Corrected for hidden rows

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index d3f513b..714eec6 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -111,8 +111,12 @@ public class OverviewPanel extends JPanel implements Runnable
             {\r
                 public void mouseDragged(MouseEvent evt)\r
                 {\r
-                  if(!av.wrapAlignment)\r
-                    doMouseDragged(evt);\r
+                  if (!av.wrapAlignment)\r
+                  {\r
+                    boxX = evt.getX();\r
+                    boxY = evt.getY();\r
+                    checkValid();\r
+                  }\r
                 }\r
             });\r
 \r
@@ -121,91 +125,17 @@ public class OverviewPanel extends JPanel implements Runnable
                 public void mousePressed(MouseEvent evt)\r
                 {\r
                   if(!av.wrapAlignment)\r
-                    doMousePressed(evt);\r
-                }\r
-\r
-                public void mouseReleased(MouseEvent evt)\r
-                {\r
-                  if(!av.wrapAlignment)\r
-                    doMouseReleased(evt);\r
+                  {\r
+                    boxX = evt.getX();\r
+                    boxY = evt.getY();\r
+                    checkValid();\r
+                  }\r
                 }\r
             });\r
 \r
         updateOverviewImage();\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param evt DOCUMENT ME!\r
-     */\r
-    public void doMousePressed(MouseEvent evt)\r
-    {\r
-        boxX = evt.getX();\r
-        boxY = evt.getY();\r
-\r
-        checkValid();\r
-        repaint();\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param evt DOCUMENT ME!\r
-     */\r
-    public void doMouseReleased(MouseEvent evt)\r
-    {\r
-        boxX = evt.getX();\r
-        boxY = evt.getY();\r
-        checkValid();\r
-\r
-        if(av.hasHiddenColumns)\r
-        {\r
-          int col = (int) ( boxX / scalew / av.getCharWidth());\r
-\r
-          if(av.getColumnSelection().isVisible(col))\r
-          {\r
-            ap.setScrollValues(\r
-                av.getColumnSelection().findColumnPosition(col),\r
-                (int) (boxY / scaleh / av.getCharHeight()));\r
-          }\r
-          else\r
-            System.out.println(col +" not visible");\r
-        }\r
-        else\r
-          ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
-                            (int) (boxY / scaleh / av.getCharHeight()));\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param evt DOCUMENT ME!\r
-     */\r
-    public void doMouseDragged(MouseEvent evt)\r
-    {\r
-        boxX = evt.getX();\r
-        boxY = evt.getY();\r
-        checkValid();\r
-\r
-        if(av.hasHiddenColumns)\r
-        {\r
-          int col = (int) ( boxX / scalew / av.getCharWidth());\r
-\r
-          if(!av.getColumnSelection().isVisible(col))\r
-          {\r
-            return;\r
-          }\r
-\r
-            ap.setScrollValues(\r
-               av.getColumnSelection().findColumnPosition( col ),\r
-                (int) (boxY / scaleh / av.getCharHeight()));\r
-        }\r
-        else\r
-        ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
-                            (int) (boxY / scaleh / av.getCharHeight()));\r
-       repaint();\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -235,9 +165,29 @@ public class OverviewPanel extends JPanel implements Runnable
             boxWidth = (int) ( (av.endRes - av.startRes + 1) *\r
                                    av.getCharWidth() * scalew);\r
           }\r
-\r
           boxX = width - boxWidth;\r
         }\r
+\r
+        int col = (int) (boxX / scalew / av.getCharWidth());\r
+        int row = (int) (boxY / scaleh / av.getCharHeight());\r
+\r
+        if (av.hasHiddenColumns)\r
+        {\r
+          if (!av.getColumnSelection().isVisible(col))\r
+          {\r
+            return;\r
+          }\r
+\r
+          col = av.getColumnSelection().findColumnPosition(col);\r
+        }\r
+\r
+        if( av.hasHiddenRows )\r
+        {\r
+          row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);\r
+        }\r
+\r
+        ap.setScrollValues( col, row );\r
+\r
     }\r
 \r
     /**\r
@@ -436,20 +386,37 @@ public class OverviewPanel extends JPanel implements Runnable
         endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);\r
       }\r
 \r
+      int startSeq = av.startSeq;\r
+      int endSeq = av.endSeq;\r
+\r
+      if (av.hasHiddenRows)\r
+      {\r
+        startSeq =\r
+            av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);\r
+\r
+        endSeq =\r
+            av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);\r
+\r
+      }\r
+\r
 \r
       scalew = (float) width / (float) fullsizeWidth;\r
       scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
 \r
         boxX = (int) (startRes * av.getCharWidth() * scalew);\r
-        boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
+        boxY = (int) (startSeq * av.getCharHeight() * scaleh);\r
+\r
+\r
 \r
         if(av.hasHiddenColumns)\r
           boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);\r
         else\r
           boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);\r
 \r
-        boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -\r
-            boxY;\r
+\r
+        boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);\r
+\r
+\r
         repaint();\r
     }\r
 \r