JAL-1191 revert to using SequenceOntologyLite due to downstream

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index ae4e55d..da83338 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -754,6 +754,23 @@ public final class MappingUtils
   public static List<AlignedCodonFrame> findMappingsForSequence(
           SequenceI sequence, List<AlignedCodonFrame> mappings)
   {
+    return findMappingsForSequenceAndOthers(sequence, mappings, null);
+  }
+
+  /**
+   * Returns a list of any mappings that are from or to the given (aligned or
+   * dataset) sequence, optionally limited to mappings involving one of a given
+   * list of sequences.
+   * 
+   * @param sequence
+   * @param mappings
+   * @param filterList
+   * @return
+   */
+  public static List<AlignedCodonFrame> findMappingsForSequenceAndOthers(
+          SequenceI sequence, List<AlignedCodonFrame> mappings,
+          List<SequenceI> filterList)
+  {
     List<AlignedCodonFrame> result = new ArrayList<AlignedCodonFrame>();
     if (sequence == null || mappings == null)
     {
@@ -763,7 +780,31 @@ public final class MappingUtils
     {
       if (mapping.involvesSequence(sequence))
       {
-        result.add(mapping);
+        if (filterList != null)
+        {
+          for (SequenceI otherseq : filterList)
+          {
+            SequenceI otherDataset = otherseq.getDatasetSequence();
+            if (otherseq == sequence
+                    || otherseq == sequence.getDatasetSequence()
+                    || (otherDataset != null && (otherDataset == sequence || otherDataset == 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;