X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceDummy.java;h=172c25fe3b5c490fd6ea4ae824de4d24b8f7f92a;hb=refs%2Fheads%2Ffeatures%2FJAL-2909_bamImport_2_11_2;hp=80b0072f2dc469f4b7a8b35640ff1cb935807731;hpb=1e13e955bb673692c0c122f6a6e3415981a6e64d;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceDummy.java b/src/jalview/datamodel/SequenceDummy.java
index 80b0072..172c25f 100644
--- a/src/jalview/datamodel/SequenceDummy.java
+++ b/src/jalview/datamodel/SequenceDummy.java
@@ -1,9 +1,63 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
-public class SequenceDummy extends Sequence implements SequenceI
+public class SequenceDummy extends Sequence
 {
   public SequenceDummy(String sequenceId)
   {
     super(sequenceId, "THISAPLACEHOLDER");
   }
+
+  private boolean dummy = true;
+
+  /**
+   * become a proxy for mseq, merging any existing annotation on this sequence
+   * 
+   * @param mseq
+   */
+  public void become(SequenceI mseq)
+  {
+    initSeqFrom(mseq, null);
+    dummy = false;
+  }
+
+  /**
+   * Test if the SequenceDummy has been promoted to a real sequence via
+   * SequenceDummy.become
+   * 
+   * @return true if this is a placeholder and contains no actual sequence data
+   */
+  public boolean isDummy()
+  {
+    return dummy;
+  }
+
+  /**
+   * Always suppress /start-end for display name as we don't know it
+   */
+  @Override
+  public String getDisplayId(boolean jvsuffix)
+  {
+    // required for correct behaviour of SequenceIdMatcher
+    return super.getDisplayId(false);
+  }
 }