Merge branch 'develop' into JAL-1705_trialMerge

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 532a11b..7b05649 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.DBRefEntryI;
 import jalview.util.StringUtils;
 
 import java.util.ArrayList;
@@ -55,6 +56,8 @@ public class Sequence extends ASequence implements SequenceI
 
   String vamsasId;
 
+  DBRefEntryI sourceDBRef;
+
   DBRefEntry[] dbrefs;
 
   RNA rna;
@@ -216,6 +219,7 @@ public class Sequence extends ASequence implements SequenceI
     initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
             seq.getEnd());
     description = seq.getDescription();
+    sourceDBRef = seq.getSourceDBRef();
     if (seq.getSequenceFeatures() != null)
     {
       SequenceFeature[] sf = seq.getSequenceFeatures();
@@ -225,10 +229,10 @@ public class Sequence extends ASequence implements SequenceI
       }
     }
     setDatasetSequence(seq.getDatasetSequence());
-    if (datasetSequence == null && seq.getDBRef() != null)
+    if (datasetSequence == null && seq.getDBRefs() != null)
     {
       // only copy DBRefs if we really are a dataset sequence
-      DBRefEntry[] dbr = seq.getDBRef();
+      DBRefEntry[] dbr = seq.getDBRefs();
       for (int i = 0; i < dbr.length; i++)
       {
         addDBRef(new DBRefEntry(dbr[i]));
@@ -284,6 +288,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public synchronized void addSequenceFeature(SequenceFeature sf)
   {
+    // TODO add to dataset sequence instead if there is one?
     if (sequenceFeatures == null)
     {
       sequenceFeatures = new SequenceFeature[0];
@@ -907,18 +912,18 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public void setDBRef(DBRefEntry[] dbref)
+  public void setDBRefs(DBRefEntry[] dbref)
   {
     dbrefs = dbref;
   }
 
   @Override
-  public DBRefEntry[] getDBRef()
+  public DBRefEntry[] getDBRefs()
   {
     if (dbrefs == null && datasetSequence != null
             && this != datasetSequence)
     {
-      return datasetSequence.getDBRef();
+      return datasetSequence.getDBRefs();
     }
     return dbrefs;
   }
@@ -926,6 +931,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
+    // TODO add to dataset sequence instead if there is one?
     if (dbrefs == null)
     {
       dbrefs = new DBRefEntry[0];
@@ -1076,8 +1082,8 @@ public class Sequence extends ASequence implements SequenceI
       datasetSequence.setDescription(getDescription());
       setSequenceFeatures(null);
       // move database references onto dataset sequence
-      datasetSequence.setDBRef(getDBRef());
-      setDBRef(null);
+      datasetSequence.setDBRefs(getDBRefs());
+      setDBRefs(null);
       datasetSequence.setPDBId(getAllPDBEntries());
       setPDBId(null);
       datasetSequence.updatePDBIds();
@@ -1252,7 +1258,7 @@ public class Sequence extends ASequence implements SequenceI
       }
     }
     // transfer database references
-    DBRefEntry[] entryRefs = entry.getDBRef();
+    DBRefEntry[] entryRefs = entry.getDBRefs();
     if (entryRefs != null)
     {
       for (int r = 0; r < entryRefs.length; r++)
@@ -1352,4 +1358,16 @@ public class Sequence extends ASequence implements SequenceI
     return null;
   }
 
+  @Override
+  public void setSourceDBRef(DBRefEntryI dbRef)
+  {
+    this.sourceDBRef = dbRef;
+  }
+
+  @Override
+  public DBRefEntryI getSourceDBRef()
+  {
+    return this.sourceDBRef;
+  }
+
 }