X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=04e5f13fc9732fe594021fae36e684c2728d00e7;hb=56b66650a5223dd79423bcebed626a8cb850fcc7;hp=244d884b50d4e2a08b87ba34757711d9a4d4fc93;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 244d884..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
@@ -23,6 +23,12 @@ import java.awt.event.*;
 import java.awt.image.*;
 import javax.swing.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class OverviewPanel
     extends JPanel implements Runnable
 {
@@ -33,28 +39,52 @@ public class OverviewPanel
   float scaleh = 1f;
   int width;
   int sequencesHeight;
-  int graphHeight = 30;
+  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)
+    {
+      graphHeight = 0;
+    }
+
     if (av.alignment.getWidth() > av.alignment.getHeight())
     {
       // wider
       width = 400;
       sequencesHeight = (int) (400f / initialScale);
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
     }
     else
     {
@@ -84,7 +114,12 @@ public class OverviewPanel
     {
       public void mouseDragged(MouseEvent evt)
       {
-        doMouseDragged(evt);
+        if (!av.wrapAlignment)
+        {
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
+        }
       }
     });
 
@@ -92,53 +127,21 @@ public class OverviewPanel
     {
       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)
@@ -158,37 +161,83 @@ public class OverviewPanel
 
     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)
     {
+      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());
     }
 
+    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();
@@ -201,125 +250,198 @@ public class OverviewPanel
                                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
+    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++)
     {
-      // 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;
-      int blocky = 0;
-      int blockw = 0;
-      int blockh = 0;
-      int eRes = 0;
-      int eSeq = 0;
-
-      av.setRenderGaps(false);
-
-      for (int sRes = 0, chunkx = 0; sRes < alwidth;
-           sRes += maxSize, chunkx++)
+      if ( (int) (row * sampleRow) == lastrow)
       {
-        eSeq = 0;
-        eRes += maxSize;
-
-        if (eRes > alwidth)
+        //No need to recalculate the colours,
+        //Just copy from the row above
+        for (col = 0; col < width; col++)
         {
-          eRes = alwidth;
+          miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
         }
+        continue;
+      }
 
-        for (int sSeq = 0, chunky = 0; sSeq < alheight;
-             sSeq += maxSize, chunky++)
-        {
-          eSeq += maxSize;
+      lastrow = (int) (row * sampleRow);
 
-          if (eSeq > alheight)
-          {
-            eSeq = alheight;
-          }
+      hiddenRow = false;
+      if (av.hasHiddenRows)
+      {
+        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        if (seq == null)
+        {
+          int index =
+              av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+              lastrow);
 
-          blocky = 0;
-          blockx = (int) ( (float) sRes / (float) alwidth * width);
+          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, 0, 0, block.getWidth(),
-                       block.getHeight(), this);
+          if (av.showSequenceFeatures)
+          {
+            color = fr.findFeatureColour(color, seq, lastcol);
+          }
+        }
+        else
+        {
+          color = -1; //White
+        }
 
-          block = null;
+        if (hiddenRow ||
+            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+        {
+          color = new Color(color).darker().darker().getRGB();
         }
+
+        miniMe.setRGB(col, row, color);
+
       }
     }
-    catch (OutOfMemoryError error)
+
+    if (av.conservation != null)
     {
-      System.err.println(
-          "Out of memory when trying to calculate the overview window image!");
+      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;
+    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();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
   public void paintComponent(Graphics g)
   {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-    g.setColor(Color.black);
-
-    if (resizing)
+    if(resizing)
     {
-      g.setFont(new Font("Verdana", Font.BOLD, 15));
-      g.drawString("Recalculating", 5, sequencesHeight / 2);
-      g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
+      g.setColor(Color.white);
+      g.fillRect(0,0,getWidth(),getHeight());
     }
-    else
+    else if (miniMe != null)
     {
-      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.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);
+
   }
 }