From 0ebcd487f08f9873987d9a32edce7df47aa27927 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 31 May 2016 17:32:08 +0100
Subject: [PATCH] JAL-2023 adjustments to mappings added for split frame to
 avoid duplication and ensure saved in project

---
 src/jalview/analysis/AlignmentUtils.java |   20 ++++++++++++++++++++
 src/jalview/datamodel/Alignment.java     |   17 +++++++++++++++++
 src/jalview/datamodel/AlignmentI.java    |    8 ++++++++
 src/jalview/gui/AlignFrame.java          |   18 ++++++++++++++++--
 4 files changed, 61 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index fba023f..081f446 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2114,6 +2114,26 @@ public class AlignmentUtils
   {
     AlignmentI copy = new Alignment(new Alignment(seqs));
 
+    /*
+     * add mappings between sequences to the new alignment
+     */
+    AlignedCodonFrame mappings = new AlignedCodonFrame();
+    copy.addCodonFrame(mappings);
+    for (int i = 0; i < copy.getHeight(); i++)
+    {
+      SequenceI from = seqs[i];
+      SequenceI to = copy.getSequenceAt(i);
+      if (to.getDatasetSequence() != null)
+      {
+        to = to.getDatasetSequence();
+      }
+      int start = from.getStart();
+      int end = from.getEnd();
+      MapList map = new MapList(new int[] { start, end }, new int[] {
+          start, end }, 1, 1);
+      mappings.addMap(to, from, map);
+    }
+
     SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
     if (xrefs != null)
     {
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index a9b0d53..f14539b 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -30,6 +30,7 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -1287,6 +1288,22 @@ public class Alignment implements AlignmentI
     }
   }
 
+  /**
+   * adds a set of mappings (while ignoring any duplicates)
+   */
+  @Override
+  public void addCodonFrames(Iterable<AlignedCodonFrame> codons)
+  {
+    if (codons != null)
+    {
+      Iterator<AlignedCodonFrame> it = codons.iterator();
+      while (it.hasNext())
+      {
+        addCodonFrame(it.next());
+      }
+    }
+  }
+
   /*
    * (non-Javadoc)
    * 
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 76d1a48..4ae8ba2 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -363,6 +363,14 @@ public interface AlignmentI extends AnnotatedCollectionI
   void addCodonFrame(AlignedCodonFrame codons);
 
   /**
+   * add a set of aligned codons mappings for this alignment, apart from any
+   * duplicates which are ignored
+   * 
+   * @param codons
+   */
+  void addCodonFrames(Iterable<AlignedCodonFrame> codons);
+
+  /**
    * remove a particular codon frame reference from this alignment
    * 
    * @param codons
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d9d5f27..d548695 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4679,6 +4679,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return showp;
   }
 
+  /**
+   * Finds and displays cross-references for the selected sequences (protein
+   * products for nucleotide sequences, dna coding sequences for peptides).
+   * 
+   * @param sel
+   *          the sequences to show cross-references for
+   * @param dna
+   *          true if from a nucleotide alignment (so showing proteins)
+   * @param source
+   *          the database to show cross-references for
+   */
   protected void showProductsFor(final SequenceI[] sel, final boolean dna,
           final String source)
   {
@@ -4749,7 +4760,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 System.err.println("Failed to make CDS alignment");
               }
               al.getCodonFrames().clear();
-              al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
+              al.addCodonFrames(copyAlignment.getCodonFrames());
+              al.addCodonFrames(cf);
 
               /*
                * pending getting Embl transcripts to 'align', 
@@ -4767,7 +4779,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             {
               copyAlignment = AlignmentUtils.makeCopyAlignment(
                       sequenceSelection, xrefs.getSequencesArray());
-              copyAlignment.getCodonFrames().addAll(cf);
+              copyAlignment.addCodonFrames(cf);
+              al.addCodonFrames(copyAlignment.getCodonFrames());
+              al.addCodonFrames(cf);
             }
             copyAlignment.setGapCharacter(AlignFrame.this.viewport
                     .getGapCharacter());
-- 
1.7.10.2