X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=d87285c63079761b69151e3125d5724bbbf8f9fc;hb=fce4313f5daea7f5b5914bfaefd11e946664942c;hp=c690490fb56614dca51184aec76a7b8d7a7c1263;hpb=d27f1ffddb3578acb603f4fa845eb499c11cde10;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index c690490..d87285c 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,377 +1,385 @@
-/*
- * 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.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class OverviewPanel extends JPanel implements Runnable
-{
-    BufferedImage miniMe;
-    AlignViewport av;
-    AlignmentPanel ap;
-    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;
-    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 );
-        fr = new FeatureRenderer(av);
-
-
-        // 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;
-            }
-        }
-
-        addComponentListener(new ComponentAdapter()
-            {
-                public void componentResized(ComponentEvent evt)
-                {
-                    if ((getWidth() != width) ||
-                            (getHeight() != (sequencesHeight + graphHeight)))
-                    {
-                        updateOverviewImage();
-                    }
-                }
-            });
-
-        addMouseMotionListener(new MouseMotionAdapter()
-            {
-                public void mouseDragged(MouseEvent evt)
-                {
-                  if(!av.wrapAlignment)
-                    doMouseDragged(evt);
-                }
-            });
-
-        addMouseListener(new MouseAdapter()
-            {
-                public void mousePressed(MouseEvent evt)
-                {
-                  if(!av.wrapAlignment)
-                    doMousePressed(evt);
-                }
-
-                public void mouseReleased(MouseEvent evt)
-                {
-                  if(!av.wrapAlignment)
-                    doMouseReleased(evt);
-                }
-            });
-
-        updateOverviewImage();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMousePressed(MouseEvent evt)
-    {
-        boxX = evt.getX();
-        boxY = evt.getY();
-
-        checkValid();
-        repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseReleased(MouseEvent evt)
-    {
-        boxX = evt.getX();
-        boxY = evt.getY();
-        checkValid();
-
-        ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),
-                (int) (boxY / scaleh / av.getCharHeight()));
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseDragged(MouseEvent evt)
-    {
-        boxX = evt.getX();
-        boxY = evt.getY();
-        checkValid();
-
-        ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
-                           (int) (boxY / scaleh / av.getCharHeight()));
-       repaint();
-    }
-
-    /**
-     * 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))
-        {
-            boxX = width - boxWidth;
-        }
-    }
-
-    /**
-     * 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));
-        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;
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void run()
-    {
-        miniMe = null;
-
-       if (av.showSequenceFeatures)
-       {
-         fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().
-             featuresDisplayed;
-         fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
-         fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
-         fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
-       }
-
-        int alwidth = av.alignment.getWidth();
-        int alheight = av.alignment.getHeight();
-
-        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;
-        Color color = Color.white;
-        for (int col = 0; col < width; col++)
-        {
-          for (int row = 0; row < sequencesHeight; row++)
-          {
-            if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
-            {
-              miniMe.setRGB(col,row,color.getRGB());
-              continue;
-            }
-
-            lastrow = (int)(row*sampleRow);
-            lastcol = (int)(col*sampleCol);
-
-            if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)
-            {
-             color = sr.getResidueBoxColour(
-                av.alignment.getSequenceAt(lastrow), lastcol);
-
-             if(av.showSequenceFeatures)
-                 color = fr.findFeatureColour(color,  av.alignment.getSequenceAt(lastrow),
-                                             lastcol);
-
-            }
-
-            miniMe.setRGB(col,row,color.getRGB());
-
-            if (av.conservation != null)
-            {
-              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();
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    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();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
-    {
-        if (miniMe != null && !resizing)
-        {
-          g.drawImage(miniMe, 0, 0, this);
-        }
-        else
-        {
-          g.setColor(Color.white);
-          g.fillRect(0, 0, getWidth(), getHeight());
-          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 ($$Version-Rel$$)
+ * 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.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;
+
+/**
+ * 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;
+
+  private 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(alPanel);
+
+    od = new OverviewDimensions(av);
+
+    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())
+        {
+          // TODO: feature: jv2.5 detect shift drag and update selection from
+          // it.
+          od.setBoxPositionByMouse(evt.getX(), evt.getY());
+          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+        }
+      }
+    });
+
+    addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent evt)
+      {
+        if (!av.getWrapAlignment())
+        {
+          od.setBoxPositionByMouse(evt.getX(), evt.getY());
+          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()); // width = getWidth();
+      od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
+    }
+
+    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 scale based on current alignment width and height
+    od.updateScales();
+
+    // 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().getHeight()
+            + av.getAlignment().getHiddenSequences().getSize();
+
+    // 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);
+
+    if (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();
+  }
+
+  private void buildImage(float sampleRow, float sampleCol)
+  {
+    int lastcol = -1;
+    int lastrow = -1;
+    int color = Color.white.getRGB();
+
+    jalview.datamodel.SequenceI seq = null;
+    final boolean hasHiddenRows = av.hasHiddenRows();
+    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;
+
+        hiddenRow = false;
+        // should be method(s) in Alignment
+        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);
+        }
+        // end of Alignment method(s)
+      }
+
+      if (seq == null)
+      {
+        System.out.println(lastrow + " null");
+        continue;
+      }
+
+      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 if ((int) (col * sampleCol) == lastcol && (int) (row *
+        // sampleRow) == lastrow))
+        // we just use the color we already have , so don't need to set it
+
+        miniMe.setRGB(col, row, color);
+      }
+    }
+  }
+
+  /*
+   * 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 (seq.getLength() > lastcol)
+    {
+      color = sr.getResidueBoxColour(seq, lastcol).getRGB();
+
+      if (av.isShowSequenceFeatures())
+      {
+        color = fr.findFeatureColour(color, seq, lastcol);
+      }
+    }
+    else
+    {
+      color = Color.white.getRGB(); // White
+    }
+
+    if (hiddenRow
+            || (hasHiddenCols && !av.getColumnSelection()
+                    .isVisible(lastcol)))
+    {
+      color = new Color(color).darker().darker().getRGB();
+    }
+
+    return color;
+  }
+
+  /**
+   * Update the overview panel box when the associated alignment panel is
+   * changed
+   * 
+   */
+  public void setBoxPosition()
+  {
+    od.setBoxPosition();
+    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());
+      }
+    }
+    // TODO: render selected regions
+    g.setColor(Color.red);
+    od.drawBox(g);
+  }
+}