From a4c795966bb5dd6dc504129aa5e07b8e962293c9 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 10 Oct 2014 14:58:37 +0100
Subject: [PATCH] JAL-1264 reverted (removed added method)

---
 src/jalview/datamodel/Alignment.java            |   28 -----------------------
 src/jalview/datamodel/AnnotatedCollectionI.java |   17 --------------
 src/jalview/datamodel/SequenceGroup.java        |   24 -------------------
 3 files changed, 69 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index bfe6406..b2d4f0f 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1528,32 +1528,4 @@ public class Alignment implements AlignmentI
   {
     return dataset;
   }
-
-  /**
-   * Returns an iterable collection of annotations on this alignment which match
-   * the given criteria.
-   */
-  @Override
-  public Iterable<AlignmentAnnotation> findAnnotation(SequenceI datasequence,
-          String calcId, String label)
-  {
-    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation ann : annotations)
-    {
-      // only sequence-linked annotations can qualify (have a datasequence)
-      if (ann.sequenceRef == null)
-      {
-        continue;
-      }
-      boolean matchDatasequence = (ann.sequenceRef.getDatasetSequence() == datasequence);
-      final String annCalcId = ann.getCalcId();
-      boolean matchCalcId = (annCalcId != null && annCalcId.equals(calcId));
-      boolean matchLabel = (ann.label != null && ann.label.equals(label));
-      if (matchDatasequence && matchCalcId && matchLabel)
-      {
-        result.add(ann);
-      }
-    }
-    return result;
-  }
 }
diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index 6bd4ab9..0b4c117 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -40,21 +40,4 @@ public interface AnnotatedCollectionI extends SequenceCollectionI
    *         alignment, parent group).
    */
   AnnotatedCollectionI getContext();
-
-  /**
-   * Return an iterable set of any annotations in the collection that match the
-   * provided criteria, i.e.
-   * <ul>
-   * <li>reference the same sequence datasequence</li>
-   * <li>have the same calcId (source of annotation)</li>
-   * <li>have the same label (type of annotation)</li>
-   * </ul>
-   * 
-   * @param datasequence
-   * @param calcId
-   * @param label
-   * @return
-   */
-  Iterable<AlignmentAnnotation> findAnnotation(SequenceI datasequence,
-          String calcId, String label);
 }
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index f8fd3ee..17348c2 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1308,28 +1308,4 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     return context;
   }
-
-  @Override
-  public Iterable<AlignmentAnnotation> findAnnotation(
-          SequenceI datasequence, String calcId, String label)
-  {
-    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation ann : getAlignmentAnnotation())
-    {
-      // only sequence-linked annotations can qualify (have a datasequence)
-      if (ann.sequenceRef == null)
-      {
-        continue;
-      }
-      boolean matchDatasequence = (ann.sequenceRef.getDatasetSequence() == datasequence);
-      final String annCalcId = ann.getCalcId();
-      boolean matchCalcId = (annCalcId != null && annCalcId.equals(calcId));
-      boolean matchLabel = (ann.label != null && ann.label.equals(label));
-      if (matchDatasequence && matchCalcId && matchLabel)
-      {
-        result.add(ann);
-      }
-    }
-    return result;
-  }
 }
-- 
1.7.10.2