merge of SIFTs Branch

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c7581d8..ac2f9c1 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]));
@@ -276,11 +280,13 @@ public class Sequence extends ASequence implements SequenceI
    * @param v
    *          DOCUMENT ME!
    */
+  @Override
   public void setSequenceFeatures(SequenceFeature[] features)
   {
     sequenceFeatures = features;
   }
 
+  @Override
   public synchronized void addSequenceFeature(SequenceFeature sf)
   {
     if (sequenceFeatures == null)
@@ -303,6 +309,7 @@ public class Sequence extends ASequence implements SequenceI
     sequenceFeatures = temp;
   }
 
+  @Override
   public void deleteFeature(SequenceFeature sf)
   {
     if (sequenceFeatures == null)
@@ -352,6 +359,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return
    */
+  @Override
   public SequenceFeature[] getSequenceFeatures()
   {
     SequenceFeature[] features = sequenceFeatures;
@@ -367,6 +375,7 @@ public class Sequence extends ASequence implements SequenceI
     return features;
   }
 
+  @Override
   public void addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
@@ -419,6 +428,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String getDisplayId(boolean jvsuffix)
   {
     StringBuffer result = new StringBuffer(name);
@@ -436,6 +446,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param name
    *          DOCUMENT ME!
    */
+  @Override
   public void setName(String name)
   {
     this.name = name;
@@ -447,6 +458,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String getName()
   {
     return this.name;
@@ -458,6 +470,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param start
    *          DOCUMENT ME!
    */
+  @Override
   public void setStart(int start)
   {
     this.start = start;
@@ -468,6 +481,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getStart()
   {
     return this.start;
@@ -479,6 +493,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param end
    *          DOCUMENT ME!
    */
+  @Override
   public void setEnd(int end)
   {
     this.end = end;
@@ -489,6 +504,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getEnd()
   {
     return this.end;
@@ -499,6 +515,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getLength()
   {
     return this.sequence.length;
@@ -510,22 +527,26 @@ public class Sequence extends ASequence implements SequenceI
    * @param seq
    *          DOCUMENT ME!
    */
+  @Override
   public void setSequence(String seq)
   {
     this.sequence = seq.toCharArray();
     checkValidRange();
   }
 
+  @Override
   public String getSequenceAsString()
   {
     return new String(sequence);
   }
 
+  @Override
   public String getSequenceAsString(int start, int end)
   {
     return new String(getSequence(start, end));
   }
 
+  @Override
   public char[] getSequence()
   {
     return sequence;
@@ -536,6 +557,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @see jalview.datamodel.SequenceI#getSequence(int, int)
    */
+  @Override
   public char[] getSequence(int start, int end)
   {
     if (start < 0)
@@ -596,6 +618,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public char getCharAt(int i)
   {
     if (i < sequence.length)
@@ -614,6 +637,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param desc
    *          DOCUMENT ME!
    */
+  @Override
   public void setDescription(String desc)
   {
     this.description = desc;
@@ -624,6 +648,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String getDescription()
   {
     return this.description;
@@ -634,6 +659,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @see jalview.datamodel.SequenceI#findIndex(int)
    */
+  @Override
   public int findIndex(int pos)
   {
     // returns the alignment position for a residue
@@ -686,6 +712,7 @@ public class Sequence extends ASequence implements SequenceI
    * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
    *         residues in SequenceI object
    */
+  @Override
   public int[] gapMap()
   {
     String seq = jalview.analysis.AlignSeq.extractGaps(
@@ -885,18 +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;
   }
@@ -973,6 +1000,7 @@ public class Sequence extends ASequence implements SequenceI
     annotation.setSequenceRef(this);
   }
 
+  @Override
   public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation != null)
@@ -1040,6 +1068,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @see jalview.datamodel.SequenceI#createDatasetSequence()
    */
+  @Override
   public SequenceI createDatasetSequence()
   {
     if (datasetSequence == null)
@@ -1051,8 +1080,8 @@ 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();
@@ -1078,6 +1107,7 @@ public class Sequence extends ASequence implements SequenceI
    * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
    * annotations)
    */
+  @Override
   public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
   {
     if (annotation != null)
@@ -1226,7 +1256,7 @@ 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++)
@@ -1250,6 +1280,7 @@ public class Sequence extends ASequence implements SequenceI
    * @return The index (zero-based) on this sequence in the MSA. It returns
    *         {@code -1} if this information is not available.
    */
+  @Override
   public int getIndex()
   {
     return index;
@@ -1263,16 +1294,19 @@ public class Sequence extends ASequence implements SequenceI
    *          position for this sequence. This value is zero-based (zero for
    *          this first sequence)
    */
+  @Override
   public void setIndex(int value)
   {
     index = value;
   }
 
+  @Override
   public void setRNA(RNA r)
   {
     rna = r;
   }
 
+  @Override
   public RNA getRNA()
   {
     return rna;
@@ -1297,6 +1331,7 @@ public class Sequence extends ASequence implements SequenceI
     return result;
   }
 
+  @Override
   public String toString()
   {
     return getDisplayId(false);
@@ -1321,4 +1356,16 @@ 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;
+  }
+
 }