X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=2c779427635f7dcb63595b9cdf97cfeddba36e88;hb=7f4da0a2b0c10f158a03dbfce8878e67e90c4a68;hp=6bc630c9a85c9b7626140028633c9db72b613fd6;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 6bc630c..2c77942 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,122 +1,103 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+import jalview.viewmodel.OverviewDimensions;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JPanel;
 
 /**
- * DOCUMENT ME!
+ * Panel displaying an overview of the full alignment, with an interactive box
+ * representing the viewport onto the alignment.
  * 
  * @author $author$
  * @version $Revision$
  */
 public class OverviewPanel extends JPanel implements Runnable
 {
-  BufferedImage miniMe;
-
-  AlignViewport av;
+  private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
 
-  AlignmentPanel ap;
+  private final AnnotationRenderer renderer = new AnnotationRenderer();
 
-  float scalew = 1f;
+  private OverviewDimensions od;
 
-  float scaleh = 1f;
+  private BufferedImage miniMe;
 
-  int width;
+  private BufferedImage lastMiniMe = null;
 
-  int sequencesHeight;
+  private AlignViewport av;
 
-  int graphHeight = 20;
+  private AlignmentPanel ap;
 
-  int boxX = -1;
+  //
+  private boolean resizing = false;
 
-  int boxY = -1;
-
-  int boxWidth = -1;
-
-  int boxHeight = -1;
-
-  boolean resizing = false;
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  private boolean resizeAgain = false;
 
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
-  SequenceRenderer sr;
+  private SequenceRenderer sr;
 
-  FeatureRenderer fr;
+  private jalview.renderer.seqfeatures.FeatureRenderer fr;
 
   /**
    * Creates a new OverviewPanel object.
    * 
-   * @param ap
-   *                DOCUMENT ME!
+   * @param alPanel
+   *          The alignment panel which is shown in the overview panel
    */
-  public OverviewPanel(AlignmentPanel ap)
+  public OverviewPanel(AlignmentPanel alPanel)
   {
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = alPanel.av;
+    this.ap = alPanel;
     setLayout(null);
 
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
     sr.forOverview = true;
-    fr = new FeatureRenderer(ap);
+    fr = new FeatureRenderer(alPanel);
 
-    // 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;
-      }
-    }
+    od = new OverviewDimensions(av.getPosProps(), av.isShowAnnotation());
 
     addComponentListener(new ComponentAdapter()
     {
+      @Override
       public void componentResized(ComponentEvent evt)
       {
-        if ((getWidth() != width)
-                || (getHeight() != (sequencesHeight + graphHeight)))
+        if ((getWidth() != od.getWidth())
+                || (getHeight() != (od.getHeight())))
         {
           updateOverviewImage();
         }
@@ -125,26 +106,30 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addMouseMotionListener(new MouseMotionAdapter()
     {
+      @Override
       public void mouseDragged(MouseEvent evt)
       {
-        if (!av.wrapAlignment)
+        if (!av.getWrapAlignment())
         {
-          boxX = evt.getX();
-          boxY = evt.getY();
-          checkValid();
+          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+                  .getAlignment().getHiddenSequences(), av
+                  .getColumnSelection(), av.getPosProps());
+          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
     });
 
     addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent evt)
       {
-        if (!av.wrapAlignment)
+        if (!av.getWrapAlignment())
         {
-          boxX = evt.getX();
-          boxY = evt.getY();
-          checkValid();
+          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+                  .getAlignment().getHiddenSequences(), av
+                  .getColumnSelection(), av.getPosProps());
+          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
     });
@@ -153,60 +138,7 @@ public class OverviewPanel extends JPanel implements Runnable
   }
 
   /**
-   * DOCUMENT ME!
-   */
-  void checkValid()
-  {
-    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;
-    }
-
-    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!
+   * Updates the overview image when the related alignment panel is updated
    */
   public void updateOverviewImage()
   {
@@ -220,239 +152,214 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if ((getWidth() > 0) && (getHeight() > 0))
     {
-      width = getWidth();
-      sequencesHeight = getHeight() - graphHeight;
+      od.setWidth(getWidth());
+      od.setHeight(getHeight());
     }
 
-    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
     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!
-   */
+  @Override
   public void run()
   {
     miniMe = null;
 
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+      fr.transferSettings(ap.getSeqPanel().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();
-    int fullsizeHeight = alheight * av.getCharHeight();
+    // why do we need to set preferred size again? was set in
+    // updateOverviewImage
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+    miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
             BufferedImage.TYPE_INT_RGB);
 
     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)
-      {
-        // 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;
-      }
-
-      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);
-
-          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;
-        }
+    mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
 
-        lastcol = (int) (col * sampleCol);
-
-        if (seq.getLength() > lastcol)
-        {
-          color = sr.getResidueBoxColour(seq, lastcol).getRGB();
+    // calculate sampleCol and sampleRow
+    // alignment width is max number of residues/bases
+    // alignment height is number of sequences
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getAbsoluteHeight();
 
-          if (av.showSequenceFeatures)
-          {
-            color = fr.findFeatureColour(color, seq, lastcol);
-          }
-        }
-        else
-        {
-          color = -1; // White
-        }
+    // sampleCol or sampleRow is the width/height allocated to each residue
+    // in particular, sometimes we may need more than one row/col of the
+    // BufferedImage allocated
+    // sampleCol is how much of a residue to assign to each pixel
+    // sampleRow is how many sequences to assign to each pixel
+    float sampleCol = alwidth / (float) od.getWidth();
+    float sampleRow = alheight / (float) od.getSequencesHeight();
 
-        if (hiddenRow
-                || (av.hasHiddenColumns && !av.getColumnSelection()
-                        .isVisible(lastcol)))
-        {
-          color = new Color(color).darker().darker().getRGB();
-        }
+    buildImage(sampleRow, sampleCol);
 
-        miniMe.setRGB(col, row, color);
-
-      }
-    }
-
-    if (av.conservation != null)
+    if (av.isShowAnnotation())
     {
-      for (col = 0; col < width; col++)
+      renderer.updateFromAlignViewport(av);
+      for (int col = 0; col < od.getWidth() && !resizeAgain; 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);
-        }
+        mg.translate(col, od.getSequencesHeight());
+        renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+                av.getAlignmentConservationAnnotation().annotations,
+                (int) (sampleCol) + 1, od.getGraphHeight(),
+                (int) (col * sampleCol), (int) (col * sampleCol) + 1);
+        mg.translate(-col, -od.getSequencesHeight());
+
       }
     }
     System.gc();
 
     resizing = false;
 
-    setBoxPosition();
-
     if (resizeAgain)
     {
       resizeAgain = false;
       updateOverviewImage();
     }
+    else
+    {
+      lastMiniMe = miniMe;
+    }
+
+    setBoxPosition();
   }
 
-  /**
-   * DOCUMENT ME!
+  /*
+   * Build the overview panel image
    */
-  public void setBoxPosition()
+  private void buildImage(float sampleRow, float sampleCol)
   {
-    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-    int fullsizeHeight = (av.alignment.getHeight() + av.alignment
-            .getHiddenSequences().getSize())
-            * av.getCharHeight();
+    int lastcol = -1;
+    int lastrow = -1;
+    int color = Color.white.getRGB();
 
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
+    SequenceI seq = null;
 
-    if (av.hasHiddenColumns)
+    final boolean hasHiddenCols = av.hasHiddenColumns();
+    boolean hiddenRow = false;
+    // get hidden row and hidden column map once at beginning.
+    // clone featureRenderer settings to avoid race conditions... if state is
+    // updated just need to refresh again
+    for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
     {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
+      boolean doCopy = true;
+      int currentrow = (int) (row * sampleRow);
+      if (currentrow != lastrow)
+      {
+        doCopy = false;
 
-    int startSeq = av.startSeq;
-    int endSeq = av.endSeq;
+        lastrow = currentrow;
 
-    if (av.hasHiddenRows)
-    {
-      startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(
-              startSeq);
+        // get the sequence which would be at alignment index 'lastrow' if no
+        // columns were hidden, and determine whether it is hidden or not
+        hiddenRow = av.getAlignment().isHidden(lastrow);
+        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
+      }
 
-      endSeq = av.alignment.getHiddenSequences()
-              .adjustForHiddenSeqs(endSeq);
+      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
+      {
+        if (doCopy)
+        {
+          color = miniMe.getRGB(col, row - 1);
+        }
+        else if ((int) (col * sampleCol) != lastcol
+                || (int) (row * sampleRow) != lastrow)
+        {
+          lastcol = (int) (col * sampleCol);
+          color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols,
+                  lastcol);
+        }
+        // else we just use the color we already have , so don't need to set it
 
+        miniMe.setRGB(col, row, color);
+      }
     }
+  }
 
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    boxX = (int) (startRes * av.getCharWidth() * scalew);
-    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+  /*
+   * Find the colour of a sequence at a specified column position
+   */
+  private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
+          boolean hiddenRow, boolean hasHiddenCols, int lastcol)
+  {
+    int color;
 
-    if (av.hasHiddenColumns)
+    if (seq == null)
     {
-      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+      color = Color.white.getRGB();
+    }
+    else if (seq.getLength() > lastcol)
+    {
+      color = sr.getResidueBoxColour(seq, lastcol).getRGB();
+
+      if (av.isShowSequenceFeatures())
+      {
+        color = fr.findFeatureColour(color, seq, lastcol);
+      }
     }
     else
     {
-      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+      color = Color.white.getRGB();
     }
 
-    boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+    if (hiddenRow
+            || (hasHiddenCols && !av.getColumnSelection()
+                    .isVisible(lastcol)))
+    {
+      color = new Color(color).darker().darker().getRGB();
+    }
 
-    repaint();
+    return color;
   }
 
   /**
-   * DOCUMENT ME!
+   * Update the overview panel box when the associated alignment panel is
+   * changed
    * 
-   * @param g
-   *                DOCUMENT ME!
    */
+  public void setBoxPosition()
+  {
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+    repaint();
+  }
+
+
+  @Override
   public void paintComponent(Graphics g)
   {
-    if (resizing)
+    if (resizing || resizeAgain)
     {
-      g.setColor(Color.white);
+      if (lastMiniMe == null)
+      {
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
+      }
+      else
+      {
+        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+      }
+      g.setColor(TRANS_GREY);
       g.fillRect(0, 0, getWidth(), getHeight());
     }
-    else if (miniMe != null)
+    else if (lastMiniMe != null)
     {
-      g.drawImage(miniMe, 0, 0, this);
+      g.drawImage(lastMiniMe, 0, 0, this);
+      if (lastMiniMe != miniMe)
+      {
+        g.setColor(TRANS_GREY);
+        g.fillRect(0, 0, getWidth(), getHeight());
+      }
     }
 
     g.setColor(Color.red);
-    g.drawRect(boxX, boxY, boxWidth, boxHeight);
-    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
-
+    od.drawBox(g);
   }
 }