X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=9397cebbeaae42116937602076ff815fb8e382d4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=3cd66851b33bddd1ff3bdd75ad1de51c3c35e84f;hpb=0ed60e8b689189f54e81d62780a2285576d36de3;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 3cd6685..9397ceb 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,192 +1,483 @@
-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, sequencesHeight;
-  int graphHeight=30;
-  int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;
-
-  public OverviewPanel(AlignmentPanel ap, AlignViewport av)
-  {
-    this.av = av;
-    this.ap = ap;
-
-    // scale the initial size of overviewpanel to shape of alignment
-
-    float initialScale = (float)av.getAlignment().getWidth()/(float)av.getAlignment().getHeight();
-    if(av.getAlignment().getWidth() > av.getAlignment().getHeight())
-    {
-      // wider
-      sequencesWidth = 400;
-      sequencesHeight = (int)(400f/initialScale);
-    }
-    else
-    {
-      // taller
-      sequencesWidth = (int)(400f*initialScale);
-      sequencesHeight = 300;
-    }
-
-
-
-    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()
-  {
-
-  boolean oldRenderGaps = av.renderGaps;
-  av.setRenderGaps(false);
-   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;
-    }
-
-    av.setRenderGaps(oldRenderGaps);
-
-  }
-
-  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 2.9)
+ * Copyright (C) 2015 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.renderer.AnnotationRenderer;
+
+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!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class OverviewPanel extends JPanel implements Runnable
+{
+  BufferedImage miniMe;
+
+  AlignViewport av;
+
+  AlignmentPanel ap;
+
+  final AnnotationRenderer renderer = new AnnotationRenderer();
+
+  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;
+
+  jalview.renderer.seqfeatures.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.getAlignment().getWidth()
+            / (float) av.getAlignment().getHeight();
+
+    if (av.getAlignmentConservationAnnotation() == null)
+    {
+      graphHeight = 0;
+    }
+
+    if (av.getAlignment().getWidth() > av.getAlignment().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()
+    {
+      @Override
+      public void componentResized(ComponentEvent evt)
+      {
+        if ((getWidth() != width)
+                || (getHeight() != (sequencesHeight + graphHeight)))
+        {
+          updateOverviewImage();
+        }
+      }
+    });
+
+    addMouseMotionListener(new MouseMotionAdapter()
+    {
+      @Override
+      public void mouseDragged(MouseEvent evt)
+      {
+        if (!av.getWrapAlignment())
+        {
+          // TODO: feature: jv2.5 detect shift drag and update selection from
+          // it.
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
+        }
+      }
+    });
+
+    addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent evt)
+      {
+        if (!av.getWrapAlignment())
+        {
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
+        }
+      }
+    });
+
+    updateOverviewImage();
+  }
+
+  /**
+   * 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.getAlignment().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!
+   */
+  @Override
+  public void run()
+  {
+    miniMe = null;
+
+    if (av.isShowSequenceFeatures())
+    {
+      fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
+    }
+
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getHeight()
+            + av.getAlignment().getHiddenSequences().getSize();
+
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+
+    int fullsizeWidth = alwidth * av.getCharWidth();
+    int fullsizeHeight = alheight * av.getCharHeight();
+
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+            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;
+    final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+            .hasHiddenColumns();
+    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 (hasHiddenRows)
+      {
+        seq = av.getAlignment().getHiddenSequences()
+                .getHiddenSequence(lastrow);
+        if (seq == null)
+        {
+          int index = av.getAlignment().getHiddenSequences()
+                  .findIndexWithoutHiddenSeqs(lastrow);
+
+          seq = av.getAlignment().getSequenceAt(index);
+        }
+        else
+        {
+          hiddenRow = true;
+        }
+      }
+      else
+      {
+        seq = av.getAlignment().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();
+
+          if (av.isShowSequenceFeatures())
+          {
+            color = fr.findFeatureColour(color, seq, lastcol);
+          }
+        }
+        else
+        {
+          color = -1; // White
+        }
+
+        if (hiddenRow
+                || (hasHiddenCols && !av.getColumnSelection().isVisible(
+                        lastcol)))
+        {
+          color = new Color(color).darker().darker().getRGB();
+        }
+
+        miniMe.setRGB(col, row, color);
+
+      }
+    }
+
+    if (av.getAlignmentConservationAnnotation() != null)
+    {
+      renderer.updateFromAlignViewport(av);
+      for (col = 0; col < width; col++)
+      {
+        lastcol = (int) (col * sampleCol);
+        {
+          mg.translate(col, sequencesHeight);
+          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+                  av.getAlignmentConservationAnnotation().annotations,
+                  (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.getAlignment().getWidth() * av.getCharWidth();
+    int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
+            .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.getAlignment().getHiddenSequences()
+              .adjustForHiddenSeqs(startSeq);
+
+      endSeq = av.getAlignment().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!
+   */
+  @Override
+  public void paintComponent(Graphics g)
+  {
+    if (resizing)
+    {
+      g.setColor(Color.white);
+      g.fillRect(0, 0, getWidth(), getHeight());
+    }
+    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);
+
+  }
+}