JAL-1641 added support for persisting and retrieveing SequenceGroup

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5e477c7..a54fa99 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -83,7 +83,7 @@ import jalview.ws.params.AutoCalcSetting;
  * @version $Revision: 1.141 $
  */
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, AlignViewportI, CommandListener
+        SelectionSource, CommandListener
 {
   Font font;
 
@@ -243,7 +243,7 @@ public class AlignViewport extends AlignmentViewport implements
     showAutocalculatedAbove = Cache.getDefault(
             Preferences.SHOW_AUTOCALC_ABOVE, false);
     viewStyle.setScaleProteinAsCdna(Cache.getDefault(
-            Preferences.SCALE_PROTEIN_TO_CDNA, false));
+            Preferences.SCALE_PROTEIN_TO_CDNA, true));
   }
 
   void init()
@@ -798,16 +798,23 @@ public class AlignViewport extends AlignmentViewport implements
     // TODO: create undo object for this JAL-1101
 
     /*
-     * If one alignment is protein and one nucleotide, with at least one
-     * sequence name in common, offer to open a linked alignment.
+     * If any cDNA/protein mappings can be made between the alignments, offer to
+     * open a linked alignment with split frame option.
      */
-    if (AlignmentUtils.isMappable(al, getAlignment()))
+    if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
     {
-      if (openLinkedAlignment(al, title))
+      if (AlignmentUtils.isMappable(al, getAlignment()))
       {
-        return;
+        if (openLinkedAlignment(al, title))
+        {
+          return;
+        }
       }
     }
+
+    /*
+     * No mappings, or offer declined - add sequences to this alignment
+     */
     // TODO: JAL-407 regardless of above - identical sequences (based on ID and
     // provenance) should share the same dataset sequence
 
@@ -815,19 +822,18 @@ public class AlignViewport extends AlignmentViewport implements
     {
       getAlignment().addSequence(al.getSequenceAt(i));
     }
-    // TODO this call was done by SequenceFetcher but not FileLoader or
-    // CutAndPasteTransfer. Is it needed?
-    // JBPComment: this repositions the view to show the new sequences
-    // JBPComment: so it is needed for UX
+
     setEndSeq(getAlignment().getHeight());
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
   /**
    * Show a dialog with the option to open and link (cDNA <-> protein) as a new
-   * alignment. Returns true if the new alignment was opened, false if not,
-   * because the user declined the offer.
+   * alignment, either as a standalone alignment or in a split frame. Returns
+   * true if the new alignment was opened, false if not, because the user
+   * declined the offer.
    * 
+   * @param al
    * @param title
    */
   protected boolean openLinkedAlignment(AlignmentI al, String title)
@@ -851,14 +857,6 @@ public class AlignViewport extends AlignmentViewport implements
     final boolean openInNewWindow = (response == 2);
 
     /*
-     * Create the AlignFrame first (which creates the new alignment's datasets),
-     * before attempting sequence mapping.
-     */
-    AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-            AlignFrame.DEFAULT_HEIGHT);
-    newAlignFrame.setTitle(title);
-
-    /*
      * Identify protein and dna alignments. Make a copy of this one if opening
      * in a new split pane.
      */
@@ -867,6 +865,23 @@ public class AlignViewport extends AlignmentViewport implements
     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.
+     */
+    al.setDataset(null);
+    AlignmentUtils.mapProteinToCdna(protein, cdna);
+
+    /*
+     * Create the AlignFrame for the added alignment. Note this will include the
+     * cDNA consensus annotation if it is protein (because the alignment holds
+     * mappings to nucleotide)
+     */
+    AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT);
+    newAlignFrame.setTitle(title);
     newAlignFrame.statusBar.setText(MessageManager.formatMessage(
             "label.successfully_loaded_file", new Object[]
             { title }));
@@ -885,13 +900,6 @@ public class AlignViewport extends AlignmentViewport implements
               AlignFrame.DEFAULT_HEIGHT);
     }
 
-    /*
-     * 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.
-     */
-    AlignmentUtils.mapProteinToCdna(protein, cdna);
-
     try
     {
       newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
@@ -933,7 +941,9 @@ public class AlignViewport extends AlignmentViewport implements
           AlignmentI complement, Set<AlignedCodonFrame> mappings)
   {
     /*
-     * Open in split pane. DNA sequence above, protein below.
+     * Make a new frame with a copy of the alignment we are adding to. If this
+     * is protein, the new frame will have a cDNA consensus annotation row
+     * added.
      */
     AlignFrame copyMe = new AlignFrame(complement,
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -951,6 +961,10 @@ public class AlignViewport extends AlignmentViewport implements
     proteinFrame.setVisible(true);
     String linkedTitle = MessageManager
             .getString("label.linked_view_title");
+
+    /*
+     * Open in split pane. DNA sequence above, protein below.
+     */
     JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
     Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);