JAL-3541 selectively merged build.gradle and gradle.properties

[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 e1340e2..d24e947 100644 (file)
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -48,12 +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();
   }
 
@@ -84,7 +84,8 @@ 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
     {
@@ -179,13 +180,13 @@ public class Datasetsequence extends DatastoreItem
     if (sq.getDatasetSequence() == null && sq.getDBRefs() != null)
     {
       // only sync database references for dataset sequences
-      DBRefEntry[] entries = sq.getDBRefs();
+      List<DBRefEntry> entries = sq.getDBRefs();
       // jalview.datamodel.DBRefEntry dbentry;
-      for (int db = 0; db < entries.length; db++)
+      for (int db = 0, dn = entries.size(); db < dn; db++)
       {
         modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
-        // dbentry =
-                entries[db], sq, (Sequence) vobj, dataset).docWasUpdated();
+                // dbentry =
+                entries.get(db), sq, (Sequence) vobj, dataset).docWasUpdated();
 
       }
 
@@ -211,7 +212,7 @@ 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();
       }
     }
@@ -221,7 +222,8 @@ public class Datasetsequence extends DatastoreItem
   @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();
   }