JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index aefb5cc..09c1b78 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,9 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
 
 public class HiddenSequences
 {
@@ -143,34 +145,34 @@ public class HiddenSequences
     alignment.deleteSequence(sequence);
   }
 
-  public Vector showAll(
+  public List<SequenceI> showAll(
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    Vector revealedSeqs = new Vector();
+    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
     for (int i = 0; i < hiddenSequences.length; i++)
     {
       if (hiddenSequences[i] != null)
       {
-        Vector tmp = showSequence(i, hiddenRepSequences);
-        for (int t = 0; t < tmp.size(); t++)
+        List<SequenceI> tmp = showSequence(i, hiddenRepSequences);
+        for (SequenceI seq : tmp)
         {
-          revealedSeqs.addElement(tmp.elementAt(t));
+          revealedSeqs.add(seq);
         }
       }
     }
     return revealedSeqs;
   }
 
-  public Vector showSequence(int alignmentIndex,
+  public List<SequenceI> showSequence(int alignmentIndex,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    Vector revealedSeqs = new Vector();
+    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
     if (repSequence != null && hiddenRepSequences != null
             && hiddenRepSequences.containsKey(repSequence))
     {
       hiddenRepSequences.remove(repSequence);
-      revealedSeqs.addElement(repSequence);
+      revealedSeqs.add(repSequence);
     }
 
     int start = adjustForHiddenSeqs(alignmentIndex - 1);
@@ -192,7 +194,7 @@ public class HiddenSequences
         {
           if (seq.getLength() > 0)
           {
-            revealedSeqs.addElement(seq);
+            revealedSeqs.add(seq);
             asequences.add(alignmentIndex, seq);
           }
           else
@@ -270,17 +272,25 @@ public class HiddenSequences
         index++;
       }
     }
+    Alignment fAlignmt = new Alignment(seq);
+    fAlignmt.annotations = alignment.getAlignmentAnnotation();
+    fAlignmt.alignmentProperties = alignment.getProperties();
+    fAlignmt.groups = alignment.getGroups();
+    fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
 
-    return new Alignment(seq);
+    return fAlignmt;
   }
 
   public boolean isHidden(SequenceI seq)
   {
-    for (int i = 0; i < hiddenSequences.length; i++)
+    if (hiddenSequences != null)
     {
-      if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+      for (int i = 0; i < hiddenSequences.length; i++)
       {
-        return true;
+        if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+        {
+          return true;
+        }
       }
     }