X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=04e5f13fc9732fe594021fae36e684c2728d00e7;hb=a4833a9c3e15e416598b61e6887ee5743c3c2734;hp=3257ce54a44e59111a6a3bded327966f733bb601;hpb=fdaf66178c7596335c3675ec3db0da8503dc61b2;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 3257ce5..04e5f13 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,149 +1,246 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import javax.swing.*;
+import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
-import java.awt.*;
+import javax.swing.*;
 
-public class OverviewPanel extends JPanel implements Runnable
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class OverviewPanel
+    extends JPanel implements Runnable
 {
   BufferedImage miniMe;
   AlignViewport av;
   AlignmentPanel ap;
   float scalew = 1f;
   float scaleh = 1f;
-
-  int width, sequencesHeight;
-  int graphHeight=30;
-  int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;
-
+  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.alignment.getWidth() > av.alignment.getHeight())
+    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);
+      sequencesHeight = (int) (400f / initialScale);
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
     }
     else
     {
       // taller
-      width = (int)(400f*initialScale);
+      width = (int) (400f * initialScale);
       sequencesHeight = 300;
-      if(width<120)
+
+      if (width < 120)
+      {
         width = 120;
+      }
     }
 
     addComponentListener(new ComponentAdapter()
-   {
-
-       public void componentResized(ComponentEvent evt)
-       {
-         if( getWidth()!=width || getHeight()!=sequencesHeight+graphHeight)
-         {
-           updateOverviewImage();
-         }
-       }
-   });
+    {
+      public void componentResized(ComponentEvent evt)
+      {
+        if ( (getWidth() != width) ||
+            (getHeight() != (sequencesHeight + graphHeight)))
+        {
+          updateOverviewImage();
+        }
+      }
+    });
 
     addMouseMotionListener(new MouseMotionAdapter()
-           {
-             public void mouseDragged(MouseEvent evt)
-             { doMouseDragged(evt);}
-           });
+    {
+      public void mouseDragged(MouseEvent evt)
+      {
+        if (!av.wrapAlignment)
+        {
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
+        }
+      }
+    });
 
     addMouseListener(new MouseAdapter()
     {
       public void mousePressed(MouseEvent evt)
-      { doMousePressed(evt);}
-      public void mouseReleased(MouseEvent evt)
-      { doMouseReleased(evt);}
+      {
+        if (!av.wrapAlignment)
+        {
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
+        }
+      }
     });
 
     updateOverviewImage();
-
-  }
-
-  public void doMousePressed(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-
-    checkValid();
-    repaint();
-  }
-
-  public void doMouseReleased(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-    if(!resizing)
-    ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),
-                        (int)(boxY/scaleh/av.getCharHeight()) );
-  }
-
-  public void doMouseDragged(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-    if(!resizing)
-    ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),
-                        (int)(boxY/scaleh/av.getCharHeight()) );
   }
 
+  /**
+   * DOCUMENT ME!
+   */
   void checkValid()
   {
     if (boxY < 0)
+    {
       boxY = 0;
+    }
 
-    if (boxY > sequencesHeight - boxHeight)
-      boxY = sequencesHeight - boxHeight+1;
+    if (boxY > (sequencesHeight - boxHeight))
+    {
+      boxY = sequencesHeight - boxHeight + 1;
+    }
 
     if (boxX < 0)
+    {
       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);
+
   }
 
+  /**
+   * DOCUMENT ME!
+   */
   public void updateOverviewImage()
   {
-    if(resizing)
+    if (resizing)
     {
+      resizeAgain = true;
       return;
     }
 
     resizing = true;
+
+    if ( (getWidth() > 0) && (getHeight() > 0))
+    {
+      width = getWidth();
+      sequencesHeight = getHeight() - graphHeight;
+    }
+
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+
     Thread thread = new Thread(this);
     thread.start();
     repaint();
   }
 
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  boolean resizeAgain = false;
+
+  /**
+   * DOCUMENT ME!
+   */
   public void run()
   {
     miniMe = null;
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight();
 
-    if(getWidth()>0 && getHeight()>0)
+    if (av.showSequenceFeatures)
     {
-      width = getWidth();
-      sequencesHeight = getHeight() - graphHeight;
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
     }
 
-    setPreferredSize (new Dimension(width, sequencesHeight+graphHeight));
+    int alwidth = av.alignment.getWidth();
+    int alheight = av.alignment.getHeight()
+        + av.alignment.getHiddenSequences().getSize();
+
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
-    int fullsizeWidth  = alwidth * av.getCharWidth();
+    int fullsizeWidth = alwidth * av.getCharWidth();
     int fullsizeHeight = alheight * av.getCharHeight();
 
     scalew = (float) width / (float) fullsizeWidth;
@@ -153,108 +250,198 @@ public class OverviewPanel extends JPanel implements Runnable
                                BufferedImage.TYPE_INT_RGB);
 
     Graphics mg = miniMe.getGraphics();
-    BufferedImage consensus = new BufferedImage(fullsizeWidth,
-                                           60,
-                                           BufferedImage.TYPE_3BYTE_BGR);
-    Graphics g = consensus.getGraphics();
-    ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);
-    mg.drawImage(consensus, 0, sequencesHeight, width,
-             sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);
-
-
-    boolean oldRenderGaps = av.renderGaps;
-    try{
-    // We'll have to draw the full size alignment in chunks, as an image of the
-    // whole alignment requires too much memory
-
-      // Max size depends on the font size, the following is a
-      // guess at a size which works
-      int maxSize = 2000 /  av.getFont().getSize();
-      BufferedImage block;
-      int blockx=0, blocky=0, blockw=0, blockh=0, eRes=0, eSeq=0;
-
-      av.setRenderGaps(false);
-      for(int sRes=0, chunkx=0; sRes<alwidth; sRes+=maxSize, chunkx++)
+    mg.setColor(Color.orange);
+    mg.fillRect(0, 0, width, miniMe.getHeight());
+
+    float sampleCol = (float) alwidth / (float) width;
+    float sampleRow = (float) alheight / (float) sequencesHeight;
+
+    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)
       {
-          eSeq = 0;
-          eRes+=maxSize;
-          if(eRes>alwidth)
-            eRes = alwidth;
+        //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;
+      }
 
-          for(int sSeq=0, chunky=0; sSeq<alheight; sSeq+=maxSize, chunky++)
-          {
-            eSeq+=maxSize;
-            if(eSeq>alheight)
-              eSeq = alheight;
+      lastrow = (int) (row * sampleRow);
 
-            blocky = 0;
-            blockx = (int)((float)sRes/(float)alwidth * width);
+      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);
+      }
 
-            block = new BufferedImage((eRes-sRes)*av.charWidth,
-              (eSeq-sSeq)*av.charHeight,
-              BufferedImage.TYPE_3BYTE_BGR);
-            g = block.getGraphics();
+      if (seq == null)
+      {
+        System.out.println(lastrow + " null");
+        continue;
+      }
 
-           ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq, 0);
+      for (col = 0; col < width; col++)
+      {
+        if ( (int) (col * sampleCol) == lastcol &&
+            (int) (row * sampleRow) == lastrow)
+        {
+          miniMe.setRGB(col, row, color);
+          continue;
+        }
 
-           blockh = (int)( (float)(eSeq-sSeq)/(float)alheight *  sequencesHeight  )+1 ;
-           blockw = (int)( (float)(eRes-sRes)/(float)alwidth  *   width )+1;
+        lastcol = (int) (col * sampleCol);
 
-           blocky += (int) ((float)sSeq/(float)alheight* sequencesHeight);
+        if (seq.getLength() > lastcol)
+        {
+          color = sr.getResidueBoxColour(
+              seq, lastcol).getRGB();
 
-           mg.drawImage(block,  blockx,
-                              blocky ,
-                            blockx + blockw,
-                            blocky + blockh,
+          if (av.showSequenceFeatures)
+          {
+            color = fr.findFeatureColour(color, seq, lastcol);
+          }
+        }
+        else
+        {
+          color = -1; //White
+        }
 
-                         0, 0, block.getWidth(),block.getHeight(), this);
+        if (hiddenRow ||
+            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+        {
+          color = new Color(color).darker().darker().getRGB();
+        }
 
-          block = null;
-          }
+        miniMe.setRGB(col, row, color);
 
       }
+    }
 
-    }catch(OutOfMemoryError error)
-    {     System.out.println("out of memory");   }
-
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
+      {
+        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();
 
-    av.setRenderGaps(oldRenderGaps);
     resizing = false;
 
     setBoxPosition();
+
+    if (resizeAgain)
+    {
+      resizeAgain = false;
+      updateOverviewImage();
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   */
   public void setBoxPosition()
   {
-      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;
-      repaint();
-  }
+    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();
 
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0,0,getWidth(),getHeight());
-    g.setColor(Color.black);
+    if (av.hasHiddenColumns)
+    {
+      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
+      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
+    }
 
-    if(resizing)
+    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) (startRes * av.getCharWidth() * scalew);
+    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+
+    if (av.hasHiddenColumns)
     {
-      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);
     }
     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);
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
     }
+
+    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
+
+    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);
+
+  }
 }