=bd033a98fbd26a1fac258df761b1f26b1d2fb178;hp=cbbfcff01821a9d80ba88030fda052f4ed339f7b;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index cbbfcff..7265489 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -43,7 +43,6 @@ public class OverviewPanel
   SequenceRenderer sr;
   FeatureRenderer fr;
 
-
   Frame nullFrame;
 
   public OverviewPanel(AlignmentPanel ap)
@@ -54,7 +53,6 @@ public class OverviewPanel
     nullFrame = new Frame();
     nullFrame.addNotify();
 
-
     sr = new SequenceRenderer(av);
     sr.graphics = nullFrame.getGraphics();
     sr.renderGaps = false;
@@ -62,22 +60,24 @@ public class OverviewPanel
     fr = new FeatureRenderer(av);
     fr.overview = true;
 
-
-
     // scale the initial size of overviewpanel to shape of alignment
     float initialScale = (float) av.alignment.getWidth() /
         (float) av.alignment.getHeight();
 
-    if(av.vconsensus==null)
-          graphHeight = 0;
+    if (av.hconsensus == null)
+    {
+      graphHeight = 0;
+    }
 
     if (av.alignment.getWidth() > av.alignment.getHeight())
     {
       // wider
       width = 400;
       sequencesHeight = (int) (400f / initialScale);
-      if(sequencesHeight<40)
-              sequencesHeight = 40;
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
     }
     else
     {
@@ -112,15 +112,18 @@ public class OverviewPanel
 
   }
 
-
   public void mouseEntered(MouseEvent evt)
   {}
+
   public void mouseExited(MouseEvent evt)
   {}
+
   public void mouseClicked(MouseEvent evt)
   {}
+
   public void mouseMoved(MouseEvent evt)
   {}
+
   public void mousePressed(MouseEvent evt)
   {
     boxX = evt.getX();
@@ -146,26 +149,26 @@ public class OverviewPanel
   {
     if (boxY < 0)
     {
-        boxY = 0;
+      boxY = 0;
     }
 
     if (boxY > (sequencesHeight - boxHeight))
     {
-        boxY = sequencesHeight - boxHeight + 1;
+      boxY = sequencesHeight - boxHeight + 1;
     }
 
     if (boxX < 0)
     {
-        boxX = 0;
+      boxX = 0;
     }
 
     if (boxX > (width - boxWidth))
     {
-      if(av.hasHiddenColumns)
+      if (av.hasHiddenColumns)
       {
         //Try smallest possible box
         boxWidth = (int) ( (av.endRes - av.startRes + 1) *
-                               av.getCharWidth() * scalew);
+                          av.getCharWidth() * scalew);
       }
       boxX = width - boxWidth;
     }
@@ -183,13 +186,13 @@ public class OverviewPanel
       col = av.getColumnSelection().findColumnPosition(col);
     }
 
-    if( av.hasHiddenRows )
+    if (av.hasHiddenRows)
     {
       row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
     }
 
-    ap.setScrollValues( col, row );
-    ap.repaint();
+    ap.setScrollValues(col, row);
+    ap.paintAlignment(false);
   }
 
   /**
@@ -199,15 +202,17 @@ public class OverviewPanel
   {
     if (resizing)
     {
-        resizeAgain = true;
-        return;
+      resizeAgain = true;
+      return;
     }
 
     if (av.showSequenceFeatures)
-   {
-     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
-     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
-   }
+    {
+      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().
+          featureGroups;
+      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().
+          featureColours;
+    }
 
     resizing = true;
 
@@ -225,7 +230,7 @@ public class OverviewPanel
 
   // This is set true if the user resizes whilst
   // the overview is being calculated
-    boolean resizeAgain = false;
+  boolean resizeAgain = false;
 
   public void run()
   {
@@ -235,7 +240,7 @@ public class OverviewPanel
 
     if (av.showSequenceFeatures)
     {
-      fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
     }
 
     if (getSize().width > 0 && getSize().height > 0)
@@ -259,17 +264,17 @@ public class OverviewPanel
     float sampleCol = (float) alwidth / (float) width;
     float sampleRow = (float) alheight / (float) sequencesHeight;
 
-    int lastcol=0, lastrow=0;
-    int xstart=0, ystart=0;
+    int lastcol = 0, lastrow = 0;
+    int xstart = 0, ystart = 0;
     Color color = Color.yellow;
     int row, col, sameRow = 0, sameCol = 0;
     jalview.datamodel.SequenceI seq;
     boolean hiddenRow = false;
     for (row = 0; row <= sequencesHeight; row++)
     {
-      if((int)(row*sampleRow)==lastrow)
+      if ( (int) (row * sampleRow) == lastrow)
       {
-        sameRow ++;
+        sameRow++;
         continue;
       }
 
@@ -280,9 +285,10 @@ public class OverviewPanel
         if (seq == null)
         {
           int index =
-             av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);
+              av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+              lastrow);
 
-         seq = av.alignment.getSequenceAt(index);
+          seq = av.alignment.getSequenceAt(index);
         }
         else
         {
@@ -290,47 +296,56 @@ public class OverviewPanel
         }
       }
       else
+      {
         seq = av.alignment.getSequenceAt(lastrow);
+      }
 
-        for (col = 0; col < width; col++)
+      for (col = 0; col < width; col++)
+      {
+        if ( (int) (col * sampleCol) == lastcol &&
+            (int) (row * sampleRow) == lastrow)
         {
-          if ( (int) (col * sampleCol) == lastcol && (int) (row * sampleRow) == lastrow)
-          {
-            sameCol ++;
-            continue;
-          }
+          sameCol++;
+          continue;
+        }
 
-          lastcol = (int) (col * sampleCol);
+        lastcol = (int) (col * sampleCol);
 
-          if (seq.getLength() > lastcol)
-          {
-            color = sr.getResidueBoxColour(
-                seq, lastcol);
+        if (seq.getLength() > lastcol)
+        {
+          color = sr.getResidueBoxColour(
+              seq, lastcol);
 
-            if (av.showSequenceFeatures)
-              color = fr.findFeatureColour(color, seq, lastcol);
-          }
-          else
+          if (av.showSequenceFeatures)
           {
-            color = Color.white; //White
+            color = fr.findFeatureColour(color, seq, lastcol);
           }
+        }
+        else
+        {
+          color = Color.white; //White
+        }
 
-          if (hiddenRow ||
-              (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
-          {
-            color = color.darker().darker();
-          }
+        if (hiddenRow ||
+            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+        {
+          color = color.darker().darker();
+        }
 
-          mg.setColor(color);
-          if (sameCol == 1 && sameRow == 1)
-            mg.drawLine(xstart, ystart, xstart, ystart);
-          else
-            mg.fillRect(xstart, ystart, sameCol, sameRow);
+        mg.setColor(color);
+        if (sameCol == 1 && sameRow == 1)
+        {
+          mg.drawLine(xstart, ystart, xstart, ystart);
+        }
+        else
+        {
+          mg.fillRect(xstart, ystart, sameCol, sameRow);
+        }
 
-          xstart = col;
-          sameCol = 1;
+        xstart = col;
+        sameCol = 1;
       }
-      lastrow = (int)(row*sampleRow);
+      lastrow = (int) (row * sampleRow);
       ystart = row;
       sameRow = 1;
     }
@@ -357,12 +372,12 @@ public class OverviewPanel
 
     setBoxPosition();
 
-    if(resizeAgain)
+    if (resizeAgain)
     {
       resizeAgain = false;
       updateOverviewImage();
     }
-}
+  }
 
   public void setBoxPosition()
   {
@@ -400,9 +415,13 @@ public class OverviewPanel
     boxY = (int) (startSeq * av.getCharHeight() * scaleh);
 
     if (av.hasHiddenColumns)
+    {
       boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
     else
+    {
       boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
 
     boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
 
@@ -423,16 +442,7 @@ public class OverviewPanel
       og.setColor(Color.red);
       og.drawRect(boxX, boxY, boxWidth, boxHeight);
       og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
-      g.drawImage(offscreen, 0,0, this);
-    }
-    else
-    {
-      g.setColor(Color.white);
-      g.fillRect(0, 0, getSize().width, getSize().height);
-      g.setColor(Color.black);
-      g.setFont(new Font("Verdana", Font.BOLD, 15));
-      g.drawString("Recalculating", 5, sequencesHeight / 2);
-      g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
+      g.drawImage(offscreen, 0, 0, this);
     }
   }