X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=c530fdce40088bba6d8aedb7830005dc76023ff8;hb=3965e9e3bc4ca05dcc82b8dc72c380f208c9a1e6;hp=2c67388020d8384241c37a76bebcd20a0440af90;hpb=8635a55d2c94dca49e62d5bda3211cb9e4f31dcc;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 2c67388..c530fdc 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,168 +1,360 @@
-package jalview.gui;
-
-import javax.swing.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import java.awt.*;
-
-public class OverviewPanel extends JPanel
-{
-  BufferedImage miniMe;
-  AlignViewport av;
-  AlignmentPanel ap;
-  float scalew = 1f;
-  float scaleh = 1f;
-
-  int sequencesWidth=400, sequencesHeight=150;
-  int graphHeight=30;
-  int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;
-
-  public OverviewPanel(AlignmentPanel ap, AlignViewport av)
-  {
-    this.av = av;
-    this.ap = ap;
-    setSize(sequencesWidth, sequencesHeight+graphHeight);
-    setLayout(null);
-
-    updateOverviewImage();
-
-    addComponentListener(new ComponentAdapter()
-   {
-
-       public void componentResized(ComponentEvent evt)
-       {
-         if( getWidth()!=sequencesWidth || getHeight()!=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 doMousePressed(MouseEvent evt)
-  {
-    checkValid(evt.getX(), evt.getY());
-    repaint();
-  }
-
-  public void doMouseReleased(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int y = evt.getY();
-    checkValid(x, y);
-    ap.setScrollValues( (int)(x/scalew/av.getCharWidth()), (int)(y/scaleh/av.getCharHeight()) );
-  }
-
-  public void doMouseDragged(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int y = evt.getY();
-    checkValid(x, y);
-    ap.setScrollValues( (int)(x/scalew/av.getCharWidth()), (int)(y/scaleh/av.getCharHeight()) );
-    repaint();
-  }
-
-  void checkValid(int x, int y)
-  {
-
-    if (y < 0)
-      y = 0;
-    if (y > sequencesHeight - boxHeight)
-      y = sequencesHeight- boxHeight;
-
-
-    if (x < 0)
-      x = 0;
-
-    if (x > sequencesWidth - boxWidth)
-      x = sequencesWidth - boxWidth;
-
-    boxX = x;
-    boxY = y;
-  }
-
-  public void updateOverviewImage()
-  {
-   miniMe = null;
-   setPreferredSize (new Dimension(sequencesWidth, sequencesHeight+graphHeight));
-   sequencesWidth=getWidth();
-   sequencesHeight=this.getHeight()-graphHeight;
-
-
-    int fullsizeWidth = (int)(av.getAlignment().getWidth()*av.getCharWidth());
-    int fullsizeHeight = av.getAlignment().getHeight()*av.getCharHeight();
-
-
-    BufferedImage fullSize = new BufferedImage(fullsizeWidth,
-                                               fullsizeHeight,
-                                               BufferedImage.TYPE_INT_RGB);
-
-    BufferedImage consensus = new BufferedImage(fullsizeWidth,
-                                               80,
-                                               BufferedImage.TYPE_INT_RGB);
-
-
-    Graphics g = fullSize.getGraphics();
-    ap.seqPanel.seqCanvas.drawPanel(g,0,av.getAlignment().getWidth(),0,av.getAlignment().getHeight(),0,0,0);
-
-    g = consensus.getGraphics();
-    ap.scorePanel.drawScorePanel(g, fullsizeWidth, 0, av.getAlignment().getWidth());
-
-    try{
-      miniMe = new BufferedImage(sequencesWidth, sequencesHeight + graphHeight,
-                                 BufferedImage.TYPE_INT_RGB);
-      Graphics mg = miniMe.getGraphics();
-
-      mg.drawImage(fullSize, 0, 0, sequencesWidth, sequencesHeight, 0, 0,
-                   fullsizeWidth, fullsizeHeight, this);
-      mg.drawImage(consensus, 0, sequencesHeight, sequencesWidth,
-                   sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);
-
-      scalew = (float) sequencesWidth / (float) fullsizeWidth;
-      scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-      setBoxPosition();
-    }catch(Exception ex)
-    {// most likely the frame size is zero
-      miniMe = null;
-    }
-
-  }
-
-  public void setBoxPosition()
-  {
-      boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);
-      boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);
-      boxWidth = (int) (av.getEndRes() * av.getCharWidth() * scalew) - boxX;
-      boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;
-      repaint();
-
-  }
-
-
-  public void paintComponent(Graphics g)
-  {
-    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);
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+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;
+
+/**
+ * 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
+{
+  private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
+
+  private final AnnotationRenderer renderer = new AnnotationRenderer();
+
+  private OverviewDimensions od;
+
+  private BufferedImage miniMe;
+
+  private BufferedImage lastMiniMe = null;
+
+  private AlignViewport av;
+
+  private AlignmentPanel ap;
+
+  //
+  private 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
+  private SequenceRenderer sr;
+
+  jalview.renderer.seqfeatures.FeatureRenderer fr;
+
+  /**
+   * Creates a new OverviewPanel object.
+   * 
+   * @param alPanel
+   *          The alignment panel which is shown in the overview panel
+   */
+  public OverviewPanel(AlignmentPanel alPanel)
+  {
+    this.av = alPanel.av;
+    this.ap = alPanel;
+    setLayout(null);
+
+    sr = new SequenceRenderer(av);
+    sr.renderGaps = false;
+    sr.forOverview = true;
+    fr = new FeatureRenderer(ap);
+
+    od = new OverviewDimensions(av.getRanges(),
+            (av.isShowAnnotation() && av
+                    .getAlignmentConservationAnnotation() != null));
+
+    addComponentListener(new ComponentAdapter()
+    {
+      @Override
+      public void componentResized(ComponentEvent evt)
+      {
+        if ((getWidth() != od.getWidth())
+                || (getHeight() != (od.getHeight())))
+        {
+          updateOverviewImage();
+        }
+      }
+    });
+
+    addMouseMotionListener(new MouseMotionAdapter()
+    {
+      @Override
+      public void mouseDragged(MouseEvent evt)
+      {
+        if (!av.getWrapAlignment())
+        {
+          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+                  .getAlignment().getHiddenSequences(), av
+                  .getColumnSelection(), av.getRanges());
+          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+        }
+      }
+    });
+
+    addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent evt)
+      {
+        if (!av.getWrapAlignment())
+        {
+          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+                  .getAlignment().getHiddenSequences(), av
+                  .getColumnSelection(), av.getRanges());
+          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+        }
+      }
+    });
+
+    updateOverviewImage();
+  }
+
+  /**
+   * Updates the overview image when the related alignment panel is updated
+   */
+  public void updateOverviewImage()
+  {
+    if (resizing)
+    {
+      resizeAgain = true;
+      return;
+    }
+
+    resizing = true;
+
+    if ((getWidth() > 0) && (getHeight() > 0))
+    {
+      od.setWidth(getWidth());
+      od.setHeight(getHeight());
+    }
+
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+
+    Thread thread = new Thread(this);
+    thread.start();
+    repaint();
+  }
+
+  @Override
+  public void run()
+  {
+    miniMe = null;
+
+    if (av.isShowSequenceFeatures())
+    {
+      fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
+    }
+
+    // why do we need to set preferred size again? was set in
+    // updateOverviewImage
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+
+    miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
+            BufferedImage.TYPE_INT_RGB);
+
+    Graphics mg = miniMe.getGraphics();
+    mg.setColor(Color.orange);
+    mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
+
+    // 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();
+
+    // 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();
+
+    buildImage(sampleRow, sampleCol);
+
+    // check for conservation annotation to make sure overview works for DNA too
+    if (av.isShowAnnotation()
+            && (av.getAlignmentConservationAnnotation() != null))
+    {
+      renderer.updateFromAlignViewport(av);
+      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
+      {
+        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;
+
+    if (resizeAgain)
+    {
+      resizeAgain = false;
+      updateOverviewImage();
+    }
+    else
+    {
+      lastMiniMe = miniMe;
+    }
+
+    setBoxPosition();
+  }
+
+  /*
+   * Build the overview panel image
+   */
+  private void buildImage(float sampleRow, float sampleCol)
+  {
+    int lastcol = -1;
+    int lastrow = -1;
+    int rgbColour = Color.white.getRGB();
+
+    SequenceI seq = null;
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+
+    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++)
+    {
+      boolean doCopy = true;
+      int currentrow = (int) (row * sampleRow);
+      if (currentrow != lastrow)
+      {
+        doCopy = false;
+
+        lastrow = currentrow;
+
+        // get the sequence which would be at alignment index 'lastrow' if no
+        // rows were hidden, and determine whether it is hidden or not
+        hiddenRow = av.getAlignment().isHidden(lastrow);
+        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
+      }
+
+      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
+      {
+        if (doCopy)
+        {
+          rgbColour = miniMe.getRGB(col, row - 1);
+        }
+        else if ((int) (col * sampleCol) != lastcol
+                || (int) (row * sampleRow) != lastrow)
+        {
+          lastcol = (int) (col * sampleCol);
+          rgbColour = getColumnColourFromSequence(seq, hiddenRow,
+                  hasHiddenCols, lastcol, finder);
+        }
+        // else we just use the color we already have , so don't need to set it
+
+        miniMe.setRGB(col, row, rgbColour);
+      }
+    }
+  }
+
+  /*
+   * Find the colour of a sequence at a specified column position
+   */
+  private int getColumnColourFromSequence(
+          jalview.datamodel.SequenceI seq,
+          boolean hiddenRow, boolean hasHiddenCols, int lastcol,
+          FeatureColourFinder finder)
+  {
+    Color color = Color.white;
+
+    if ((seq != null) && (seq.getLength() > lastcol))
+    {
+    	color = sr.getResidueColour(seq, lastcol, finder);
+    }
+
+    if (hiddenRow
+            || (hasHiddenCols && !av.getColumnSelection()
+                    .isVisible(lastcol)))
+    {
+      color = color.darker().darker();
+    }
+
+    return color.getRGB();
+  }
+
+  /**
+   * Update the overview panel box when the associated alignment panel is
+   * changed
+   * 
+   */
+  public void setBoxPosition()
+  {
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
+    repaint();
+  }
+
+
+  @Override
+  public void paintComponent(Graphics g)
+  {
+    if (resizing || resizeAgain)
+    {
+      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 (lastMiniMe != null)
+    {
+      g.drawImage(lastMiniMe, 0, 0, this);
+      if (lastMiniMe != miniMe)
+      {
+        g.setColor(TRANS_GREY);
+        g.fillRect(0, 0, getWidth(), getHeight());
+      }
+    }
+
+    g.setColor(Color.red);
+    od.drawBox(g);
+  }
+}