X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=f73e250528d0f7771225137b261b6574ee8e810c;hb=d518f19c8d411d365085962d4ec8dadc78e773f9;hp=3ef721003a82c83babb5a951563de6ff79ff3c2a;hpb=a79f9e113c51c032070c670e45ce3eb464691166;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 3ef7210..f73e250 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,19 +1,22 @@
/*
- * 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.io;
@@ -21,6 +24,7 @@ import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
import java.io.IOException;
import java.util.Enumeration;
@@ -65,6 +69,10 @@ public abstract class AlignFile extends FileParse
*/
public AlignFile()
{
+ // Shouldn't we init data structures (JBPNote: not sure - initData is for
+ // initialising the structures used for reading from a datasource, and the
+ // bare constructor hasn't got any datasource)
+ initData();
}
/**
@@ -81,8 +89,9 @@ public abstract class AlignFile extends FileParse
initData();
parse();
// sets the index of each sequence in the alignment
- for( int i=0,c=seqs.size(); i