Faster

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 7ffac1e..a4127bd 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -161,8 +161,22 @@ public class OverviewPanel extends JPanel implements Runnable
         boxY = evt.getY();\r
         checkValid();\r
 \r
-        ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),\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
@@ -176,8 +190,22 @@ public class OverviewPanel extends JPanel implements Runnable
         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
+                            (int) (boxY / scaleh / av.getCharHeight()));\r
        repaint();\r
     }\r
 \r
@@ -203,7 +231,14 @@ public class OverviewPanel extends JPanel implements Runnable
 \r
         if (boxX > (width - boxWidth))\r
         {\r
-            boxX = width - boxWidth;\r
+          if(av.hasHiddenColumns)\r
+          {\r
+            //Try smallest possible box\r
+            boxWidth = (int) ( (av.endRes - av.startRes + 1) *\r
+                                   av.getCharWidth() * scalew);\r
+          }\r
+\r
+          boxX = width - boxWidth;\r
         }\r
     }\r
 \r
@@ -227,7 +262,7 @@ public class OverviewPanel extends JPanel implements Runnable
         }\r
 \r
         setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
-        setBoxPosition();\r
+       // setBoxPosition();\r
 \r
         Thread thread = new Thread(this);\r
         thread.start();\r
@@ -254,7 +289,8 @@ public class OverviewPanel extends JPanel implements Runnable
        }\r
 \r
         int alwidth = av.alignment.getWidth();\r
-        int alheight = av.alignment.getHeight();\r
+        int alheight = av.alignment.getHeight()\r
+            +av.alignment.getHiddenSequences().getSize();\r
 \r
         setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
 \r
@@ -278,8 +314,50 @@ public class OverviewPanel extends JPanel implements Runnable
         int lastcol=-1, lastrow=-1;\r
         int color = Color.white.getRGB();\r
         int row, col;\r
+        jalview.datamodel.SequenceI seq;\r
+        boolean hiddenRow = false;\r
         for (row = 0; row < sequencesHeight; row++)\r
         {\r
+          if((int)(row*sampleRow)==lastrow)\r
+          {\r
+            //No need to recalculate the colours,\r
+            //Just copy from the row above\r
+            for (col = 0; col < width; col++)\r
+            {\r
+              miniMe.setRGB(col, row, miniMe.getRGB(col, row-1));\r
+            }\r
+            continue;\r
+          }\r
+\r
+          lastrow = (int)(row*sampleRow);\r
+\r
+          hiddenRow = false;\r
+          if (av.hasHiddenRows)\r
+          {\r
+            seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);\r
+            if (seq == null)\r
+            {\r
+\r
+              int index =\r
+                 av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);\r
+\r
+\r
+             seq = av.alignment.getSequenceAt(index);\r
+            }\r
+            else\r
+            {\r
+              hiddenRow = true;\r
+            }\r
+          }\r
+          else\r
+            seq = av.alignment.getSequenceAt(lastrow);\r
+\r
+          if(seq==null)\r
+          {\r
+            System.out.println(lastrow+" null");\r
+            continue;\r
+          }\r
+\r
             for (col = 0; col < width; col++)\r
             {\r
             if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
@@ -288,22 +366,28 @@ public class OverviewPanel extends JPanel implements Runnable
               continue;\r
             }\r
 \r
-            lastrow = (int)(row*sampleRow);\r
+\r
             lastcol = (int)(col*sampleCol);\r
 \r
-            if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
+            if (seq.getLength() > lastcol)\r
             {\r
-             color = sr.getResidueBoxColour(\r
-                av.alignment.getSequenceAt(lastrow), lastcol).getRGB();\r
+              color = sr.getResidueBoxColour(\r
+                  seq, lastcol).getRGB();\r
 \r
-             if(av.showSequenceFeatures)\r
-                 color = fr.findFeatureColour(color,  lastrow, lastcol);\r
+              if (av.showSequenceFeatures)\r
+                color = fr.findFeatureColour(color, lastrow, lastcol);\r
+            }\r
+            else\r
+            {\r
+              color = -1; //White\r
+            }\r
+\r
+            if(hiddenRow ||\r
+               (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))\r
+            {\r
+              color = new Color(color).darker().darker().getRGB();\r
+            }\r
 \r
-             }\r
-             else\r
-             {\r
-               color = -1; //White\r
-             }\r
 \r
             miniMe.setRGB(col,row,color);\r
 \r
@@ -346,14 +430,30 @@ public class OverviewPanel extends JPanel implements Runnable
     public void setBoxPosition()\r
     {\r
       int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();\r
-      int fullsizeHeight = av.alignment.getHeight() * av.getCharHeight();\r
+      int fullsizeHeight = (av.alignment.getHeight()\r
+                   +av.alignment.getHiddenSequences().getSize()) * av.getCharHeight();\r
+\r
+      int startRes = av.getStartRes();\r
+      int endRes = av.getEndRes();\r
+\r
+      if(av.hasHiddenColumns)\r
+      {\r
+        startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);\r
+        endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);\r
+      }\r
+\r
 \r
       scalew = (float) width / (float) fullsizeWidth;\r
       scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
 \r
-        boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
+        boxX = (int) (startRes * av.getCharWidth() * scalew);\r
         boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
-        boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1) * av.getCharWidth() * scalew);\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
         repaint();\r