X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewCanvas.java;fp=src%2Fjalview%2Fappletgui%2FOverviewCanvas.java;h=dea8ddc6e09c649daa1ca4066f7643dd589470d8;hb=3b5d07562d8974f2fde820a1390c404d8734ebeb;hp=0000000000000000000000000000000000000000;hpb=fd45447c22c4bb229e2383ab8010d3a60a48f86d;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewCanvas.java b/src/jalview/appletgui/OverviewCanvas.java
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+/*
+ * 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.appletgui;
+
+import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.viewmodel.OverviewDimensions;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+
+import javax.swing.JComponent;
+
+public class OverviewCanvas extends JComponent
+{
+  // This is set true if the alignment view changes whilst
+  // the overview is being calculated
+  private volatile boolean restart = false;
+
+  private volatile boolean updaterunning = false;
+
+  private OverviewDimensions od;
+
+  private Image miniMe;
+
+  private Image offscreen;
+
+  private AlignViewport av;
+
+  private AlignmentPanel ap;
+
+  // Can set different properties in this seqCanvas than
+  // main visible SeqCanvas
+  private SequenceRenderer sr;
+
+  private FeatureRenderer fr;
+
+  private Frame nullFrame;
+
+  public OverviewCanvas(OverviewDimensions overviewDims,
+          AlignViewport alignvp, AlignmentPanel alignp)
+  {
+    od = overviewDims;
+    av = alignp.av;
+    ap = alignp;
+
+    nullFrame = new Frame();
+    nullFrame.addNotify();
+
+    sr = new SequenceRenderer(av);
+    sr.graphics = nullFrame.getGraphics();
+    sr.renderGaps = false;
+    sr.forOverview = true;
+    fr = new FeatureRenderer(av);
+  }
+
+  /*
+   * Signals to drawing code that the associated alignment viewport
+   * has changed and a redraw will be required
+   */
+  public boolean restartDraw()
+  {
+    synchronized (this)
+    {
+      if (updaterunning)
+      {
+        restart = true;
+      }
+      else
+      {
+        updaterunning = true;
+      }
+      return restart;
+    }
+  }
+
+  public void draw(boolean showSequenceFeatures, boolean showAnnotation)
+  {
+    miniMe = null;
+
+    if (av.isShowSequenceFeatures())
+    {
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+    }
+
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+
+    miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
+    offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
+
+    Graphics mg = miniMe.getGraphics();
+
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getAbsoluteHeight();
+    float sampleCol = alwidth / (float) od.getWidth();
+    float sampleRow = alheight / (float) od.getSequencesHeight();
+
+    buildImage(sampleRow, sampleCol, mg);
+
+    // check for conservation annotation to make sure overview works for DNA too
+    if (showAnnotation)
+    {
+      for (int col = 0; col < od.getWidth() && !restart; col++)
+      {
+        mg.translate(col, od.getSequencesHeight());
+        ap.annotationPanel.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();
+
+    if (restart)
+    {
+      restart = false;
+      draw(showSequenceFeatures, showAnnotation);
+    }
+    else
+    {
+      updaterunning = false;
+    }
+  }
+
+  /*
+   * Build the overview panel image
+   */
+  private void buildImage(float sampleRow, float sampleCol, Graphics mg)
+  {
+    int lastcol = 0;
+    int lastrow = 0;
+    int xstart = 0;
+    int ystart = 0;
+    Color color = Color.yellow;
+    int sameRow = 0;
+    int sameCol = 0;
+
+    SequenceI seq = null;
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+
+    final boolean hasHiddenCols = av.hasHiddenColumns();
+    boolean hiddenRow = false;
+
+    for (int row = 0; row < od.getSequencesHeight() && !restart; row++)
+    {
+      if ((int) (row * sampleRow) == lastrow)
+      {
+        sameRow++;
+      }
+      else
+      {
+        // 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(); col++)
+        {
+          if ((int) (col * sampleCol) == lastcol
+                  && (int) (row * sampleRow) == lastrow)
+          {
+            sameCol++;
+          }
+          else
+          {
+            lastcol = (int) (col * sampleCol);
+
+            color = getColumnColourFromSequence(seq, hiddenRow,
+                    hasHiddenCols, lastcol, finder);
+
+            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;
+      }
+    }
+  }
+
+  /*
+   * Find the colour of a sequence at a specified column position
+   */
+  private Color getColumnColourFromSequence(
+          jalview.datamodel.SequenceI seq, boolean hiddenRow,
+          boolean hasHiddenCols, int lastcol, FeatureColourFinder finder)
+  {
+    Color color = Color.white;
+    if (seq.getLength() > lastcol)
+    {
+      color = sr.getResidueColour(seq, lastcol, finder);
+    }
+
+    if (hiddenRow
+            || (hasHiddenCols && !av.getColumnSelection()
+                    .isVisible(lastcol)))
+    {
+      color = color.darker().darker();
+    }
+    return color;
+  }
+
+  @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);
+      od.drawBox(og);
+      g.drawImage(offscreen, 0, 0, this);
+    }
+  }
+
+}