X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=72654893e7efe75edce5d3967a32daa468fff902;hb=56ad3ae1c8b2fefd7af371049e344acfc1f23944;hp=23bfd095ca189f8fd8741086a29f45ae61005c82;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 23bfd09..7265489 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/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) 2007 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
@@ -23,9 +23,10 @@ import java.awt.*;
 import java.awt.event.*;
 
 public class OverviewPanel
-    extends Panel implements Runnable
+    extends Panel implements Runnable, MouseMotionListener, MouseListener
 {
   Image miniMe;
+  Image offscreen;
   AlignViewport av;
   AlignmentPanel ap;
   float scalew = 1f;
@@ -40,8 +41,7 @@ public class OverviewPanel
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
   SequenceRenderer sr;
-  //FeatureRenderer fr;
-
+  FeatureRenderer fr;
 
   Frame nullFrame;
 
@@ -53,30 +53,31 @@ public class OverviewPanel
     nullFrame = new Frame();
     nullFrame.addNotify();
 
-
     sr = new SequenceRenderer(av);
     sr.graphics = nullFrame.getGraphics();
-    sr.renderGaps( false );
-    //fr = new FeatureRenderer(av);
-    //fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
-    //fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
-
-
+    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();
 
-    if(av.vconsensus==null)
-          graphHeight = 0;
+    if (av.hconsensus == null)
+    {
+      graphHeight = 0;
+    }
 
     if (av.alignment.getWidth() > av.alignment.getHeight())
     {
       // wider
       width = 400;
       sequencesHeight = (int) (400f / initialScale);
-      if(sequencesHeight<40)
-              sequencesHeight = 40;
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
     }
     else
     {
@@ -103,59 +104,45 @@ public class OverviewPanel
       }
     });
 
-    addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseDragged(MouseEvent evt)
-      {
-        doMouseDragged(evt);
-      }
-    });
-
-    addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent evt)
-      {
-        doMousePressed(evt);
-      }
+    addMouseMotionListener(this);
 
-      public void mouseReleased(MouseEvent evt)
-      {
-        doMouseReleased(evt);
-      }
-    });
+    addMouseListener(this);
 
     updateOverviewImage();
 
   }
 
-  public void doMousePressed(MouseEvent evt)
+  public void mouseEntered(MouseEvent evt)
+  {}
+
+  public void mouseExited(MouseEvent evt)
+  {}
+
+  public void mouseClicked(MouseEvent evt)
+  {}
+
+  public void mouseMoved(MouseEvent evt)
+  {}
+
+  public void mousePressed(MouseEvent evt)
   {
     boxX = evt.getX();
     boxY = evt.getY();
-
     checkValid();
-    repaint();
   }
 
-  public void doMouseReleased(MouseEvent evt)
+  public void mouseReleased(MouseEvent evt)
   {
     boxX = evt.getX();
     boxY = evt.getY();
     checkValid();
-    ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                         (int) (boxY / scaleh / av.getCharHeight()));
   }
 
-  public void doMouseDragged(MouseEvent evt)
+  public void mouseDragged(MouseEvent evt)
   {
     boxX = evt.getX();
     boxY = evt.getY();
     checkValid();
-    ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                         (int) (boxY / scaleh / av.getCharHeight()));
-
-    repaint();
-    ap.repaint();
   }
 
   void checkValid()
@@ -165,7 +152,7 @@ public class OverviewPanel
       boxY = 0;
     }
 
-    if (boxY > sequencesHeight - boxHeight)
+    if (boxY > (sequencesHeight - boxHeight))
     {
       boxY = sequencesHeight - boxHeight + 1;
     }
@@ -175,10 +162,37 @@ public class OverviewPanel
       boxX = 0;
     }
 
-    if (boxX > width - boxWidth)
+    if (boxX > (width - boxWidth))
     {
+      if (av.hasHiddenColumns)
+      {
+        //Try smallest possible box
+        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);
+    ap.paintAlignment(false);
   }
 
   /**
@@ -188,8 +202,16 @@ public class OverviewPanel
   {
     if (resizing)
     {
-        resizeAgain = true;
-        return;
+      resizeAgain = true;
+      return;
+    }
+
+    if (av.showSequenceFeatures)
+    {
+      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().
+          featureGroups;
+      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().
+          featureColours;
     }
 
     resizing = true;
@@ -200,16 +222,15 @@ public class OverviewPanel
       sequencesHeight = getSize().height - graphHeight;
     }
     setSize(new Dimension(width, sequencesHeight + graphHeight));
-    setBoxPosition();
 
     Thread thread = new Thread(this);
     thread.start();
-        repaint();
+    repaint();
   }
 
   // This is set true if the user resizes whilst
   // the overview is being calculated
-    boolean resizeAgain = false;
+  boolean resizeAgain = false;
 
   public void run()
   {
@@ -217,6 +238,11 @@ public class OverviewPanel
     int alwidth = av.alignment.getWidth();
     int alheight = av.alignment.getHeight();
 
+    if (av.showSequenceFeatures)
+    {
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+    }
+
     if (getSize().width > 0 && getSize().height > 0)
     {
       width = getSize().width;
@@ -232,33 +258,103 @@ public class OverviewPanel
     scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
     miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
+    offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
 
     Graphics mg = miniMe.getGraphics();
     float sampleCol = (float) alwidth / (float) width;
     float sampleRow = (float) alheight / (float) sequencesHeight;
 
-    int lastcol=-1, lastrow=-1;
-    Color color = Color.white;
-    for (int col = 0; col < width; col++)
+    int lastcol = 0, lastrow = 0;
+    int xstart = 0, ystart = 0;
+    Color color = Color.yellow;
+    int row, col, sameRow = 0, sameCol = 0;
+    jalview.datamodel.SequenceI seq;
+    boolean hiddenRow = false;
+    for (row = 0; row <= sequencesHeight; row++)
     {
-      for (int row = 0; row < sequencesHeight; row++)
+      if ( (int) (row * sampleRow) == lastrow)
       {
-        if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
+        sameRow++;
+        continue;
+      }
+
+      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
         {
-          mg.setColor(color);
-          mg.fillRect(col,row,1,1);
+          hiddenRow = true;
+        }
+      }
+      else
+      {
+        seq = av.alignment.getSequenceAt(lastrow);
+      }
+
+      for (col = 0; col < width; col++)
+      {
+        if ( (int) (col * sampleCol) == lastcol &&
+            (int) (row * sampleRow) == lastrow)
+        {
+          sameCol++;
           continue;
         }
 
-        lastrow = (int)(row*sampleRow);
-        lastcol = (int)(col*sampleCol);
+        lastcol = (int) (col * sampleCol);
+
+        if (seq.getLength() > lastcol)
+        {
+          color = sr.getResidueBoxColour(
+              seq, lastcol);
+
+          if (av.showSequenceFeatures)
+          {
+            color = fr.findFeatureColour(color, seq, lastcol);
+          }
+        }
+        else
+        {
+          color = Color.white; //White
+        }
 
-        color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);
+        if (hiddenRow ||
+            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+        {
+          color = color.darker().darker();
+        }
 
         mg.setColor(color);
-        mg.fillRect(col,row,1,1);
+        if (sameCol == 1 && sameRow == 1)
+        {
+          mg.drawLine(xstart, ystart, xstart, ystart);
+        }
+        else
+        {
+          mg.fillRect(xstart, ystart, sameCol, sameRow);
+        }
+
+        xstart = col;
+        sameCol = 1;
+      }
+      lastrow = (int) (row * sampleRow);
+      ystart = row;
+      sameRow = 1;
+    }
 
-        if (av.conservation != null)
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
+      {
+        lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
           ap.annotationPanel.drawGraph(mg, av.conservation,
@@ -266,18 +362,17 @@ public class OverviewPanel
                                        graphHeight,
                                        (int) (col * sampleCol),
                                        (int) (col * sampleCol) + 1);
-          mg.translate(-col, -sequencesHeight);
+          mg.translate( -col, -sequencesHeight);
         }
       }
     }
-
     System.gc();
 
     resizing = false;
 
     setBoxPosition();
 
-    if(resizeAgain)
+    if (resizeAgain)
     {
       resizeAgain = false;
       updateOverviewImage();
@@ -287,16 +382,49 @@ public class OverviewPanel
   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);
+    }
+
+    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) (av.getStartRes() * av.getCharWidth() * scalew);
-    boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);
-    boxWidth = (int) ( (av.getEndRes() - av.getStartRes() + 1) *
-                      av.getCharWidth() * scalew);
-    boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;
+    boxX = (int) (startRes * av.getCharWidth() * scalew);
+    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) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
+
     repaint();
   }
 
@@ -307,23 +435,15 @@ public class OverviewPanel
 
   public void paint(Graphics g)
   {
+    Graphics og = offscreen.getGraphics();
     if (miniMe != null)
     {
-      g.drawImage(miniMe, 0, 0, this);
-    }
-    else
-    {
-      g.setColor(Color.white);
-      g.fillRect(0, 0, getSize().width, getSize().height);
-      g.setColor(Color.black);
-      g.setFont(new Font("Verdana", Font.BOLD, 15));
-      g.drawString("Recalculating", 5, sequencesHeight / 2);
-      g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
+      og.drawImage(miniMe, 0, 0, this);
+      og.setColor(Color.red);
+      og.drawRect(boxX, boxY, boxWidth, boxHeight);
+      og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+      g.drawImage(offscreen, 0, 0, this);
     }
-
-    g.setColor(Color.red);
-    g.drawRect(boxX, boxY, boxWidth, boxHeight);
-    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
   }
 
 }