X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewCanvas.java;h=07f591971754be002438eb8392145dba1f51bdec;hb=2a86b2b3d7b5e8ad3f23d7895637cbfb24685fac;hp=2fbdeabf2395258ad4874d331e956b6a7b49f1a7;hpb=536a4a9c407a4c07b71e86e75135eaa2ba5e8850;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewCanvas.java b/src/jalview/appletgui/OverviewCanvas.java
index 2fbdeab..07f5919 100644
--- a/src/jalview/appletgui/OverviewCanvas.java
+++ b/src/jalview/appletgui/OverviewCanvas.java
@@ -20,19 +20,18 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.SequenceI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
+import java.awt.Component;
 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
+public class OverviewCanvas extends Component
 {
   // This is set true if the alignment view changes whilst
   // the overview is being calculated
@@ -42,17 +41,15 @@ public class OverviewCanvas extends JComponent
 
   private OverviewDimensions od;
 
+  private OverviewRenderer or = null;
+
   private Image miniMe;
 
   private Image offscreen;
 
   private AlignViewport av;
 
-  // Can set different properties in this seqCanvas than
-  // main visible SeqCanvas
-  private SequenceRenderer sr;
-
-  private FeatureRenderer fr;
+  private jalview.renderer.seqfeatures.FeatureRenderer fr;
 
   private Frame nullFrame;
 
@@ -65,16 +62,23 @@ public class OverviewCanvas extends JComponent
     nullFrame = new Frame();
     nullFrame.addNotify();
 
-    sr = new SequenceRenderer(av);
-    sr.graphics = nullFrame.getGraphics();
-    sr.renderGaps = false;
-    sr.forOverview = true;
-    fr = new FeatureRenderer(av);
+    fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
+  }
+
+  /**
+   * Update the overview dimensions object used by the canvas (e.g. if we change
+   * from showing hidden columns to hiding them or vice versa)
+   * 
+   * @param overviewDims
+   */
+  public void resetOviewDims(OverviewDimensions overviewDims)
+  {
+    od = overviewDims;
   }
 
-  /*
-   * Signals to drawing code that the associated alignment viewport
-   * has changed and a redraw will be required
+  /**
+   * Signals to drawing code that the associated alignment viewport has changed
+   * and a redraw will be required
    */
   public boolean restartDraw()
   {
@@ -83,6 +87,10 @@ public class OverviewCanvas extends JComponent
       if (updaterunning)
       {
         restart = true;
+        if (or != null)
+        {
+          or.setRedraw(true);
+        }
       }
       else
       {
@@ -93,49 +101,41 @@ public class OverviewCanvas extends JComponent
   }
 
   public void draw(boolean showSequenceFeatures, boolean showAnnotation,
-          AlignmentPanel ap)
+          FeatureRenderer transferRenderer)
   {
     miniMe = null;
 
-    if (av.isShowSequenceFeatures())
+    if (showSequenceFeatures)
     {
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+      fr.transferSettings(transferRenderer);
     }
 
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
+    or = new OverviewRenderer(fr, od, av.getAlignment(),
+            av.getResidueShading(), new OverviewResColourFinder());
     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();
+    miniMe = or.draw(od.getRows(av.getAlignment()),
+            od.getColumns(av.getAlignment()));
 
-    buildImage(sampleRow, sampleCol, mg);
+    Graphics mg = miniMe.getGraphics();
 
-    // check for conservation annotation to make sure overview works for DNA too
+    // checks 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());
-      }
+      mg.translate(0, od.getSequencesHeight());
+      or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+              od.getGraphHeight(), od.getColumns(av.getAlignment()));
+      mg.translate(0, -od.getSequencesHeight());
     }
-    System.gc();
 
     if (restart)
     {
       restart = false;
-      draw(showSequenceFeatures, showAnnotation, ap);
+      draw(showSequenceFeatures, showAnnotation, transferRenderer);
     }
     else
     {
@@ -143,95 +143,6 @@ public class OverviewCanvas extends JComponent
     }
   }
 
-  /*
-   * 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.getAlignment().getHiddenColumns()
-                    .isVisible(lastcol)))
-    {
-      color = color.darker().darker();
-    }
-    return color;
-  }
-
   @Override
   public void update(Graphics g)
   {
@@ -251,4 +162,12 @@ public class OverviewCanvas extends JComponent
     }
   }
 
+  /**
+   * Nulls references to protect against potential memory leaks
+   */
+  void dispose()
+  {
+    od = null;
+  }
+
 }