JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / appletgui / SplitFrame.java

diff --git a/src/jalview/appletgui/SplitFrame.java b/src/jalview/appletgui/SplitFrame.java
index 59b66c6..cbad148 100644 (file)
--- a/src/jalview/appletgui/SplitFrame.java
+++ b/src/jalview/appletgui/SplitFrame.java
@@ -1,16 +1,36 @@
+/*
+ * 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 java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.GridLayout;
-import java.awt.Panel;
-
-import jalview.analysis.AlignmentUtils;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
 import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.Panel;
 
 public class SplitFrame extends EmbmenuFrame
 {
@@ -23,12 +43,14 @@ public class SplitFrame extends EmbmenuFrame
   private Panel outermost;
 
   /**
-   * Constructor
+   * Constructs the split frame placing cdna in the top half. No 'alignment' is
+   * performed here, this should be done by the calling client if wanted.
    */
   public SplitFrame(AlignFrame af1, AlignFrame af2)
   {
-    topFrame = af1;
-    bottomFrame = af2;
+    boolean af1IsNucleotide = af1.viewport.getAlignment().isNucleotide();
+    topFrame = af1IsNucleotide ? af1 : af2;
+    bottomFrame = topFrame == af1 ? af2 : af1;
     init();
   }
 
@@ -49,25 +71,20 @@ public class SplitFrame extends EmbmenuFrame
     final AlignViewport bottomViewport = bottomFrame.viewport;
     final AlignmentI topAlignment = topViewport.getAlignment();
     final AlignmentI bottomAlignment = bottomViewport.getAlignment();
-    AlignViewport cdna = topAlignment.isNucleotide() ? topViewport
+    AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
             : (bottomAlignment.isNucleotide() ? bottomViewport : null);
-    AlignViewport protein = !topAlignment.isNucleotide() ? topViewport
+    AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
             : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
 
-    boolean mapped = AlignmentUtils.mapProteinToCdna(
-            protein.getAlignment(), cdna.getAlignment());
-    if (mapped)
-    {
-      final StructureSelectionManager ssm = StructureSelectionManager
-              .getStructureSelectionManager(topViewport.applet);
-      ssm.addMappings(protein.getAlignment().getCodonFrames());
-      topViewport.setCodingComplement(bottomViewport);
-      ssm.addCommandListener(cdna);
-      ssm.addCommandListener(protein);
-    }
+    final StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(topViewport.applet);
+    ssm.registerMappings(protein.getAlignment().getCodonFrames());
+    topViewport.setCodingComplement(bottomViewport);
+    ssm.addCommandListener(cdna);
+    ssm.addCommandListener(protein);
 
     /*
-     * Now mappings exist, can compute cDNA consensus on protein alignment
+     * Compute cDNA consensus on protein alignment
      */
     protein.initComplementConsensus();
     AlignmentViewPanel ap = topAlignment.isNucleotide() ? bottomFrame.alignPanel
@@ -99,9 +116,9 @@ public class SplitFrame extends EmbmenuFrame
    */
   protected void adjustLayout()
   {
-    AlignViewport cdna = topFrame.getAlignViewport().getAlignment()
+    AlignmentViewport cdna = topFrame.getAlignViewport().getAlignment()
             .isNucleotide() ? topFrame.viewport : bottomFrame.viewport;
-    AlignViewport protein = cdna == topFrame.viewport ? bottomFrame.viewport
+    AlignmentViewport protein = cdna == topFrame.viewport ? bottomFrame.viewport
             : topFrame.viewport;
 
     /*
@@ -126,12 +143,13 @@ public class SplitFrame extends EmbmenuFrame
     }
 
     /*
-     * Expand protein to 3 times character width of dna
+     * Scale protein to either 1 or 3 times character width of dna
      */
     if (protein != null && cdna != null)
     {
       ViewStyleI vs = protein.getViewStyle();
-      vs.setCharWidth(3 * vs.getCharWidth());
+      int scale = vs.isScaleProteinAsCdna() ? 3 : 1;
+      vs.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
       protein.setViewStyle(vs);
     }
   }
@@ -152,6 +170,8 @@ public class SplitFrame extends EmbmenuFrame
     panel.add(menuPanel, BorderLayout.NORTH);
     panel.add(af.statusBar, BorderLayout.SOUTH);
     panel.add(af.alignPanel, BorderLayout.CENTER);
+
+    af.setSplitFrame(this);
   }
 
   /**
@@ -187,11 +207,30 @@ public class SplitFrame extends EmbmenuFrame
     else
     {
       this.add(outermost);
-      int width = Math.max(topFrame.frameWidth,
-              bottomFrame.frameWidth);
+      int width = Math.max(topFrame.frameWidth, bottomFrame.frameWidth);
       int height = topFrame.frameHeight + bottomFrame.frameHeight;
       jalview.bin.JalviewLite
               .addFrame(this, this.getTitle(), width, height);
     }
   }
+
+  /**
+   * Returns the contained AlignFrame complementary to the one given (or null if
+   * no match to top or bottom component).
+   * 
+   * @param af
+   * @return
+   */
+  public AlignFrame getComplement(AlignFrame af)
+  {
+    if (topFrame == af)
+    {
+      return bottomFrame;
+    }
+    else if (bottomFrame == af)
+    {
+      return topFrame;
+    }
+    return null;
+  }
 }