Merge remote-tracking branch 'origin/develop' into

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index d15ec40..ac2138f 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,7 +20,9 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -69,7 +71,7 @@ public class OverviewPanel extends JPanel implements Runnable
   // main visible SeqCanvas
   private SequenceRenderer sr;
 
-  private jalview.renderer.seqfeatures.FeatureRenderer fr;
+  jalview.renderer.seqfeatures.FeatureRenderer fr;
 
   /**
    * Creates a new OverviewPanel object.
@@ -86,16 +88,9 @@ public class OverviewPanel extends JPanel implements Runnable
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
     sr.forOverview = true;
-    fr = new FeatureRenderer(alPanel);
+    fr = new FeatureRenderer(ap);
 
-    boolean showAnnotation = false;
-    // TODO: in applet this was getSequenceConsensusHash()
-    // check if it makes any functional difference: hconsensus or conservation
-    if (av.getAlignmentConservationAnnotation() == null)
-    {
-      showAnnotation = true;
-    }
-    od = new OverviewDimensions(av, showAnnotation);
+    od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
 
     addComponentListener(new ComponentAdapter()
     {
@@ -117,9 +112,9 @@ public class OverviewPanel extends JPanel implements Runnable
       {
         if (!av.getWrapAlignment())
         {
-          // TODO: feature: jv2.5 detect shift drag and update selection from
-          // it.
-          od.updateViewportFromMouse(evt.getX(), evt.getY());
+          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+                  .getAlignment().getHiddenSequences(), av
+                  .getColumnSelection(), av.getRanges());
           ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
@@ -132,7 +127,9 @@ public class OverviewPanel extends JPanel implements Runnable
       {
         if (!av.getWrapAlignment())
         {
-          od.updateViewportFromMouse(evt.getX(), evt.getY());
+          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+                  .getAlignment().getHiddenSequences(), av
+                  .getColumnSelection(), av.getRanges());
           ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
@@ -156,8 +153,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if ((getWidth() > 0) && (getHeight() > 0))
     {
-      od.setWidth(getWidth()); // width = getWidth();
-      od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
+      od.setWidth(getWidth());
+      od.setHeight(getHeight());
     }
 
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
@@ -204,7 +201,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     buildImage(sampleRow, sampleCol);
 
-    if (av.getAlignmentConservationAnnotation() != null)
+    if (av.isShowAnnotation())
     {
       renderer.updateFromAlignViewport(av);
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
@@ -235,13 +232,17 @@ public class OverviewPanel extends JPanel implements Runnable
     setBoxPosition();
   }
 
+  /*
+   * Build the overview panel image
+   */
   private void buildImage(float sampleRow, float sampleCol)
   {
     int lastcol = -1;
     int lastrow = -1;
-    int color = Color.white.getRGB();
+    int rgbColour = Color.white.getRGB();
 
-    jalview.datamodel.SequenceI seq = null;
+    SequenceI seq = null;
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
 
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
@@ -259,35 +260,27 @@ public class OverviewPanel extends JPanel implements Runnable
         lastrow = currentrow;
 
         // get the sequence which would be at alignment index 'lastrow' if no
-        // columns were hidden, and determine whether it is hidden or not
+        // rows were hidden, and determine whether it is hidden or not
         hiddenRow = av.getAlignment().isHidden(lastrow);
         seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
       }
 
-      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);
+          rgbColour = 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);
+          rgbColour = getColumnColourFromSequence(seq, hiddenRow,
+                  hasHiddenCols, lastcol, finder);
         }
-        // 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
+        // else we just use the color we already have , so don't need to set it
 
-        miniMe.setRGB(col, row, color);
+        miniMe.setRGB(col, row, rgbColour);
       }
     }
   }
@@ -295,33 +288,26 @@ public class OverviewPanel extends JPanel implements Runnable
   /*
    * Find the colour of a sequence at a specified column position
    */
-  private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
-          boolean hiddenRow, boolean hasHiddenCols, int lastcol)
+  private int getColumnColourFromSequence(
+          jalview.datamodel.SequenceI seq,
+          boolean hiddenRow, boolean hasHiddenCols, int lastcol,
+          FeatureColourFinder finder)
   {
-    int color;
+    Color color = Color.white;
 
-    if (seq.getLength() > lastcol)
+    if ((seq != null) && (seq.getLength() > lastcol))
     {
-      color = sr.getResidueBoxColour(seq, lastcol).getRGB();
-
-      if (av.isShowSequenceFeatures())
-      {
-        color = fr.findFeatureColour(color, seq, lastcol);
-      }
-    }
-    else
-    {
-      color = Color.white.getRGB(); // White
+       color = sr.getResidueColour(seq, lastcol, finder);
     }
 
     if (hiddenRow
             || (hasHiddenCols && !av.getColumnSelection()
                     .isVisible(lastcol)))
     {
-      color = new Color(color).darker().darker().getRGB();
+      color = color.darker().darker();
     }
 
-    return color;
+    return color.getRGB();
   }
 
   /**
@@ -331,7 +317,8 @@ public class OverviewPanel extends JPanel implements Runnable
    */
   public void setBoxPosition()
   {
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
     repaint();
   }
 
@@ -362,7 +349,7 @@ public class OverviewPanel extends JPanel implements Runnable
         g.fillRect(0, 0, getWidth(), getHeight());
       }
     }
-    // TODO: render selected regions
+
     g.setColor(Color.red);
     od.drawBox(g);
   }