X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=7c4b3c71c7693f8b717d72f9ce1e880a5013baac;hb=ec669c13867d001e07c9cef157c268afe03be9f3;hp=c1f3c2ab87a22aa44e96be38a3f0477834173abd;hpb=7850b5cdcf8f8b19fdf8c1e29498b35f609f754f;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index c1f3c2a..7c4b3c7 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.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.
@@ -147,7 +147,9 @@ public class Alignment implements AlignmentI
   public SequenceI[] getSequencesArray()
   {
     if (sequences == null)
+    {
       return null;
+    }
     synchronized (sequences)
     {
       return sequences.toArray(new SequenceI[sequences.size()]);
@@ -211,7 +213,9 @@ public class Alignment implements AlignmentI
       }
     }
     if (hiddenSequences != null)
+    {
       hiddenSequences.adjustHeightSequenceAdded();
+    }
   }
 
   /**
@@ -245,7 +249,9 @@ public class Alignment implements AlignmentI
   public void finalize()
   {
     if (getDataset() != null)
+    {
       getDataset().removeAlignmentRef();
+    }
 
     dataset = null;
     sequences = null;
@@ -754,7 +760,9 @@ public class Alignment implements AlignmentI
         continue;
       }
       if (tIndex < temp.length)
+      {
         temp[tIndex++] = annotations[i];
+      }
     }
 
     if (swap)
@@ -1171,7 +1179,9 @@ public class Alignment implements AlignmentI
   public void setProperty(Object key, Object value)
   {
     if (alignmentProperties == null)
+    {
       alignmentProperties = new Hashtable();
+    }
 
     alignmentProperties.put(key, value);
   }
@@ -1180,9 +1190,13 @@ public class Alignment implements AlignmentI
   public Object getProperty(Object key)
   {
     if (alignmentProperties != null)
+    {
       return alignmentProperties.get(key);
+    }
     else
+    {
       return null;
+    }
   }
 
   @Override
@@ -1204,7 +1218,9 @@ public class Alignment implements AlignmentI
   public void addCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null)
+    {
       return;
+    }
     if (codonFrameList == null)
     {
       codonFrameList = new AlignedCodonFrame[]
@@ -1238,15 +1254,21 @@ public class Alignment implements AlignmentI
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
   {
     if (seq == null || codonFrameList == null)
+    {
       return null;
+    }
     Vector cframes = new Vector();
     for (int f = 0; f < codonFrameList.length; f++)
     {
       if (codonFrameList[f].involvesSequence(seq))
+      {
         cframes.addElement(codonFrameList[f]);
+      }
     }
     if (cframes.size() == 0)
+    {
       return null;
+    }
     AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
     cframes.copyInto(cfr);
     return cfr;
@@ -1273,7 +1295,9 @@ public class Alignment implements AlignmentI
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null || codonFrameList == null)
+    {
       return false;
+    }
     boolean removed = false;
     int i = 0, iSize = codonFrameList.length;
     while (i < iSize)
@@ -1465,6 +1489,27 @@ public class Alignment implements AlignmentI
     return aa;
   }
 
+  /**
+   * Returns an iterable collection of any annotations that match on given
+   * sequence ref, calcId and label (ignoring null values).
+   */
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+          String calcId, String label)
+  {
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation ann : getAlignmentAnnotation())
+    {
+      if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+              && ann.sequenceRef != null && ann.sequenceRef == seq
+              && ann.label != null && ann.label.equals(label))
+      {
+        aa.add(ann);
+      }
+    }
+    return aa;
+  }
+
   @Override
   public void moveSelectedSequencesByOne(SequenceGroup sg,
           Map<SequenceI, SequenceCollectionI> map, boolean up)