JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings

[jalview.git] / src / jalview / analysis / SequenceIdMatcher.java

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index b89287c..70defb0 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -46,7 +46,7 @@ public class SequenceIdMatcher
   }
 
   /**
-   * add more sequences to this matcher - also used by the constructor
+   * Adds sequences to this matcher
    * 
    * @param seqs
    */
@@ -54,26 +54,36 @@ public class SequenceIdMatcher
   {
     for (SequenceI seq : seqs)
     {
-      // TODO: deal with ID collisions - SequenceI should be appended to list
-      // associated with this key.
-      names.put(new SeqIdName(seq.getDisplayId(true)), seq);
-      SequenceI dbseq = seq;
-      while (dbseq.getDatasetSequence() != null)
-      {
-        dbseq = dbseq.getDatasetSequence();
-      }
-      // add in any interesting identifiers
-      if (dbseq.getDBRefs() != null)
+      add(seq);
+    }
+  }
+
+  /**
+   * Adds one sequence to this matcher
+   * 
+   * @param seq
+   */
+  public void add(SequenceI seq)
+  {
+    // TODO: deal with ID collisions - SequenceI should be appended to list
+    // associated with this key.
+    names.put(new SeqIdName(seq.getDisplayId(true)), seq);
+    SequenceI dbseq = seq;
+    while (dbseq.getDatasetSequence() != null)
+    {
+      dbseq = dbseq.getDatasetSequence();
+    }
+    // add in any interesting identifiers
+    if (dbseq.getDBRefs() != null)
+    {
+      DBRefEntry dbr[] = dbseq.getDBRefs();
+      SeqIdName sid = null;
+      for (int r = 0; r < dbr.length; r++)
       {
-        DBRefEntry dbr[] = dbseq.getDBRefs();
-        SeqIdName sid = null;
-        for (int r = 0; r < dbr.length; r++)
+        sid = new SeqIdName(dbr[r].getAccessionId());
+        if (!names.containsKey(sid))
         {
-          sid = new SeqIdName(dbr[r].getAccessionId());
-          if (!names.containsKey(sid))
-          {
-            names.put(sid, seq);
-          }
+          names.put(sid, seq);
         }
       }
     }