X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=fd3c334ccb62b91e5a2e6004e275b3f6d05a5f58;hb=b3b59df08fc4183bb35e4ed5a54841a990b71346;hp=3257ce54a44e59111a6a3bded327966f733bb601;hpb=fdaf66178c7596335c3675ec3db0da8503dc61b2;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 3257ce5..fd3c334 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,260 +1,448 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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.*;
+
+
+/**
+ * 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;
-
-  boolean resizing = false;
-
-  public OverviewPanel(AlignmentPanel ap)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-    setLayout(null);
-
-    // 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())
+    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)
     {
-      // wider
-      width = 400;
-      sequencesHeight = (int)(400f/initialScale);
+        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();
     }
-    else
+
+
+    /**
+     * DOCUMENT ME!
+     */
+    void checkValid()
     {
-      // taller
-      width = (int)(400f*initialScale);
-      sequencesHeight = 300;
-      if(width<120)
-        width = 120;
-    }
+        if (boxY < 0)
+        {
+            boxY = 0;
+        }
+
+        if (boxY > (sequencesHeight - boxHeight))
+        {
+            boxY = sequencesHeight - boxHeight + 1;
+        }
+
+        if (boxX < 0)
+        {
+            boxX = 0;
+        }
+
+        if (boxX > (width - boxWidth))
+        {
+          if(av.hasHiddenColumns)
+          {
+            //Try smallest possible box
+            boxWidth = (int) ( (av.endRes - av.startRes + 1) *
+                                   av.getCharWidth() * scalew);
+          }
+          boxX = width - boxWidth;
+        }
 
-    addComponentListener(new ComponentAdapter()
-   {
+        int col = (int) (boxX / scalew / av.getCharWidth());
+        int row = (int) (boxY / scaleh / av.getCharHeight());
 
-       public void componentResized(ComponentEvent evt)
-       {
-         if( getWidth()!=width || getHeight()!=sequencesHeight+graphHeight)
-         {
-           updateOverviewImage();
-         }
-       }
-   });
+        if (av.hasHiddenColumns)
+        {
+          if (!av.getColumnSelection().isVisible(col))
+          {
+            return;
+          }
 
-    addMouseMotionListener(new MouseMotionAdapter()
-           {
-             public void mouseDragged(MouseEvent evt)
-             { doMouseDragged(evt);}
-           });
+          col = av.getColumnSelection().findColumnPosition(col);
+        }
 
-    addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent evt)
-      { doMousePressed(evt);}
-      public void mouseReleased(MouseEvent evt)
-      { doMouseReleased(evt);}
-    });
-
-    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()) );
-  }
-
-  void checkValid()
-  {
-    if (boxY < 0)
-      boxY = 0;
-
-    if (boxY > sequencesHeight - boxHeight)
-      boxY = sequencesHeight - boxHeight+1;
-
-    if (boxX < 0)
-      boxX = 0;
-
-    if (boxX > width - boxWidth)
-      boxX = width - boxWidth;
-  }
-
-  public void updateOverviewImage()
-  {
-    if(resizing)
-    {
-      return;
-    }
+        if( av.hasHiddenRows )
+        {
+          row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
+        }
 
-    resizing = true;
-    Thread thread = new Thread(this);
-    thread.start();
-    repaint();
-  }
+        ap.setScrollValues( col, row );
 
-  public void run()
-  {
-    miniMe = null;
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight();
+    }
 
-    if(getWidth()>0 && getHeight()>0)
+    /**
+     * DOCUMENT ME!
+     */
+    public void updateOverviewImage()
     {
-      width = getWidth();
-      sequencesHeight = getHeight() - graphHeight;
+        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();
     }
 
-    setPreferredSize (new Dimension(width, sequencesHeight+graphHeight));
+    // This is set true if the user resizes whilst
+    // the overview is being calculated
+    boolean resizeAgain = false;
 
-    int fullsizeWidth  = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
+    /**
+     * DOCUMENT ME!
+     */
+    public void run()
+    {
+        miniMe = null;
 
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+       if (av.showSequenceFeatures)
+       {
+         fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
+       }
 
-    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
-                               BufferedImage.TYPE_INT_RGB);
+        int alwidth = av.alignment.getWidth();
+        int alheight = av.alignment.getHeight()
+            +av.alignment.getHiddenSequences().getSize();
 
-    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);
+        setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
+        int fullsizeWidth = alwidth * av.getCharWidth();
+        int fullsizeHeight = alheight * av.getCharHeight();
 
-    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
+        scalew = (float) width / (float) fullsizeWidth;
+        scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
-      // 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;
+        miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+                BufferedImage.TYPE_INT_RGB);
 
-      av.setRenderGaps(false);
-      for(int sRes=0, chunkx=0; sRes<alwidth; sRes+=maxSize, chunkx++)
-      {
-          eSeq = 0;
-          eRes+=maxSize;
-          if(eRes>alwidth)
-            eRes = alwidth;
 
-          for(int sSeq=0, chunky=0; sSeq<alheight; sSeq+=maxSize, chunky++)
+        Graphics mg = miniMe.getGraphics();
+        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+=maxSize;
-            if(eSeq>alheight)
-              eSeq = alheight;
+            //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;
+          }
 
-            blocky = 0;
-            blockx = (int)((float)sRes/(float)alwidth * width);
+          lastrow = (int)(row*sampleRow);
 
-            block = new BufferedImage((eRes-sRes)*av.charWidth,
-              (eSeq-sSeq)*av.charHeight,
-              BufferedImage.TYPE_3BYTE_BGR);
-            g = block.getGraphics();
+          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)
+            {
+              miniMe.setRGB(col,row,color);
+              continue;
+            }
+
+
+            lastcol = (int)(col*sampleCol);
+
+            if (seq.getLength() > lastcol)
+            {
+              color = sr.getResidueBoxColour(
+                  seq, lastcol).getRGB();
 
-           ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq, 0);
+              if (av.showSequenceFeatures)
+                color = fr.findFeatureColour(color, seq, lastcol);
+            }
+            else
+            {
+              color = -1; //White
+            }
 
-           blockh = (int)( (float)(eSeq-sSeq)/(float)alheight *  sequencesHeight  )+1 ;
-           blockw = (int)( (float)(eRes-sRes)/(float)alwidth  *   width )+1;
+            if(hiddenRow ||
+               (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+            {
+              color = new Color(color).darker().darker().getRGB();
+            }
 
-           blocky += (int) ((float)sSeq/(float)alheight* sequencesHeight);
 
-           mg.drawImage(block,  blockx,
-                              blocky ,
-                            blockx + blockw,
-                            blocky + blockh,
+            miniMe.setRGB(col,row,color);
 
-                         0, 0, block.getWidth(),block.getHeight(), this);
 
-          block = 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,
+                                           (int) (sampleCol) + 1,
+                                           graphHeight,
+                                           (int) (col * sampleCol),
+                                           (int) (col * sampleCol) + 1);
+              mg.translate( -col, -sequencesHeight);
+            }
+          }
+        }
+        System.gc();
+
+        resizing = false;
+
+        setBoxPosition();
+
+        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);
       }
 
-    }catch(OutOfMemoryError error)
-    {     System.out.println("out of memory");   }
+      int startSeq = av.startSeq;
+      int endSeq = av.endSeq;
 
+      if (av.hasHiddenRows)
+      {
+        startSeq =
+            av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
+
+        endSeq =
+            av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
 
-    av.setRenderGaps(oldRenderGaps);
-    resizing = false;
+      }
 
-    setBoxPosition();
-  }
 
-  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();
-  }
+      scalew = (float) width / (float) fullsizeWidth;
+      scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
+        boxX = (int) (startRes * av.getCharWidth() * scalew);
+        boxY = (int) (startSeq * av.getCharHeight() * scaleh);
 
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0,0,getWidth(),getHeight());
-    g.setColor(Color.black);
 
-    if(resizing)
-    {
-      g.setFont(new Font("Verdana", Font.BOLD, 15));
-      g.drawString("Recalculating", 5, sequencesHeight/2);
-      g.drawString("Overview.....", 5, sequencesHeight/2 +20);
+
+        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();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
     {
-      if(miniMe!=null)
-        g.drawImage(miniMe, 0,0,this);
+        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);
+        }
+
+
+        g.setColor(Color.red);
+        g.drawRect(boxX, boxY, boxWidth, boxHeight);
+        g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
 
-      g.setColor(Color.red);
-      g.drawRect(boxX, boxY, boxWidth, boxHeight);
-      g.drawRect(boxX+1, boxY+1, boxWidth-2, boxHeight-2);
     }
-  }
-
 }