Merge branch 'bug/JAL-2722' into releases/Release_2_10_2b1_Branch

[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..462f5af 100644 (file)
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -1,19 +1,21 @@
 /*
- * 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;
@@ -21,6 +23,7 @@ package jalview.io.vamsas;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;
+
 import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Sequence;
@@ -76,7 +79,8 @@ public class Datasetsequence extends DatastoreItem
     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
     {
@@ -137,8 +141,8 @@ public class Datasetsequence extends DatastoreItem
       {
         modified |= new jalview.io.vamsas.Sequencefeature(datastore,
                 (jalview.datamodel.SequenceFeature) sq
-                        .getSequenceFeatures()[sf], dataset,
-                (Sequence) vobj).docWasUpdated();
+                        .getSequenceFeatures()[sf],
+                dataset, (Sequence) vobj).docWasUpdated();
       }
     }
     return modified;
@@ -172,15 +176,15 @@ 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();
 
       }
@@ -207,7 +211,7 @@ 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();
       }
     }
@@ -216,7 +220,8 @@ public class Datasetsequence extends DatastoreItem
 
   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();
   }