X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=cbbfcff01821a9d80ba88030fda052f4ed339f7b;hb=8240aa86ee94d4c372af7deb1452a8294ff8800b;hp=94bff0e8510d29cbf9664711e56f0874a4076844;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 94bff0e..cbbfcff 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,22 +1,49 @@
+/*
+ * 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.appletgui;
 
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
 
-public class OverviewPanel extends Panel implements Runnable
+public class OverviewPanel
+    extends Panel implements Runnable, MouseMotionListener, MouseListener
 {
   Image miniMe;
+  Image offscreen;
   AlignViewport av;
   AlignmentPanel ap;
   float scalew = 1f;
   float scaleh = 1f;
 
   public int width, sequencesHeight;
-  int graphHeight=30;
-  int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;
+  int graphHeight = 20;
+  int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
 
   boolean resizing = false;
 
+  // Can set different properties in this seqCanvas than
+  // main visible SeqCanvas
+  SequenceRenderer sr;
+  FeatureRenderer fr;
+
+
   Frame nullFrame;
 
   public OverviewPanel(AlignmentPanel ap)
@@ -27,237 +54,385 @@ public class OverviewPanel extends Panel implements Runnable
     nullFrame = new Frame();
     nullFrame.addNotify();
 
+
+    sr = new SequenceRenderer(av);
+    sr.graphics = nullFrame.getGraphics();
+    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.alignment.getWidth() > av.alignment.getHeight())
+    float initialScale = (float) av.alignment.getWidth() /
+        (float) av.alignment.getHeight();
+
+    if(av.vconsensus==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;
+      }
     }
 
-    setSize (new Dimension(width, sequencesHeight+graphHeight));
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
     addComponentListener(new ComponentAdapter()
-   {
-
-       public void componentResized(ComponentEvent evt)
-       {
-         if( getSize().width!=width || getSize().height!=sequencesHeight+graphHeight)
-         {
-           updateOverviewImage();
-         }
-       }
-   });
-
-    addMouseMotionListener(new MouseMotionAdapter()
-           {
-             public void mouseDragged(MouseEvent evt)
-             { doMouseDragged(evt);}
-           });
-
-    addMouseListener(new MouseAdapter()
     {
-      public void mousePressed(MouseEvent evt)
-      { doMousePressed(evt);}
-      public void mouseReleased(MouseEvent evt)
-      { doMouseReleased(evt);}
+
+      public void componentResized(ComponentEvent evt)
+      {
+        if (getSize().width != width ||
+            getSize().height != sequencesHeight + graphHeight)
+        {
+          updateOverviewImage();
+        }
+      }
     });
 
+    addMouseMotionListener(this);
+
+    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();
-    if(!resizing)
-    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();
-    if(!resizing)
-    ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),
-                        (int)(boxY/scaleh/av.getCharHeight()) );
-    repaint();
-    ap.repaint();
   }
 
   void checkValid()
   {
     if (boxY < 0)
-      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;
+    {
+        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.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   */
   public void updateOverviewImage()
   {
-    if(resizing)
+    if (resizing)
     {
-      return;
+        resizeAgain = true;
+        return;
     }
 
+    if (av.showSequenceFeatures)
+   {
+     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
+     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+   }
+
     resizing = true;
+
+    if ( (getSize().width > 0) && (getSize().height > 0))
+    {
+      width = getSize().width;
+      sequencesHeight = getSize().height - graphHeight;
+    }
+    setSize(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;
+
   public void run()
   {
     miniMe = null;
     int alwidth = av.alignment.getWidth();
     int alheight = av.alignment.getHeight();
 
-    if(getSize().width>0 && getSize().height>0)
+    if (av.showSequenceFeatures)
+    {
+      fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
+    }
+
+    if (getSize().width > 0 && getSize().height > 0)
     {
       width = getSize().width;
       sequencesHeight = getSize().height - graphHeight;
     }
 
-    setSize (new Dimension(width, sequencesHeight+graphHeight));
+    setSize(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;
     scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
     miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
+    offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
 
     Graphics mg = miniMe.getGraphics();
-    Image consensus = nullFrame.createImage(fullsizeWidth, 60);
-    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();
-      Image 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++)
+    float sampleCol = (float) alwidth / (float) width;
+    float sampleRow = (float) alheight / (float) sequencesHeight;
+
+    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++)
+    {
+      if((int)(row*sampleRow)==lastrow)
       {
-          eSeq = 0;
-          eRes+=maxSize;
-          if(eRes>alwidth)
-            eRes = alwidth;
-
-          for(int sSeq=0, chunky=0; sSeq<alheight; sSeq+=maxSize, chunky++)
-          {
-            eSeq+=maxSize;
-            if(eSeq>alheight)
-              eSeq = alheight;
-
-            blocky = 0;
-            blockx = (int)((float)sRes/(float)alwidth * width);
-
-            block = nullFrame.createImage((eRes-sRes)*av.charWidth, (eSeq-sSeq)*av.charHeight);
-            g = block.getGraphics();
+        sameRow ++;
+        continue;
+      }
 
-           ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq, 0);
+      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);
 
-           blockh = (int)( (float)(eSeq-sSeq)/(float)alheight *  sequencesHeight  )+1 ;
-           blockw = (int)( (float)(eRes-sRes)/(float)alwidth  *   width )+1;
+        for (col = 0; col < width; col++)
+        {
+          if ( (int) (col * sampleCol) == lastcol && (int) (row * sampleRow) == lastrow)
+          {
+            sameCol ++;
+            continue;
+          }
 
-           blocky += (int) ((float)sSeq/(float)alheight* sequencesHeight);
+          lastcol = (int) (col * sampleCol);
 
-           mg.drawImage(block,  blockx,
-                              blocky ,
-                            blockx + blockw,
-                            blocky + blockh,
+          if (seq.getLength() > lastcol)
+          {
+            color = sr.getResidueBoxColour(
+                seq, lastcol);
 
-                         0, 0, block.getWidth(null),block.getHeight(null), this);
+            if (av.showSequenceFeatures)
+              color = fr.findFeatureColour(color, seq, lastcol);
+          }
+          else
+          {
+            color = Color.white; //White
+          }
 
-          block = null;
+          if (hiddenRow ||
+              (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+          {
+            color = color.darker().darker();
           }
 
-      }
+          mg.setColor(color);
+          if (sameCol == 1 && sameRow == 1)
+            mg.drawLine(xstart, ystart, xstart, ystart);
+          else
+            mg.fillRect(xstart, ystart, sameCol, sameRow);
 
-    }catch(OutOfMemoryError error)
-    {     System.err.println("Out of memory when trying to calculate the overview window image!");   }
+          xstart = col;
+          sameCol = 1;
+      }
+      lastrow = (int)(row*sampleRow);
+      ystart = row;
+      sameRow = 1;
+    }
 
+    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();
+    }
+}
 
   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();
+
+    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) (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();
   }
 
- public void update(Graphics g)
- {
-   paint(g);
- }
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
 
   public void paint(Graphics g)
   {
-    if(resizing)
+    Graphics og = offscreen.getGraphics();
+    if (miniMe != null)
+    {
+      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);
+    }
+    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);
-    }
-    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);
+      g.drawString("Recalculating", 5, sequencesHeight / 2);
+      g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
     }
   }