From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:28:41 +0000 (+0000)
Subject: Faster
X-Git-Tag: Root_VamJalview_2_07b+~43
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cb5acd3e551c2f9e67f8db366a93828f110c15fa;p=jalview.git

Faster
---

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