X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDatasetsequence.java;h=e1340e27f775cff08ce04b6cf05b4bb54a43ab33;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=9c86557d1f1242e87280f8def13b015e2d15ca6c;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/io/vamsas/Datasetsequence.java b/src/jalview/io/vamsas/Datasetsequence.java
index 9c86557..e1340e2 100644
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -21,8 +21,12 @@
 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;
@@ -60,6 +64,7 @@ public class Datasetsequence extends DatastoreItem
     doJvUpdate();
   }
 
+  @Override
   public void addFromDocument()
   {
     Sequence vseq = (Sequence) vobj;
@@ -72,6 +77,7 @@ public class Datasetsequence extends DatastoreItem
     modified = true;
   }
 
+  @Override
   public void updateFromDoc()
   {
     Sequence sq = (Sequence) vobj;
@@ -127,25 +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;
@@ -174,10 +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++)
       {
@@ -216,6 +218,7 @@ public class Datasetsequence extends DatastoreItem
     return modifiedtheseq;
   }
 
+  @Override
   public void conflict()
   {
     log.warn("Conflict in dataset sequence update to document. Overwriting document");
@@ -225,6 +228,7 @@ public class Datasetsequence extends DatastoreItem
 
   boolean modified = false;
 
+  @Override
   public void updateToDoc()
   {
     SequenceI sq = (SequenceI) jvobj;