JAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 0652fb5..cf1c983 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -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];
@@ -685,11 +681,7 @@ public class Sequence implements SequenceI
     return map;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#deleteChars(int, int)
-   */
+  @Override
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;
@@ -768,16 +760,7 @@ 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 +790,31 @@ 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 +825,7 @@ public class Sequence implements SequenceI
     return dbrefs;
   }
 
+  @Override
   public void addDBRef(DBRefEntry entry)
   {
     if (dbrefs == null)
@@ -869,40 +858,33 @@ public class Sequence implements SequenceI
     dbrefs = temp;
   }
 
+  @Override
   public void setDatasetSequence(SequenceI seq)
   {
     datasetSequence = seq;
   }
 
+  @Override
   public SequenceI getDatasetSequence()
   {
     return datasetSequence;
   }
 
-  /**
-   * Returns a new array containing this sequence's annotations, or null.
-   */
+  @Override
   public AlignmentAnnotation[] getAnnotation()
   {
     return annotation == null ? null : annotation
             .toArray(new AlignmentAnnotation[annotation.size()]);
   }
 
-  /**
-   * Returns true if this sequence has the given annotation (by object
-   * identity).
-   */
+
   @Override
   public boolean hasAnnotation(AlignmentAnnotation ann)
   {
     return annotation == null ? false : annotation.contains(ann);
   }
 
-  /**
-   * Add the given annotation, if not already added, and set its sequence ref to
-   * 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)
@@ -948,11 +930,7 @@ public class Sequence implements SequenceI
     return true;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#deriveSequence()
-   */
+  @Override
   public SequenceI deriveSequence()
   {
     SequenceI seq = new Sequence(this);
@@ -1043,11 +1021,7 @@ public class Sequence implements SequenceI
     }
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
-   */
+  @Override
   public AlignmentAnnotation[] getAnnotation(String label)
   {
     if (annotation == null || annotation.size() == 0)
@@ -1080,6 +1054,7 @@ public class Sequence implements SequenceI
     return anns;
   }
 
+  @Override
   public boolean updatePDBIds()
   {
     if (datasetSequence != null)
@@ -1133,13 +1108,7 @@ public class Sequence implements SequenceI
     return false;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see
-   * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
-   * jalview.datamodel.Mapping)
-   */
+  @Override
   public void transferAnnotation(SequenceI entry, Mapping mp)
   {
     if (datasetSequence != null)
@@ -1235,13 +1204,6 @@ public class Sequence implements SequenceI
     return rna;
   }
 
-  /**
-   * Returns a (possibly empty) list of any annotations that match on given
-   * calcId (source) and label (type). Null values do not match.
-   * 
-   * @param calcId
-   * @param label
-   */
   @Override
   public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
           String label)

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index fc67efd..46669ae 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -315,10 +315,22 @@ public interface SequenceI
 
   public SequenceI getDatasetSequence();
 
+  /**
+   * Returns a new array containing this sequence's annotations, or null.
+   */
   public AlignmentAnnotation[] getAnnotation();
 
+  /**
+   * Returns true if this sequence has the given annotation (by object
+   * identity).
+   */
   public boolean hasAnnotation(AlignmentAnnotation ann);
 
+  /**
+   * Add the given annotation, if not already added, and set its sequence ref to
+   * be this sequence. Does nothing if this sequence's annotations already
+   * include this annotation (by identical object reference).
+   */
   public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
   public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
@@ -347,12 +359,11 @@ public interface SequenceI
   public AlignmentAnnotation[] getAnnotation(String label);
 
   /**
-   * Return a list of any annotations which match the given calcId (source) and
-   * label (type). Null values do not match.
+   * Returns a (possibly empty) list of any annotations that match on given
+   * calcId (source) and label (type). Null values do not match.
    * 
    * @param calcId
    * @param label
-   * @return
    */
   public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
           String label);