Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / io / vamsas / Datasetsequence.java

diff --git a/src/jalview/io/vamsas/Datasetsequence.java b/src/jalview/io/vamsas/Datasetsequence.java
index 08e6288..e1340e2 100644 (file)
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -1,26 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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/>.
+ * 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.io.vamsas;
 
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;
+
+import java.util.List;
+
 import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Sequence;
@@ -58,6 +64,7 @@ public class Datasetsequence extends DatastoreItem
     doJvUpdate();
   }
 
+  @Override
   public void addFromDocument()
   {
     Sequence vseq = (Sequence) vobj;
@@ -70,6 +77,7 @@ public class Datasetsequence extends DatastoreItem
     modified = true;
   }
 
+  @Override
   public void updateFromDoc()
   {
     Sequence sq = (Sequence) vobj;
@@ -125,25 +133,21 @@ public class Datasetsequence extends DatastoreItem
    */
   private boolean updateSqFeatures()
   {
-    boolean modified = false;
+    boolean changed = false;
     SequenceI sq = (SequenceI) jvobj;
 
     // add or update any new features/references on dataset sequence
-    if (sq.getSequenceFeatures() != null)
+    List<SequenceFeature> sfs = sq.getSequenceFeatures();
+    for (SequenceFeature sf : sfs)
     {
-      int sfSize = sq.getSequenceFeatures().length;
-
-      for (int sf = 0; sf < sfSize; sf++)
-      {
-        modified |= new jalview.io.vamsas.Sequencefeature(datastore,
-                (jalview.datamodel.SequenceFeature) sq
-                        .getSequenceFeatures()[sf], dataset,
-                (Sequence) vobj).docWasUpdated();
-      }
+      changed |= new jalview.io.vamsas.Sequencefeature(datastore, sf,
+              dataset, (Sequence) vobj).docWasUpdated();
     }
-    return modified;
+
+    return changed;
   }
 
+  @Override
   public void addToDocument()
   {
     SequenceI sq = (SequenceI) jvobj;
@@ -172,10 +176,10 @@ public class Datasetsequence extends DatastoreItem
     boolean modifiedthedoc = false;
     SequenceI sq = (SequenceI) jvobj;
 
-    if (sq.getDatasetSequence() == null && sq.getDBRef() != null)
+    if (sq.getDatasetSequence() == null && sq.getDBRefs() != null)
     {
       // only sync database references for dataset sequences
-      DBRefEntry[] entries = sq.getDBRef();
+      DBRefEntry[] entries = sq.getDBRefs();
       // jalview.datamodel.DBRefEntry dbentry;
       for (int db = 0; db < entries.length; db++)
       {
@@ -214,6 +218,7 @@ public class Datasetsequence extends DatastoreItem
     return modifiedtheseq;
   }
 
+  @Override
   public void conflict()
   {
     log.warn("Conflict in dataset sequence update to document. Overwriting document");
@@ -223,6 +228,7 @@ public class Datasetsequence extends DatastoreItem
 
   boolean modified = false;
 
+  @Override
   public void updateToDoc()
   {
     SequenceI sq = (SequenceI) jvobj;