From 43e966997685777da741087d56c2067a46757806 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 5 Aug 2020 09:13:33 +0100
Subject: [PATCH] JAL-3700 fix for propagation of sort commands

---
 src/jalview/datamodel/AlignedCodonFrame.java |   20 ++++++++++++++------
 src/jalview/util/MappingUtils.java           |   18 +++++++++++-------
 2 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 7fa8b29..6103df5 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -311,8 +311,8 @@ public class AlignedCodonFrame
 
   /**
    * Return the corresponding aligned or dataset dna sequence for given amino
-   * acid sequence, or null if not found. returns the sequence from
-   * the first mapping found that involves the protein sequence.
+   * acid sequence, or null if not found. returns the sequence from the first
+   * mapping found that involves the protein sequence.
    * 
    * @param aaSeqRef
    * @return
@@ -819,7 +819,7 @@ public class AlignedCodonFrame
    * Two AlignedCodonFrame objects are equal if they hold the same ordered list
    * of mappings
    * 
-   * @see SequenceToSequenceMapping#
+   * @see SequenceToSequenceMapping#equals
    */
   @Override
   public boolean equals(Object obj)
@@ -836,12 +836,20 @@ public class AlignedCodonFrame
     return mappings;
   }
 
-  public SequenceToSequenceMapping getCoveringMapping(SequenceI cds,
-          SequenceI peptide)
+  /**
+   * Returns the first mapping found which is between the two given sequences,
+   * and covers the full extent of both.
+   * 
+   * @param seq1
+   * @param seq2
+   * @return
+   */
+  public SequenceToSequenceMapping getCoveringMapping(SequenceI seq1,
+          SequenceI seq2)
   {
     for (SequenceToSequenceMapping mapping : mappings)
     {
-      if (mapping.covers(peptide) && mapping.covers(cds))
+      if (mapping.covers(seq2) && mapping.covers(seq1))
       {
         return mapping;
       }
diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index cf90bf9..499fc6b 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -22,6 +22,7 @@ package jalview.util;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -79,7 +80,7 @@ public final class MappingUtils
       action = action.getUndoAction();
     }
     // TODO write this
-    System.err.println("MappingUtils.mapCutOrPaste not yet implemented");
+    Cache.log.error("MappingUtils.mapCutOrPaste not yet implemented");
   }
 
   /**
@@ -443,20 +444,23 @@ public final class MappingUtils
     {
       for (AlignedCodonFrame acf : mappings)
       {
-        SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
-                : acf.getAaForDnaSeq(seq);
-        if (mappedSeq != null)
-        {
           for (SequenceI seq2 : mapTo.getSequences())
           {
-            if (seq2.getDatasetSequence() == mappedSeq)
+            /*
+             * the corresponding peptide / CDS is the one for which there is
+             * a complete ('covering') mapping to 'seq'
+             */
+            SequenceI peptide = mappingToNucleotide ? seq2 : seq;
+            SequenceI cds = mappingToNucleotide ? seq : seq2;
+            SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
+                    peptide);
+            if (s2s != null)
             {
               mappedOrder.add(seq2);
               j++;
               break;
             }
           }
-        }
       }
     }
 
-- 
1.7.10.2