X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=d56764b0bec5879d701a374bb6a03851f51159ee;hb=9d465da4f21e403c20b835264929906b538c0c9b;hp=fea74db0ce48d12520463f6772638f8b1d854a22;hpb=a7bc89415a6749ff89eb97f75fbc950a433a4935;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fea74db..d56764b 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -745,6 +745,11 @@ public class AlignViewport extends AlignmentViewport
    */
   public void addFile(File file, FileFormatI format)
   {
+    addFile(file, format, true);
+  }
+
+  public void addFile(File file, FileFormatI format, boolean async)
+  {
     DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
 
     if (format == null)
@@ -769,7 +774,8 @@ public class AlignViewport extends AlignmentViewport
       }
     }
 
-    new FileLoader().LoadFile(this, file, DataSourceType.FILE, format);
+    new FileLoader().LoadFile(this, file, DataSourceType.FILE, format,
+            async);
   }
 
   public void addFile(File file)
@@ -803,13 +809,10 @@ public class AlignViewport extends AlignmentViewport
     JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
             .setResponseHandler(0, () -> {
               addDataToAlignment(al);
-              return null;
             }).setResponseHandler(1, () -> {
               us.openLinkedAlignmentAs(al, title, true);
-              return null;
             }).setResponseHandler(2, () -> {
               us.openLinkedAlignmentAs(al, title, false);
-              return null;
             });
     dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
@@ -827,18 +830,31 @@ public class AlignViewport extends AlignmentViewport
     AlignmentI thisAlignment = newWindowOrSplitPane
             ? new Alignment(getAlignment())
             : getAlignment();
-    AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
-    final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
-
-    /*
-     * Map sequences. At least one should get mapped as we have already passed
-     * the test for 'mappability'. Any mappings made will be added to the
-     * protein alignment. Note creating dataset sequences on the new alignment
-     * is a pre-requisite for building mappings.
-     */
+    
+    // always create dataset for imported alignment before doing anything else..
     al.setDataset(null);
-    AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
+    
+    if (!al.isNucleotide() && !thisAlignment.isNucleotide())
+    {
+      // link AA to 3di or other kind of 'alternative' 1:1 mapping alignment
+      AlignmentUtils.map3diPeptideToProteinAligment(thisAlignment,al);
 
+    }
+    else
+    {
+      // link CODON triplets to Protein
+      AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+      final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+      /*
+       * Map sequences. At least one should get mapped as we have already passed
+       * the test for 'mappability'. Any mappings made will be added to the
+       * protein alignment. Note creating dataset sequences on the new alignment
+       * is a pre-requisite for building mappings.
+       */
+      AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
+    }
+    
     /*
      * Create the AlignFrame for the added alignment. If it is protein, mappings
      * are registered with StructureSelectionManager as a side-effect.
@@ -873,7 +889,7 @@ public class AlignViewport extends AlignmentViewport
     if (newWindowOrSplitPane)
     {
       al.alignAs(thisAlignment);
-      protein = openSplitFrame(newAlignFrame, thisAlignment);
+      AlignmentI mapped = openSplitFrame(newAlignFrame, thisAlignment);
     }
   }
 
@@ -994,7 +1010,7 @@ public class AlignViewport extends AlignmentViewport
    */
   protected boolean noReferencesTo(AlignedCodonFrame acf)
   {
-    AlignFrame[] frames = Desktop.getAlignFrames();
+    AlignFrame[] frames = Desktop.getDesktopAlignFrames();
     if (frames == null)
     {
       return true;
@@ -1155,4 +1171,5 @@ public class AlignViewport extends AlignmentViewport
   {
     this.viewName = viewName;
   }
+
 }