Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / gui / OverviewCanvas.java

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 8e67992..0827208 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -20,22 +20,35 @@
  */
 package jalview.gui;
 
-import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
-import jalview.renderer.OverviewRenderer;
-import jalview.renderer.OverviewResColourFinder;
-import jalview.viewmodel.OverviewDimensions;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Graphics;
 import java.awt.image.BufferedImage;
+import java.awt.image.RasterFormatException;
 
 import javax.swing.JPanel;
 
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
+import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+
 public class OverviewCanvas extends JPanel
 {
+  public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
+
+  public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+
+  public static final Color OVERVIEW_DEFAULT_RESIDUE = Color.white;
+
+  public static final Color OVERVIEW_DEFAULT_LEGACY_RESIDUE = Color.lightGray;
+
+  public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
+          .darker();
+
   private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
 
   // This is set true if the alignment view changes whilst
@@ -79,10 +92,13 @@ public class OverviewCanvas extends JPanel
 
     boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
     Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+            OVERVIEW_DEFAULT_GAP);
     Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
-    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
+            OVERVIEW_DEFAULT_HIDDEN);
+    Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE
+            : OVERVIEW_DEFAULT_RESIDUE;
+
+    cf = new OverviewResColourFinder(gapCol, residueCol, hiddenCol);
 
     setSize(od.getWidth(), od.getHeight());
   }
@@ -182,7 +198,7 @@ public class OverviewCanvas extends JPanel
   @Override
   public void paintComponent(Graphics g)
   {
-    //super.paintComponent(g);
+    // super.paintComponent(g);
 
     if (restart)
     {
@@ -207,31 +223,39 @@ public class OverviewCanvas extends JPanel
       {
         // if there is annotation, scale the alignment and annotation
         // separately
-        if (od.getGraphHeight() > 0 
-                       && od.getSequencesHeight() > 0  // BH 2019
-                       )
+        if (od.getGraphHeight() > 0 && od.getSequencesHeight() > 0 // BH 2019
+        )
         {
-          BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
-                  od.getWidth(), od.getSequencesHeight());
-          BufferedImage bottomImage = lastMiniMe.getSubimage(0,
-                  od.getSequencesHeight(), od.getWidth(),
-                  od.getGraphHeight());
-
-          // must be done at this point as we rely on using old width/height
-          // above, and new width/height below
-          od.setWidth(getWidth());
-          od.setHeight(getHeight());
-
-          // stick the images back together so lastMiniMe is consistent in the
-          // event of a repaint - BUT probably not thread safe
-          lastMiniMe = new BufferedImage(od.getWidth(), od.getHeight(),
-                  BufferedImage.TYPE_INT_RGB);
-          Graphics lg = lastMiniMe.getGraphics();
-          lg.drawImage(topImage, 0, 0, od.getWidth(),
-                  od.getSequencesHeight(), null);
-          lg.drawImage(bottomImage, 0, od.getSequencesHeight(),
-                  od.getWidth(), od.getGraphHeight(), this);
-          lg.dispose();
+          try
+          {
+            BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
+                    od.getWidth(), od.getSequencesHeight());
+            BufferedImage bottomImage = lastMiniMe.getSubimage(0,
+                    od.getSequencesHeight(), od.getWidth(),
+                    od.getGraphHeight());
+
+            // must be done at this point as we rely on using old width/height
+            // above, and new width/height below
+            od.setWidth(getWidth());
+            od.setHeight(getHeight());
+
+            // stick the images back together so lastMiniMe is consistent in the
+            // event of a repaint - BUT probably not thread safe
+            lastMiniMe = new BufferedImage(od.getWidth(), od.getHeight(),
+                    BufferedImage.TYPE_INT_RGB);
+            Graphics lg = lastMiniMe.getGraphics();
+            lg.drawImage(topImage, 0, 0, od.getWidth(),
+                    od.getSequencesHeight(), null);
+            lg.drawImage(bottomImage, 0, od.getSequencesHeight(),
+                    od.getWidth(), od.getGraphHeight(), this);
+            lg.dispose();
+          } catch (RasterFormatException e)
+          {
+            Console.debug(
+                    "Scaling miscalculation resizing Overview window");
+            od.setWidth(getWidth());
+            od.setHeight(getHeight());
+          }
         }
         else
         {
@@ -250,13 +274,12 @@ public class OverviewCanvas extends JPanel
     {
       g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
     }
-    
+
     // draw the box
     g.setColor(Color.red);
     od.drawBox(g);
   }
 
-
   public void dispose()
   {
     dispose = true;
@@ -270,4 +293,31 @@ public class OverviewCanvas extends JPanel
       }
     }
   }
+
+  public Color getGapColour()
+  {
+    return cf.getGapColour();
+  }
+
+  public Color getHiddenColour()
+  {
+    return cf.getHiddenColour();
+  }
+
+  public Color getResidueColour()
+  {
+    return cf.getResidueColour();
+  }
+
+  /**
+   * Sets the colours to use for gaps, residues and hidden regions
+   * 
+   * @param gaps
+   * @param residues
+   * @param hidden
+   */
+  public void setColours(Color gaps, Color residues, Color hidden)
+  {
+    cf = new OverviewResColourFinder(gaps, residues, hidden);
+  }
 }