From 1c5dc1d944711fe6b6fdf5ddee60806ac364f638 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 7 Jul 2006 13:07:04 +0000
Subject: [PATCH 1/1] Corrected for hidden rows

---
 src/jalview/gui/OverviewPanel.java |  137 ++++++++++++++----------------------
 1 file changed, 52 insertions(+), 85 deletions(-)

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index d3f513b..714eec6 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -111,8 +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();
+                  }
                 }
             });
 
@@ -121,91 +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!
@@ -235,9 +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 );
+
     }
 
     /**
@@ -436,20 +386,37 @@ 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();
     }
 
-- 
1.7.10.2