X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=bfeafd6629a9458527b2a05a2782b7122ae75f16;hb=0b2e0f52baa343973a6c9b1e652ff584ce418fa0;hp=e9f6d1f3becf742506e04f4dece6794d93fbbb45;hpb=d6509fcf3a8cc90616e18cb22cec97f85c722bb8;p=jalview.git
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index e9f6d1f..bfeafd6 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,23 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
public class HiddenSequences
{
@@ -140,32 +145,34 @@ public class HiddenSequences
alignment.deleteSequence(sequence);
}
- public Vector showAll(Map hiddenRepSequences)
+ public List showAll(
+ Map hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List revealedSeqs = new ArrayList();
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 tmp = showSequence(i, hiddenRepSequences);
+ for (SequenceI seq : tmp)
{
- revealedSeqs.addElement(tmp.elementAt(t));
+ revealedSeqs.add(seq);
}
}
}
return revealedSeqs;
}
- public Vector showSequence(int alignmentIndex, Map hiddenRepSequences)
+ public List showSequence(int alignmentIndex,
+ Map hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List revealedSeqs = new ArrayList();
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);
@@ -187,7 +194,7 @@ public class HiddenSequences
{
if (seq.getLength() > 0)
{
- revealedSeqs.addElement(seq);
+ revealedSeqs.add(seq);
asequences.add(alignmentIndex, seq);
}
else