X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAnnotatedCollectionI.java;h=755333ce509c033d72b6e28c0486187de041f649;hb=cfbb94908f5b2d247b763e2663f180058efda7aa;hp=74568e45fd4a4ce2f3e1ee4a88e63142e488b3dc;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index 74568e4..755333c 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -31,8 +31,26 @@ public interface AnnotatedCollectionI extends SequenceCollectionI
    */
   AlignmentAnnotation[] getAlignmentAnnotation();
 
+  /**
+   * Returns a list of annotations matching the given calc id, or an empty list
+   * if calcId is null
+   * 
+   * @param calcId
+   * @return
+   */
   Iterable<AlignmentAnnotation> findAnnotation(String calcId);
 
+  /**
+   * Returns an iterable collection of any annotations that match on given
+   * sequence ref, calcId and label (ignoring null values).
+   * 
+   * @param seq
+   *          null or reference sequence to select annotation for
+   * @param calcId
+   *          null or the calcId to select annotation for
+   * @param label
+   *          null or the label to select annotation for
+   */
   Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label);
 
@@ -43,4 +61,22 @@ public interface AnnotatedCollectionI extends SequenceCollectionI
    *         alignment, parent group).
    */
   AnnotatedCollectionI getContext();
+
+  /**
+   * Returns the number of the highest annotation graph group attached to this
+   * alignment.
+   */
+  default int getLastGraphGroup()
+  {
+    var annots = getAlignmentAnnotation();
+    if (annots == null)
+      return 1;
+    int graphGroup = 1;
+    for (AlignmentAnnotation ala : annots)
+    {
+      graphGroup = Math.max(graphGroup, ala.graphGroup);
+    }
+    return graphGroup;
+  }
+
 }