From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 23 Feb 2015 15:48:13 +0000 (+0000)
Subject: JAL-845 repaint of complementary selection (applet)
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4618ad78a2bb127995d1eb92fd2286d24ec3c87a;p=jalview.git

JAL-845 repaint of complementary selection (applet)
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index dc4539e..447f5e3 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -23,6 +23,7 @@ package jalview.appletgui;
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
@@ -64,6 +65,7 @@ import jalview.schemes.TurnColourScheme;
 import jalview.schemes.ZappoColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -1585,6 +1587,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return originalSource;
   }
 
+  /**
+   * Move the currently selected sequences up or down one position in the
+   * alignment
+   * 
+   * @param up
+   */
   public void moveSelectedSequences(boolean up)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
@@ -1595,6 +1603,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             up ? null : viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true);
+
+    /*
+     * Also move cDNA/protein complement sequences
+     */
+    AlignViewportI complement = viewport.getCodingComplement();
+    if (complement != null)
+    {
+      SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
+              viewport, complement);
+      complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
+              up ? null : complement.getHiddenRepSequences(), up);
+      // TODO need to trigger a repaint of the complementary panel - how?
+      // would prefer to handle in SplitFrame but it is not overriding key
+      // listener chiz
+    }
   }
 
   synchronized void slideSequences(boolean right, int size)
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 8a526ac..090779e 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1965,8 +1965,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     av.setColumnSelection(cs);
     av.isColSelChanged(true);
   
-    firePropertyChange("alignment", null, av.getAlignment().getSequences());
-    // PaintRefresher.Refresh(this, av.getSequenceSetId());
+    ap.scalePanelHolder.repaint();
+    ap.repaint();
   
     return true;
   }
diff --git a/src/jalview/appletgui/SplitFrame.java b/src/jalview/appletgui/SplitFrame.java
index 4f61f4a..fb11a5c 100644
--- a/src/jalview/appletgui/SplitFrame.java
+++ b/src/jalview/appletgui/SplitFrame.java
@@ -8,8 +8,12 @@ import jalview.datamodel.AlignmentI;
 import jalview.structure.StructureSelectionManager;
 
 import java.awt.BorderLayout;
+import java.awt.Component;
 import java.awt.GridLayout;
+import java.awt.MouseInfo;
 import java.awt.Panel;
+import java.awt.Point;
+import java.awt.Rectangle;
 
 public class SplitFrame extends EmbmenuFrame
 {
@@ -39,16 +43,7 @@ public class SplitFrame extends EmbmenuFrame
    */
   public void init()
   {
-    setMenuBar(null);
-    outermost = new Panel(new GridLayout(2, 1));
-
-    Panel topPanel = new Panel();
-    Panel bottomPanel = new Panel();
-    outermost.add(topPanel);
-    outermost.add(bottomPanel);
-
-    addAlignFrameComponents(topFrame, topPanel);
-    addAlignFrameComponents(bottomFrame, bottomPanel);
+    constructSplit();
 
     /*
      * Try to make and add dna/protein sequence mappings
@@ -74,16 +69,40 @@ public class SplitFrame extends EmbmenuFrame
       ssm.addCommandListener(protein);
     }
 
-    /*
-     * Expand protein to 3 times character width of dna
-     */
+    setCharacterWidth(protein, cdna);
+  }
+
+  /**
+   * 
+   */
+  protected void constructSplit()
+  {
+    setMenuBar(null);
+    outermost = new Panel(new GridLayout(2, 1));
+
+    Panel topPanel = new Panel();
+    Panel bottomPanel = new Panel();
+    outermost.add(topPanel);
+    outermost.add(bottomPanel);
+
+    addAlignFrameComponents(topFrame, topPanel);
+    addAlignFrameComponents(bottomFrame, bottomPanel);
+  }
+
+  /**
+   * Expand protein to 3 times character width of dna
+   * 
+   * @param protein
+   * @param cdna
+   */
+  protected void setCharacterWidth(AlignViewport protein, AlignViewport cdna)
+  {
     if (protein != null && cdna != null)
     {
       ViewStyleI vs = protein.getViewStyle();
       vs.setCharWidth(3 * vs.getCharWidth());
       protein.setViewStyle(vs);
     }
-
   }
 
   /**