X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=3d5bd1b343a9742da080d0968b38982feab122f9;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=a4b7f06bef72dfbd9d385662896aaecb5ef6c41e;hpb=c5ae36527ac4366160ba09b88e5e74568f71b836;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index a4b7f06..3d5bd1b 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,374 +1,473 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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.*;
-import java.awt.event.*;
-
-public class OverviewPanel
-    extends Panel implements Runnable, MouseMotionListener, MouseListener
-{
-  Image miniMe;
-  AlignViewport av;
-  AlignmentPanel ap;
-  float scalew = 1f;
-  float scaleh = 1f;
-
-  public int width, sequencesHeight;
-  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)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-    setLayout(null);
-    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.vconsensus==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;
-      }
-    }
-
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-    addComponentListener(new ComponentAdapter()
-    {
-
-      public void componentResized(ComponentEvent evt)
-      {
-        if (getSize().width != width ||
-            getSize().height != sequencesHeight + graphHeight)
-        {
-          updateOverviewImage();
-        }
-      }
-    });
-
-    addMouseMotionListener(this);
-
-    addMouseListener(this);
-
-    updateOverviewImage();
-
-  }
-
-
-  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 mouseReleased(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-    ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                         (int) (boxY / scaleh / av.getCharHeight()));
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-    ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                         (int) (boxY / scaleh / av.getCharHeight()));
-
-    repaint();
-    ap.repaint();
-  }
-
-  void checkValid()
-  {
-    if (boxY < 0)
-    {
-      boxY = 0;
-    }
-
-    if (boxY > sequencesHeight - boxHeight)
-    {
-      boxY = sequencesHeight - boxHeight + 1;
-    }
-
-    if (boxX < 0)
-    {
-      boxX = 0;
-    }
-
-    if (boxX > width - boxWidth)
-    {
-      boxX = width - boxWidth;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateOverviewImage()
-  {
-    if (resizing)
-    {
-        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));
-    setBoxPosition();
-
-    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 (av.showSequenceFeatures)
-    {
-      fr.renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
-      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
-      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
-      fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
-    }
-
-    if (getSize().width > 0 && getSize().height > 0)
-    {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
-    }
-
-    setSize(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 = nullFrame.createImage(width, sequencesHeight + graphHeight);
-
-    Graphics mg = miniMe.getGraphics();
-    float sampleCol = (float) alwidth / (float) width;
-    float sampleRow = (float) alheight / (float) sequencesHeight;
-
-    int lastcol=0, lastseq=0;
-    int xstart=0, ystart=0;
-    Color color = Color.yellow;
-    int col, sameRow = 0, sameCol = 0;
-    jalview.datamodel.SequenceI sequence;
-
-    for (int row = 0; row <= sequencesHeight; row++)
-    {
-      if((int)(row*sampleRow)==lastseq)
-      {
-        sameRow ++;
-        continue;
-      }
-
-      sequence = av.getAlignment().getSequenceAt(lastseq);
-
-      for (col = 0; col < width; col++)
-      {
-        if((int)(col*sampleCol) == lastcol)
-        {
-          sameCol ++;
-          continue;
-        }
-
-        lastcol = (int)(col*sampleCol);
-
-        if(sequence.getLength()>lastcol)
-        {
-          color = sr.findSequenceColour(sequence, lastcol);
-
-          if (av.showSequenceFeatures)
-            color = fr.findFeatureColour(color,
-                                        sequence,
-                                        lastcol);
-        }
-        else
-          color = color.white;
-
-        mg.setColor(color);
-        if (sameCol == 1 && sameRow == 1)
-          mg.drawLine(xstart, ystart, xstart, ystart);
-        else
-          mg.fillRect(xstart, ystart, sameCol, sameRow);
-
-        xstart = col;
-        sameCol = 1;
-      }
-
-
-      lastseq = (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();
-
-    resizing = false;
-
-    setBoxPosition();
-
-    if(resizeAgain)
-    {
-      resizeAgain = false;
-      updateOverviewImage();
-    }
-  }
-
-  public void setBoxPosition()
-  {
-    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-    int fullsizeHeight = av.alignment.getHeight() * av.getCharHeight();
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    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();
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    if (miniMe != null)
-    {
-      g.drawImage(miniMe, 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);
-    }
-
-    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 2.8.2b1)
+ * Copyright (C) 2014 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.appletgui;
+
+import jalview.datamodel.AlignmentI;
+
+import java.awt.*;
+import java.awt.event.*;
+
+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 = 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)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+    setLayout(null);
+    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.getAlignment().getWidth()
+            / (float) av.getAlignment().getHeight();
+
+    if (av.getSequenceConsensusHash() == 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;
+      }
+    }
+
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
+    addComponentListener(new ComponentAdapter()
+    {
+
+      @Override
+      public void componentResized(ComponentEvent evt)
+      {
+        if (getSize().width != width
+                || getSize().height != sequencesHeight + graphHeight)
+        {
+          updateOverviewImage();
+        }
+      }
+    });
+
+    addMouseMotionListener(this);
+
+    addMouseListener(this);
+
+    updateOverviewImage();
+
+  }
+
+  @Override
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  @Override
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+
+  @Override
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  @Override
+  public void mouseMoved(MouseEvent evt)
+  {
+  }
+
+  @Override
+  public void mousePressed(MouseEvent evt)
+  {
+    boxX = evt.getX();
+    boxY = evt.getY();
+    checkValid();
+  }
+
+  @Override
+  public void mouseReleased(MouseEvent evt)
+  {
+    boxX = evt.getX();
+    boxY = evt.getY();
+    checkValid();
+  }
+
+  @Override
+  public void mouseDragged(MouseEvent evt)
+  {
+    boxX = evt.getX();
+    boxY = evt.getY();
+    checkValid();
+  }
+
+  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);
+    ap.paintAlignment(false);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateOverviewImage()
+  {
+    if (resizing)
+    {
+      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;
+
+  @Override
+  public void run()
+  {
+    miniMe = null;
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getHeight();
+
+    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));
+
+    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();
+    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;
+    AlignmentI alignment = av.getAlignment();
+    for (row = 0; row <= sequencesHeight; row++)
+    {
+      if ((int) (row * sampleRow) == lastrow)
+      {
+        sameRow++;
+        continue;
+      }
+
+      hiddenRow = false;
+      if (av.hasHiddenRows())
+      {
+        seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        if (seq == null)
+        {
+          int index = alignment.getHiddenSequences()
+                  .findIndexWithoutHiddenSeqs(lastrow);
+
+          seq = alignment.getSequenceAt(index);
+        }
+        else
+        {
+          hiddenRow = true;
+        }
+      }
+      else
+      {
+        seq = alignment.getSequenceAt(lastrow);
+      }
+
+      for (col = 0; col < width; col++)
+      {
+        if ((int) (col * sampleCol) == lastcol
+                && (int) (row * sampleRow) == lastrow)
+        {
+          sameCol++;
+          continue;
+        }
+
+        lastcol = (int) (col * sampleCol);
+
+        if (seq.getLength() > lastcol)
+        {
+          color = sr.getResidueBoxColour(seq, lastcol);
+
+          if (av.showSequenceFeatures)
+          {
+            color = fr.findFeatureColour(color, seq, lastcol);
+          }
+        }
+        else
+        {
+          color = Color.white; // White
+        }
+
+        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);
+        }
+
+        xstart = col;
+        sameCol = 1;
+      }
+      lastrow = (int) (row * sampleRow);
+      ystart = row;
+      sameRow = 1;
+    }
+
+    if (av.getAlignmentConservationAnnotation() != null)
+    {
+      for (col = 0; col < width; col++)
+      {
+        lastcol = (int) (col * sampleCol);
+        {
+          mg.translate(col, sequencesHeight);
+          ap.annotationPanel.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();
+    }
+  }
+
+  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();
+  }
+
+  @Override
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  @Override
+  public void paint(Graphics g)
+  {
+    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);
+    }
+  }
+
+}