X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=fd3c334ccb62b91e5a2e6004e275b3f6d05a5f58;hb=ec012cb44879af718f1f9d88d669ebdc763712f2;hp=a4127bd86fee6b1fc41b67e2f4831f7c9d36a321;hpb=cb5acd3e551c2f9e67f8db366a93828f110c15fa;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index a4127bd..fd3c334 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -64,11 +64,9 @@ public class OverviewPanel extends JPanel implements Runnable
         setLayout(null);
 
         sr = new SequenceRenderer(av);
-        sr.renderGaps( false );
+        sr.renderGaps = false;
         sr.forOverview = true;
         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();
@@ -113,8 +111,12 @@ public class OverviewPanel extends JPanel implements Runnable
             {
                 public void mouseDragged(MouseEvent evt)
                 {
-                  if(!av.wrapAlignment)
-                    doMouseDragged(evt);
+                  if (!av.wrapAlignment)
+                  {
+                    boxX = evt.getX();
+                    boxY = evt.getY();
+                    checkValid();
+                  }
                 }
             });
 
@@ -123,91 +125,17 @@ public class OverviewPanel extends JPanel implements Runnable
                 public void mousePressed(MouseEvent evt)
                 {
                   if(!av.wrapAlignment)
-                    doMousePressed(evt);
-                }
-
-                public void mouseReleased(MouseEvent evt)
-                {
-                  if(!av.wrapAlignment)
-                    doMouseReleased(evt);
+                  {
+                    boxX = evt.getX();
+                    boxY = evt.getY();
+                    checkValid();
+                  }
                 }
             });
 
         updateOverviewImage();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMousePressed(MouseEvent evt)
-    {
-        boxX = evt.getX();
-        boxY = evt.getY();
-
-        checkValid();
-        repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseReleased(MouseEvent evt)
-    {
-        boxX = evt.getX();
-        boxY = evt.getY();
-        checkValid();
-
-        if(av.hasHiddenColumns)
-        {
-          int col = (int) ( boxX / scalew / av.getCharWidth());
-
-          if(av.getColumnSelection().isVisible(col))
-          {
-            ap.setScrollValues(
-                av.getColumnSelection().findColumnPosition(col),
-                (int) (boxY / scaleh / av.getCharHeight()));
-          }
-          else
-            System.out.println(col +" not visible");
-        }
-        else
-          ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                            (int) (boxY / scaleh / av.getCharHeight()));
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseDragged(MouseEvent evt)
-    {
-        boxX = evt.getX();
-        boxY = evt.getY();
-        checkValid();
-
-        if(av.hasHiddenColumns)
-        {
-          int col = (int) ( boxX / scalew / av.getCharWidth());
-
-          if(!av.getColumnSelection().isVisible(col))
-          {
-            return;
-          }
-
-            ap.setScrollValues(
-               av.getColumnSelection().findColumnPosition( col ),
-                (int) (boxY / scaleh / av.getCharHeight()));
-        }
-        else
-        ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                            (int) (boxY / scaleh / av.getCharHeight()));
-       repaint();
-    }
 
     /**
      * DOCUMENT ME!
@@ -237,9 +165,29 @@ public class OverviewPanel extends JPanel implements Runnable
             boxWidth = (int) ( (av.endRes - av.startRes + 1) *
                                    av.getCharWidth() * scalew);
           }
-
           boxX = width - boxWidth;
         }
+
+        int col = (int) (boxX / scalew / av.getCharWidth());
+        int row = (int) (boxY / scaleh / av.getCharHeight());
+
+        if (av.hasHiddenColumns)
+        {
+          if (!av.getColumnSelection().isVisible(col))
+          {
+            return;
+          }
+
+          col = av.getColumnSelection().findColumnPosition(col);
+        }
+
+        if( av.hasHiddenRows )
+        {
+          row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
+        }
+
+        ap.setScrollValues( col, row );
+
     }
 
     /**
@@ -262,7 +210,6 @@ public class OverviewPanel extends JPanel implements Runnable
         }
 
         setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-       // setBoxPosition();
 
         Thread thread = new Thread(this);
         thread.start();
@@ -282,10 +229,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
        if (av.showSequenceFeatures)
        {
-         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;
+         fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
        }
 
         int alwidth = av.alignment.getWidth();
@@ -337,11 +281,9 @@ public class OverviewPanel extends JPanel implements Runnable
             seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
             if (seq == null)
             {
-
               int index =
                  av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);
 
-
              seq = av.alignment.getSequenceAt(index);
             }
             else
@@ -375,7 +317,7 @@ public class OverviewPanel extends JPanel implements Runnable
                   seq, lastcol).getRGB();
 
               if (av.showSequenceFeatures)
-                color = fr.findFeatureColour(color, lastrow, lastcol);
+                color = fr.findFeatureColour(color, seq, lastcol);
             }
             else
             {
@@ -442,20 +384,37 @@ public class OverviewPanel extends JPanel implements Runnable
         endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
       }
 
+      int startSeq = av.startSeq;
+      int endSeq = av.endSeq;
+
+      if (av.hasHiddenRows)
+      {
+        startSeq =
+            av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
+
+        endSeq =
+            av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
+
+      }
+
 
       scalew = (float) width / (float) fullsizeWidth;
       scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
         boxX = (int) (startRes * av.getCharWidth() * scalew);
-        boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);
+        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) (av.getEndSeq() * av.getCharHeight() * scaleh) -
-            boxY;
+
+        boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+
+
         repaint();
     }