Merge branch 'bug/JAL-2750' into develop

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index deabf46..fc8ac49 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -30,6 +30,7 @@ import java.awt.Color;
 import java.beans.PropertyChangeListener;
 import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 
@@ -1196,9 +1197,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       if (consensus.annotations[i] != null)
       {
-        if (consensus.annotations[i].description.charAt(0) == '[')
+        String desc = consensus.annotations[i].description;
+        if (desc.length() > 1 && desc.charAt(0) == '[')
         {
-          seqs.append(consensus.annotations[i].description.charAt(1));
+          seqs.append(desc.charAt(1));
         }
         else
         {
@@ -1324,39 +1326,16 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<>();
-    if (calcId == null)
-    {
-      return aa;
-    }
-    for (AlignmentAnnotation a : getAlignmentAnnotation())
-    {
-      if (calcId.equals(a.getCalcId()))
-      {
-        aa.add(a);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotation(
+            Arrays.asList(getAlignmentAnnotation()), calcId);
   }
 
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
-    for (AlignmentAnnotation ann : getAlignmentAnnotation())
-    {
-      if ((calcId == null || (ann.getCalcId() != null
-              && ann.getCalcId().equals(calcId)))
-              && (seq == null || (ann.sequenceRef != null
-                      && ann.sequenceRef == seq))
-              && (label == null
-                      || (ann.label != null && ann.label.equals(label))))
-      {
-        aa.add(ann);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotations(
+            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
   }
 
   /**
@@ -1367,17 +1346,8 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public boolean hasAnnotation(String calcId)
   {
-    if (calcId != null && !"".equals(calcId))
-    {
-      for (AlignmentAnnotation a : getAlignmentAnnotation())
-      {
-        if (a.getCalcId() == calcId)
-        {
-          return true;
-        }
-      }
-    }
-    return false;
+    return AlignmentAnnotation
+            .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId);
   }
 
   /**