X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=04e5f13fc9732fe594021fae36e684c2728d00e7;hb=cbfa4d2bc1282662ad88756f1b0b2d8b3b82bd11;hp=2933841e7706d6790ccd603753007df449f12a1a;hpb=ef36c8bbd6c5eef95e4d1a2cff57ea772af5110b;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 2933841..04e5f13 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/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
@@ -21,428 +21,427 @@ package jalview.gui;
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
-
 import javax.swing.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class OverviewPanel extends JPanel implements Runnable
+public class OverviewPanel
+    extends JPanel implements Runnable
 {
-    BufferedImage miniMe;
-    AlignViewport av;
-    AlignmentPanel ap;
-    float scalew = 1f;
-    float scaleh = 1f;
-    int width;
-    int sequencesHeight;
-    int graphHeight = 20;
-    int boxX = -1;
-    int boxY = -1;
-    int boxWidth = -1;
-    int boxHeight = -1;
-    boolean resizing = false;
-
-    // Can set different properties in this seqCanvas than
-    // main visible SeqCanvas
-    SequenceRenderer sr;
-    FeatureRenderer fr;
-
-    /**
-     * Creates a new OverviewPanel object.
-     *
-     * @param ap DOCUMENT ME!
-     */
-    public OverviewPanel(AlignmentPanel ap)
+  BufferedImage miniMe;
+  AlignViewport av;
+  AlignmentPanel ap;
+  float scalew = 1f;
+  float scaleh = 1f;
+  int width;
+  int sequencesHeight;
+  int graphHeight = 20;
+  int boxX = -1;
+  int boxY = -1;
+  int boxWidth = -1;
+  int boxHeight = -1;
+  boolean resizing = false;
+
+  // Can set different properties in this seqCanvas than
+  // main visible SeqCanvas
+  SequenceRenderer sr;
+  FeatureRenderer fr;
+
+  /**
+   * Creates a new OverviewPanel object.
+   *
+   * @param ap DOCUMENT ME!
+   */
+  public OverviewPanel(AlignmentPanel ap)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+    setLayout(null);
+
+    sr = new SequenceRenderer(av);
+    sr.renderGaps = false;
+    sr.forOverview = true;
+    fr = new FeatureRenderer(ap);
+
+    // scale the initial size of overviewpanel to shape of alignment
+    float initialScale = (float) av.alignment.getWidth() /
+        (float) av.alignment.getHeight();
+
+    if (av.conservation == null)
     {
-        this.av = ap.av;
-        this.ap = ap;
-        setLayout(null);
-
-        sr = new SequenceRenderer(av);
-        sr.renderGaps = false;
-        sr.forOverview = true;
-        fr = new FeatureRenderer(av);
-
-        // scale the initial size of overviewpanel to shape of alignment
-        float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();
-
-        if(av.conservation==null)
-          graphHeight = 0;
-
-
-        if (av.alignment.getWidth() > av.alignment.getHeight())
-        {
-            // wider
-            width = 400;
-            sequencesHeight = (int) (400f / initialScale);
-            if(sequencesHeight<40)
-              sequencesHeight = 40;
-        }
-        else
-        {
-            // taller
-            width = (int) (400f * initialScale);
-            sequencesHeight = 300;
-
-            if (width < 120)
-            {
-                width = 120;
-            }
-        }
-
-        addComponentListener(new ComponentAdapter()
-            {
-                public void componentResized(ComponentEvent evt)
-                {
-                    if ((getWidth() != width) ||
-                            (getHeight() != (sequencesHeight + graphHeight)))
-                    {
-                        updateOverviewImage();
-                    }
-                }
-            });
-
-        addMouseMotionListener(new MouseMotionAdapter()
-            {
-                public void mouseDragged(MouseEvent evt)
-                {
-                  if (!av.wrapAlignment)
-                  {
-                    boxX = evt.getX();
-                    boxY = evt.getY();
-                    checkValid();
-                  }
-                }
-            });
-
-        addMouseListener(new MouseAdapter()
-            {
-                public void mousePressed(MouseEvent evt)
-                {
-                  if(!av.wrapAlignment)
-                  {
-                    boxX = evt.getX();
-                    boxY = evt.getY();
-                    checkValid();
-                  }
-                }
-            });
-
-        updateOverviewImage();
+      graphHeight = 0;
     }
 
-
-    /**
-     * DOCUMENT ME!
-     */
-    void checkValid()
+    if (av.alignment.getWidth() > av.alignment.getHeight())
     {
-        if (boxY < 0)
-        {
-            boxY = 0;
-        }
+      // wider
+      width = 400;
+      sequencesHeight = (int) (400f / initialScale);
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
+    }
+    else
+    {
+      // taller
+      width = (int) (400f * initialScale);
+      sequencesHeight = 300;
 
-        if (boxY > (sequencesHeight - boxHeight))
-        {
-            boxY = sequencesHeight - boxHeight + 1;
-        }
+      if (width < 120)
+      {
+        width = 120;
+      }
+    }
 
-        if (boxX < 0)
+    addComponentListener(new ComponentAdapter()
+    {
+      public void componentResized(ComponentEvent evt)
+      {
+        if ( (getWidth() != width) ||
+            (getHeight() != (sequencesHeight + graphHeight)))
         {
-            boxX = 0;
+          updateOverviewImage();
         }
+      }
+    });
 
-        if (boxX > (width - boxWidth))
+    addMouseMotionListener(new MouseMotionAdapter()
+    {
+      public void mouseDragged(MouseEvent evt)
+      {
+        if (!av.wrapAlignment)
         {
-          if(av.hasHiddenColumns)
-          {
-            //Try smallest possible box
-            boxWidth = (int) ( (av.endRes - av.startRes + 1) *
-                                   av.getCharWidth() * scalew);
-          }
-          boxX = width - boxWidth;
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
         }
+      }
+    });
 
-        int col = (int) (boxX / scalew / av.getCharWidth());
-        int row = (int) (boxY / scaleh / av.getCharHeight());
-
-        if (av.hasHiddenColumns)
+    addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        if (!av.wrapAlignment)
         {
-          if (!av.getColumnSelection().isVisible(col))
-          {
-            return;
-          }
-
-          col = av.getColumnSelection().findColumnPosition(col);
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
         }
+      }
+    });
 
-        if( av.hasHiddenRows )
-        {
-          row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
-        }
+    updateOverviewImage();
+  }
 
-        ap.setScrollValues( col, row );
+  /**
+   * DOCUMENT ME!
+   */
+  void checkValid()
+  {
+    if (boxY < 0)
+    {
+      boxY = 0;
+    }
 
+    if (boxY > (sequencesHeight - boxHeight))
+    {
+      boxY = sequencesHeight - boxHeight + 1;
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateOverviewImage()
+    if (boxX < 0)
     {
-        if (resizing)
-        {
-            resizeAgain = true;
-            return;
-        }
+      boxX = 0;
+    }
 
-        resizing = true;
+    if (boxX > (width - boxWidth))
+    {
+      if (av.hasHiddenColumns)
+      {
+        //Try smallest possible box
+        boxWidth = (int) ( (av.endRes - av.startRes + 1) *
+                          av.getCharWidth() * scalew);
+      }
+      boxX = width - boxWidth;
+    }
 
-        if ( (getWidth() > 0) && (getHeight() > 0))
-        {
-          width = getWidth();
-          sequencesHeight = getHeight() - graphHeight;
-        }
+    int col = (int) (boxX / scalew / av.getCharWidth());
+    int row = (int) (boxY / scaleh / av.getCharHeight());
 
-        setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+    if (av.hasHiddenColumns)
+    {
+      if (!av.getColumnSelection().isVisible(col))
+      {
+        return;
+      }
 
-        Thread thread = new Thread(this);
-        thread.start();
-        repaint();
+      col = av.getColumnSelection().findColumnPosition(col);
     }
 
-    // This is set true if the user resizes whilst
-    // the overview is being calculated
-    boolean resizeAgain = false;
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void run()
+    if (av.hasHiddenRows)
     {
-        miniMe = null;
+      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
+    }
 
-       if (av.showSequenceFeatures)
-       {
-         fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
-       }
+    ap.setScrollValues(col, row);
 
-        int alwidth = av.alignment.getWidth();
-        int alheight = av.alignment.getHeight()
-            +av.alignment.getHiddenSequences().getSize();
+  }
 
-        setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateOverviewImage()
+  {
+    if (resizing)
+    {
+      resizeAgain = true;
+      return;
+    }
 
-        int fullsizeWidth = alwidth * av.getCharWidth();
-        int fullsizeHeight = alheight * av.getCharHeight();
+    resizing = true;
 
-        scalew = (float) width / (float) fullsizeWidth;
-        scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+    if ( (getWidth() > 0) && (getHeight() > 0))
+    {
+      width = getWidth();
+      sequencesHeight = getHeight() - graphHeight;
+    }
 
-        miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
-                BufferedImage.TYPE_INT_RGB);
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
+    Thread thread = new Thread(this);
+    thread.start();
+    repaint();
+  }
 
-        Graphics mg = miniMe.getGraphics();
-        mg.setColor(Color.orange);
-        mg.fillRect(0,0,width, miniMe.getHeight());
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  boolean resizeAgain = false;
 
-        float sampleCol = (float) alwidth / (float) width;
-        float sampleRow = (float) alheight / (float) sequencesHeight;
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    miniMe = null;
 
-        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;
-          }
+    if (av.showSequenceFeatures)
+    {
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+    }
 
-          lastrow = (int)(row*sampleRow);
+    int alwidth = av.alignment.getWidth();
+    int alheight = av.alignment.getHeight()
+        + av.alignment.getHiddenSequences().getSize();
 
-          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);
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
-          if(seq==null)
-          {
-            System.out.println(lastrow+" null");
-            continue;
-          }
+    int fullsizeWidth = alwidth * av.getCharWidth();
+    int fullsizeHeight = alheight * av.getCharHeight();
 
-            for (col = 0; col < width; col++)
-            {
-            if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
-            {
-              miniMe.setRGB(col,row,color);
-              continue;
-            }
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
+    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+                               BufferedImage.TYPE_INT_RGB);
 
-            lastcol = (int)(col*sampleCol);
+    Graphics mg = miniMe.getGraphics();
+    mg.setColor(Color.orange);
+    mg.fillRect(0, 0, width, miniMe.getHeight());
 
-            if (seq.getLength() > lastcol)
-            {
-              color = sr.getResidueBoxColour(
-                  seq, lastcol).getRGB();
+    float sampleCol = (float) alwidth / (float) width;
+    float sampleRow = (float) alheight / (float) sequencesHeight;
 
-              if (av.showSequenceFeatures)
-                color = fr.findFeatureColour(color, seq, lastcol);
-            }
-            else
-            {
-              color = -1; //White
-            }
+    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;
+      }
 
-            if(hiddenRow ||
-               (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
-            {
-              color = new Color(color).darker().darker().getRGB();
-            }
+      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);
 
-            miniMe.setRGB(col,row,color);
+          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)
+        {
+          miniMe.setRGB(col, row, color);
+          continue;
         }
 
-        if (av.conservation != null)
+        lastcol = (int) (col * sampleCol);
+
+        if (seq.getLength() > lastcol)
         {
-          for (col = 0; col < width; col++)
+          color = sr.getResidueBoxColour(
+              seq, lastcol).getRGB();
+
+          if (av.showSequenceFeatures)
           {
-            lastcol = (int) (col * sampleCol);
-            {
-              mg.translate(col, sequencesHeight);
-              ap.annotationPanel.drawGraph(mg, av.conservation,
-                                           (int) (sampleCol) + 1,
-                                           graphHeight,
-                                           (int) (col * sampleCol),
-                                           (int) (col * sampleCol) + 1);
-              mg.translate( -col, -sequencesHeight);
-            }
+            color = fr.findFeatureColour(color, seq, lastcol);
           }
         }
-        System.gc();
-
-        resizing = false;
-
-        setBoxPosition();
-
-        if(resizeAgain)
+        else
         {
-          resizeAgain = false;
-          updateOverviewImage();
+          color = -1; //White
         }
-    }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void setBoxPosition()
-    {
-      int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-      int fullsizeHeight = (av.alignment.getHeight()
-                   +av.alignment.getHiddenSequences().getSize()) * av.getCharHeight();
+        if (hiddenRow ||
+            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+        {
+          color = new Color(color).darker().darker().getRGB();
+        }
 
-      int startRes = av.getStartRes();
-      int endRes = av.getEndRes();
+        miniMe.setRGB(col, row, color);
 
-      if(av.hasHiddenColumns)
-      {
-        startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-        endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
       }
+    }
 
-      int startSeq = av.startSeq;
-      int endSeq = av.endSeq;
-
-      if (av.hasHiddenRows)
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
       {
-        startSeq =
-            av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
-
-        endSeq =
-            av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
-
+        lastcol = (int) (col * sampleCol);
+        {
+          mg.translate(col, sequencesHeight);
+          ap.annotationPanel.drawGraph(mg, av.conservation,
+                                       (int) (sampleCol) + 1,
+                                       graphHeight,
+                                       (int) (col * sampleCol),
+                                       (int) (col * sampleCol) + 1);
+          mg.translate( -col, -sequencesHeight);
+        }
       }
+    }
+    System.gc();
 
+    resizing = false;
 
-      scalew = (float) width / (float) fullsizeWidth;
-      scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+    setBoxPosition();
 
-        boxX = (int) (startRes * av.getCharWidth() * scalew);
-        boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+    if (resizeAgain)
+    {
+      resizeAgain = false;
+      updateOverviewImage();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void setBoxPosition()
+  {
+    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
+    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);
 
-        if(av.hasHiddenColumns)
-          boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
-        else
-          boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+      endSeq =
+          av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
 
+    }
 
-        boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
+    boxX = (int) (startRes * av.getCharWidth() * scalew);
+    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
 
-        repaint();
+    if (av.hasHiddenColumns)
+    {
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
+    else
     {
-        if (miniMe != null && !resizing)
-        {
-          g.drawImage(miniMe, 0, 0, this);
-        }
-        else
-        {
-          g.setColor(Color.white);
-          g.fillRect(0, 0, getWidth(), getHeight());
-          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);
-        }
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
 
+    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
 
-        g.setColor(Color.red);
-        g.drawRect(boxX, boxY, boxWidth, boxHeight);
-        g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+    repaint();
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    if(resizing)
+    {
+      g.setColor(Color.white);
+      g.fillRect(0,0,getWidth(),getHeight());
     }
+    else if (miniMe != null)
+    {
+      g.drawImage(miniMe, 0, 0, this);
+    }
+
+    g.setColor(Color.red);
+    g.drawRect(boxX, boxY, boxWidth, boxHeight);
+    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+
+  }
 }