JAL-1681 ensure cDNA consensus computed on startup (project/applet)

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

diff --git a/src/jalview/appletgui/SplitFrame.java b/src/jalview/appletgui/SplitFrame.java
index ccfa432..68da6cf 100644 (file)
--- a/src/jalview/appletgui/SplitFrame.java
+++ b/src/jalview/appletgui/SplitFrame.java
@@ -1,17 +1,17 @@
 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.analysis.AlignmentUtils.MappingResult;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
 import jalview.structure.StructureSelectionManager;
 
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.GridLayout;
-import java.awt.Panel;
-
 public class SplitFrame extends EmbmenuFrame
 {
   private static final long serialVersionUID = 1L;
@@ -54,9 +54,9 @@ public class SplitFrame extends EmbmenuFrame
     AlignViewport protein = !topAlignment.isNucleotide() ? topViewport
             : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
 
-    MappingResult mapped = AlignmentUtils.mapProteinToCdna(
+    boolean mapped = AlignmentUtils.mapProteinToCdna(
             protein.getAlignment(), cdna.getAlignment());
-    if (mapped != MappingResult.NotMapped)
+    if (mapped)
     {
       final StructureSelectionManager ssm = StructureSelectionManager
               .getStructureSelectionManager(topViewport.applet);
@@ -64,6 +64,14 @@ public class SplitFrame extends EmbmenuFrame
       topViewport.setCodingComplement(bottomViewport);
       ssm.addCommandListener(cdna);
       ssm.addCommandListener(protein);
+
+      /*
+       * Now mappings exist, can compute cDNA consensus on protein alignment
+       */
+      protein.initComplementConsensus();
+      AlignmentViewPanel ap = topAlignment.isNucleotide() ? bottomFrame.alignPanel
+              : topFrame.alignPanel;
+      protein.updateConsensus(ap);
     }
 
     adjustLayout();
@@ -179,9 +187,9 @@ public class SplitFrame extends EmbmenuFrame
     else
     {
       this.add(outermost);
-      int width = Math.max(topFrame.DEFAULT_WIDTH,
-              bottomFrame.DEFAULT_WIDTH);
-      int height = topFrame.DEFAULT_HEIGHT + bottomFrame.DEFAULT_HEIGHT;
+      int width = Math.max(topFrame.frameWidth,
+              bottomFrame.frameWidth);
+      int height = topFrame.frameHeight + bottomFrame.frameHeight;
       jalview.bin.JalviewLite
               .addFrame(this, this.getTitle(), width, height);
     }