JAL-1712 fixes/tests for Castor binding and 'show flanking regions'

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 338aa62..c7b40c6 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.AlignSeq;
-
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.List;
@@ -29,6 +27,8 @@ import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
 
+import jalview.analysis.AlignSeq;
+
 /**
  * 
  * Implements the SequenceI interface for a char[] based sequence object.
@@ -339,7 +339,7 @@ public class Sequence implements SequenceI
   {
     if (pdbIds == null)
     {
-      pdbIds = new Vector();
+      pdbIds = new Vector<PDBEntry>();
     }
     if (!pdbIds.contains(entry))
     {
@@ -363,7 +363,7 @@ public class Sequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getPDBId()
+  public Vector<PDBEntry> getPDBId()
   {
     return pdbIds;
   }
@@ -661,11 +661,7 @@ public class Sequence implements SequenceI
     return map;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#findPositionMap()
-   */
+  @Override
   public int[] findPositionMap()
   {
     int map[] = new int[sequence.length];
@@ -690,6 +686,7 @@ public class Sequence implements SequenceI
    * 
    * @see jalview.datamodel.SequenceI#deleteChars(int, int)
    */
+   @Override
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;
@@ -768,16 +765,7 @@ public class Sequence implements SequenceI
     sequence = tmp;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   * @param c
-   *          DOCUMENT ME!
-   * @param chop
-   *          DOCUMENT ME!
-   */
+   @Override
   public void insertCharAt(int i, int length, char c)
   {
     char[] tmp = new char[sequence.length + length];
@@ -807,26 +795,31 @@ public class Sequence implements SequenceI
     sequence = tmp;
   }
 
+  @Override
   public void insertCharAt(int i, char c)
   {
     insertCharAt(i, 1, c);
   }
 
+  @Override
   public String getVamsasId()
   {
     return vamsasId;
   }
 
+  @Override
   public void setVamsasId(String id)
   {
     vamsasId = id;
   }
 
+  @Override
   public void setDBRef(DBRefEntry[] dbref)
   {
     dbrefs = dbref;
   }
 
+  @Override
   public DBRefEntry[] getDBRef()
   {
     if (dbrefs == null && datasetSequence != null
@@ -837,6 +830,7 @@ public class Sequence implements SequenceI
     return dbrefs;
   }
 
+  @Override
   public void addDBRef(DBRefEntry entry)
   {
     if (dbrefs == null)
@@ -869,11 +863,13 @@ public class Sequence implements SequenceI
     dbrefs = temp;
   }
 
+  @Override
   public void setDatasetSequence(SequenceI seq)
   {
     datasetSequence = seq;
   }
 
+  @Override
   public SequenceI getDatasetSequence()
   {
     return datasetSequence;
@@ -882,6 +878,7 @@ public class Sequence implements SequenceI
   /**
    * Returns a new array containing this sequence's annotations, or null.
    */
+  @Override
   public AlignmentAnnotation[] getAnnotation()
   {
     return annotation == null ? null : annotation
@@ -903,6 +900,7 @@ public class Sequence implements SequenceI
    * be this sequence. Does nothing if this sequence's annotations already
    * include this annotation (by identical object reference).
    */
+  @Override
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)
@@ -953,6 +951,7 @@ public class Sequence implements SequenceI
    * 
    * @see jalview.datamodel.SequenceI#deriveSequence()
    */
+  @Override
   public SequenceI deriveSequence()
   {
     SequenceI seq = new Sequence(this);
@@ -987,6 +986,7 @@ public class Sequence implements SequenceI
    * 
    * @see jalview.datamodel.SequenceI#createDatasetSequence()
    */
+  @Override
   public SequenceI createDatasetSequence()
   {
     if (datasetSequence == null)
@@ -1048,6 +1048,7 @@ public class Sequence implements SequenceI
    * 
    * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
    */
+  @Override
   public AlignmentAnnotation[] getAnnotation(String label)
   {
     if (annotation == null || annotation.size() == 0)
@@ -1080,6 +1081,7 @@ public class Sequence implements SequenceI
     return anns;
   }
 
+  @Override
   public boolean updatePDBIds()
   {
     if (datasetSequence != null)
@@ -1140,6 +1142,7 @@ public class Sequence implements SequenceI
    * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
    * jalview.datamodel.Mapping)
    */
+  @Override
   public void transferAnnotation(SequenceI entry, Mapping mp)
   {
     if (datasetSequence != null)