JAL-2147 findMappingsBetweenSequenceAndOthers for scoping search to sequences in...

[jalview.git] / src / jalview / util / MappingUtils.java

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index ae4e55d..515ff51 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -754,6 +754,13 @@ public final class MappingUtils
   public static List<AlignedCodonFrame> findMappingsForSequence(
           SequenceI sequence, List<AlignedCodonFrame> mappings)
   {
+    return findMappingsForSequenceAndOthers(sequence, mappings, null);
+  }
+
+  public static List<AlignedCodonFrame> findMappingsForSequenceAndOthers(
+          SequenceI sequence, List<AlignedCodonFrame> mappings,
+          AlignmentI alignment)
+  {
     List<AlignedCodonFrame> result = new ArrayList<AlignedCodonFrame>();
     if (sequence == null || mappings == null)
     {
@@ -763,7 +770,31 @@ public final class MappingUtils
     {
       if (mapping.involvesSequence(sequence))
       {
-        result.add(mapping);
+        if (alignment != null)
+        {
+          for (SequenceI otherseq : alignment.getSequences())
+          {
+            if (otherseq == sequence
+                    || (otherseq.getDatasetSequence() != null && (otherseq
+                            .getDatasetSequence() == sequence || otherseq
+                            .getDatasetSequence() == sequence
+                            .getDatasetSequence())))
+            {
+              // skip sequences in subset which directly relate to sequence
+              continue;
+            }
+            if (mapping.involvesSequence(otherseq))
+            {
+              // selected a mapping contained in subselect alignment
+              result.add(mapping);
+              break;
+            }
+          }
+        }
+        else
+        {
+          result.add(mapping);
+        }
       }
     }
     return result;