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 6b449ee..a399c04 100644 (file)
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
  * 
@@ -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;
@@ -44,12 +48,12 @@ public class Datasetsequence extends DatastoreItem
   // private AlignmentI jvdset;
 
   public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,
-          SequenceI sq, String dict, DataSet dataset)
+          SequenceI sq, String theDict, DataSet theDataset)
   {
     super(vamsasAppDatastore, sq, uk.ac.vamsas.objects.core.Sequence.class);
-    this.dataset = dataset;
+    this.dataset = theDataset;
     // this.jvdset = jvdset;
-    this.dict = dict;
+    this.dict = theDict;
     doSync();
   }
 
@@ -60,6 +64,7 @@ public class Datasetsequence extends DatastoreItem
     doJvUpdate();
   }
 
+  @Override
   public void addFromDocument()
   {
     Sequence vseq = (Sequence) vobj;
@@ -72,13 +77,15 @@ public class Datasetsequence extends DatastoreItem
     modified = true;
   }
 
+  @Override
   public void updateFromDoc()
   {
     Sequence sq = (Sequence) vobj;
     SequenceI sequence = (SequenceI) jvobj;
     if (!sequence.getSequenceAsString().equals(sq.getSequence()))
     {
-      log.warn("Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
+      log.warn(
+              "Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
     }
     else
     {
@@ -127,25 +134,21 @@ 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;
@@ -174,15 +177,15 @@ 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++)
       {
         modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
-        // dbentry =
+                // dbentry =
                 entries[db], sq, (Sequence) vobj, dataset).docWasUpdated();
 
       }
@@ -209,22 +212,25 @@ public class Datasetsequence extends DatastoreItem
       for (int db = 0; db < entries.length; db++)
       {
         modifiedtheseq |= new jalview.io.vamsas.Dbref(datastore,
-        // dbentry =
+                // dbentry =
                 entries[db], vsq, sq).jvWasUpdated();
       }
     }
     return modifiedtheseq;
   }
 
+  @Override
   public void conflict()
   {
-    log.warn("Conflict in dataset sequence update to document. Overwriting document");
+    log.warn(
+            "Conflict in dataset sequence update to document. Overwriting document");
     // TODO: could try to import from document data to jalview first. and then
     updateToDoc();
   }
 
   boolean modified = false;
 
+  @Override
   public void updateToDoc()
   {
     SequenceI sq = (SequenceI) jvobj;