JAL-1620 version bump and release notes

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 945a9d4..338aa62 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -22,7 +22,9 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
 
+import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.List;
 import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
@@ -491,7 +493,9 @@ public class Sequence implements SequenceI
   public char[] getSequence(int start, int end)
   {
     if (start < 0)
+    {
       start = 0;
+    }
     // JBPNote - left to user to pad the result here (TODO:Decide on this
     // policy)
     if (start >= sequence.length)
@@ -510,16 +514,7 @@ public class Sequence implements SequenceI
     return reply;
   }
 
-  /**
-   * make a new Sequence object from start to end (including gaps) over this
-   * seqeunce
-   * 
-   * @param start
-   *          int
-   * @param end
-   *          int
-   * @return SequenceI
-   */
+  @Override
   public SequenceI getSubSequence(int start, int end)
   {
     if (start < 0)
@@ -619,14 +614,7 @@ public class Sequence implements SequenceI
     }
   }
 
-  /**
-   * Returns the sequence position for an alignment position
-   * 
-   * @param i
-   *          column index in alignment (from 1)
-   * 
-   * @return residue number for residue (left of and) nearest ith column
-   */
+  @Override
   public int findPosition(int i)
   {
     int j = 0;
@@ -891,22 +879,30 @@ public class Sequence implements SequenceI
     return datasetSequence;
   }
 
+  /**
+   * Returns a new array containing this sequence's annotations, or null.
+   */
   public AlignmentAnnotation[] getAnnotation()
   {
-    if (annotation == null)
-    {
-      return null;
-    }
-
-    AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
-    for (int r = 0; r < ret.length; r++)
-    {
-      ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
-    }
+    return annotation == null ? null : annotation
+            .toArray(new AlignmentAnnotation[annotation.size()]);
+  }
 
-    return ret;
+  /**
+   * 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).
+   */
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)
@@ -926,7 +922,9 @@ public class Sequence implements SequenceI
     {
       this.annotation.removeElement(annotation);
       if (this.annotation.size() == 0)
+      {
         this.annotation = null;
+      }
     }
   }
 
@@ -1038,7 +1036,9 @@ public class Sequence implements SequenceI
       for (int i = 0; i < annotations.length; i++)
       {
         if (annotations[i] != null)
+        {
           addAlignmentAnnotation(annotations[i]);
+        }
       }
     }
   }
@@ -1235,4 +1235,28 @@ 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)
+  {
+    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+    if (this.annotation != null) {
+      for (AlignmentAnnotation ann : annotation) {
+        if (ann.calcId != null && ann.calcId.equals(calcId)
+                && ann.label != null && ann.label.equals(label))
+        {
+          result.add(ann);
+        }
+      }
+    }
+    return result;
+  }
+
 }