Merge branch 'bug/JAL-2541cutWithFeatures' into features/JAL-2446NCList

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 9994675..9f3e7b8 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -22,6 +22,8 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.DBRefEntryI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
@@ -88,6 +90,8 @@ public class Sequence extends ASequence implements SequenceI
   /** array of sequence features - may not be null for a valid sequence object */
   public SequenceFeature[] sequenceFeatures;
 
+  private SequenceFeatures sequenceFeatureStore;
+
   /**
    * Creates a new Sequence object.
    * 
@@ -127,6 +131,7 @@ public class Sequence extends ASequence implements SequenceI
     this.sequence = sequence2;
     this.start = start2;
     this.end = end2;
+    sequenceFeatureStore = new SequenceFeatures();
     parseId();
     checkValidRange();
   }
@@ -324,6 +329,13 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public synchronized boolean addSequenceFeature(SequenceFeature sf)
   {
+    if (sf.getType() == null)
+    {
+      System.err.println("SequenceFeature type may not be null: "
+              + sf.toString());
+      return false;
+    }
+
     if (sequenceFeatures == null && datasetSequence != null)
     {
       return datasetSequence.addSequenceFeature(sf);
@@ -346,6 +358,8 @@ public class Sequence extends ASequence implements SequenceI
     temp[sequenceFeatures.length] = sf;
 
     sequenceFeatures = temp;
+
+    sequenceFeatureStore.add(sf);
     return true;
   }
 
@@ -361,6 +375,14 @@ public class Sequence extends ASequence implements SequenceI
       return;
     }
 
+    /*
+     * new way
+     */
+    sequenceFeatureStore.delete(sf);
+
+    /*
+     * old way - to be removed
+     */
     int index = 0;
     for (index = 0; index < sequenceFeatures.length; index++)
     {
@@ -420,6 +442,13 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
+  public SequenceFeaturesI getFeatures()
+  {
+    return datasetSequence != null ? datasetSequence.getFeatures()
+            : sequenceFeatureStore;
+  }
+
+  @Override
   public boolean addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
@@ -1164,6 +1193,8 @@ public class Sequence extends ASequence implements SequenceI
       // move features and database references onto dataset sequence
       dsseq.sequenceFeatures = sequenceFeatures;
       sequenceFeatures = null;
+      dsseq.sequenceFeatureStore = sequenceFeatureStore;
+      sequenceFeatureStore = null;
       dsseq.dbrefs = dbrefs;
       dbrefs = null;
       // TODO: search and replace any references to this sequence with
@@ -1483,4 +1514,17 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> findFeatures(int from, int to,
+          String... types)
+  {
+    if (datasetSequence != null)
+    {
+      return datasetSequence.findFeatures(from, to, types);
+    }
+    return sequenceFeatureStore.findFeatures(from, to, types);
+  }
 }