JAL-1264 added getAlignmentAnnotations(calcId, label)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 945a9d4..f628699 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -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;
@@ -901,7 +903,7 @@ public class Sequence implements SequenceI
     AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
     for (int r = 0; r < ret.length; r++)
     {
-      ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
+      ret[r] = annotation.elementAt(r);
     }
 
     return ret;
@@ -1080,6 +1082,33 @@ public class Sequence implements SequenceI
     return anns;
   }
 
+  /**
+   * Returns a list of any annotations on the sequence that match the given
+   * calcId (source) and label (type). Null values do not match.
+   * 
+   * @param calcId
+   * @param label
+   * @return
+   */
+  @Override
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label)
+  {
+    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+    if (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;
+  }
+
   public boolean updatePDBIds()
   {
     if (datasetSequence != null)

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index b10a4d4..366b776 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,6 +20,7 @@
  */\r
 package jalview.datamodel;\r
 \r
+import java.util.List;\r
 import java.util.Vector;\r
 \r
 import fr.orsay.lri.varna.models.rna.RNA;\r
@@ -342,6 +343,17 @@ public interface SequenceI
   public AlignmentAnnotation[] getAnnotation(String label);\r
 \r
   /**\r
+   * Return a list of any annotations which match the given calcId (source) and\r
+   * label (type). Null values do not match.\r
+   * \r
+   * @param calcId\r
+   * @param label\r
+   * @return\r
+   */\r
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,\r
+          String label);\r
+\r
+  /**\r
    * create a new dataset sequence (if necessary) for this sequence and sets\r
    * this sequence to refer to it. This call will move any features or\r
    * references on the sequence onto the dataset. It will also make a duplicate\r