JAL-4366 provide options for updating (or not) the linked alignment or existing align...

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d56764b..91dded1 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import java.awt.Container;
 import java.awt.Dimension;
+import java.awt.FlowLayout;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Rectangle;
@@ -795,8 +796,13 @@ public class AlignViewport extends AlignmentViewport
   protected void openLinkedAlignment(AlignmentI al, String title)
   {
     String[] options = new String[] { MessageManager.getString("action.no"),
-        MessageManager.getString("label.split_window"),
-        MessageManager.getString("label.new_window"), };
+        MessageManager.getString("label.split_window")
+                + "(update new alignment)",
+        MessageManager.getString("label.new_window"),
+        MessageManager.getString(
+                "label.split_window") + "(update this alignment)",
+        MessageManager.getString(
+                "label.split_window") + "(leave both unchanged)" };
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
     final AlignViewport us = this;
@@ -810,18 +816,33 @@ public class AlignViewport extends AlignmentViewport
             .setResponseHandler(0, () -> {
               addDataToAlignment(al);
             }).setResponseHandler(1, () -> {
-              us.openLinkedAlignmentAs(al, title, true);
+              us.openLinkedAlignmentAs(al, title, true, 1);
             }).setResponseHandler(2, () -> {
-              us.openLinkedAlignmentAs(al, title, false);
+              us.openLinkedAlignmentAs(al, title, false, 1);
+            }).setResponseHandler(3, () -> {
+              us.openLinkedAlignmentAs(al, title, true, 2);
+            }).setResponseHandler(4, () -> {
+              us.openLinkedAlignmentAs(al, title, true, 0);
             });
+    dialog.setLayout(new FlowLayout(FlowLayout.CENTER));
+    dialog.setPreferredSize(new Dimension(350,300));
     dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
             JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
   }
 
-  protected void openLinkedAlignmentAs(AlignmentI al, String title,
-          boolean newWindowOrSplitPane)
+  /**
+   * link given alignment to the alignment in this viewport and open
+   * @param al - alignment containing sequences to link to this alignment
+   * @param title
+   * @param newWindowOrSplitPane
+   * @param alignAs TODO
+   * @param alignAs - 0 - don't modify either alignment, 1 - align al according to us, 2- align us according to al
+   * @return alignFrame holding al
+   */
+  protected AlignFrame openLinkedAlignmentAs(AlignmentI al, String title,
+          boolean newWindowOrSplitPane, int alignAs)
   {
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
@@ -831,18 +852,26 @@ public class AlignViewport extends AlignmentViewport
             ? new Alignment(getAlignment())
             : getAlignment();
     
-    // always create dataset for imported alignment before doing anything else..
-    al.setDataset(null);
     
     if (!al.isNucleotide() && !thisAlignment.isNucleotide())
     {
       // link AA to 3di or other kind of 'alternative' 1:1 mapping alignment
+      if (al.getDataset()==null)
+      {
+        al.setDataset(thisAlignment.getDataset());
+      }
       AlignmentUtils.map3diPeptideToProteinAligment(thisAlignment,al);
+      if (thisAlignment.getCodonFrames().isEmpty()) {thisAlignment.getCodonFrames().addAll(al.getCodonFrames()); }
+      else {al.getCodonFrames().addAll(thisAlignment.getCodonFrames()); };
+
 
     }
     else
     {
-      // link CODON triplets to Protein
+      // shouldn't we be merging dataset here ?
+      // always create dataset for imported alignment before doing anything else..
+        al.setDataset(null);
+        // link CODON triplets to Protein
       AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
       final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
 
@@ -888,9 +917,15 @@ public class AlignViewport extends AlignmentViewport
 
     if (newWindowOrSplitPane)
     {
-      al.alignAs(thisAlignment);
+      if (alignAs==1) {
+        al.alignAs(thisAlignment);
+      }
+      if (alignAs==2) {
+        thisAlignment.alignAs(al);
+      }
       AlignmentI mapped = openSplitFrame(newAlignFrame, thisAlignment);
     }
+    return newAlignFrame;
   }
 
   /**