/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
/**
* Additional formatting methods used by the application in a number of places.
afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX",
true));
}
+ else if (format.equalsIgnoreCase("MEGA"))
+ {
+ afile = new MegaFile();
+ afile.addJVSuffix(jalview.bin.Cache.getDefault("MEGA_JVSUFFIX",
+ true));
+ }
/*
* amsa is not supported by this function - it requires an alignment
* rather than a sequence vector else if (format.equalsIgnoreCase("AMSA"))
{
// TODO consider using AlignmentView to prune to visible region
// TODO prune sequence annotation and groups to visible region
- // TODO: JAL-1486 - set start and end for output correctly. basically, AlignmentView.getVisibleContigs does this.
+ // TODO: JAL-1486 - set start and end for output correctly. basically,
+ // AlignmentView.getVisibleContigs does this.
Alignment alv = new Alignment(replaceStrings(
alignment.getSequencesArray(), omitHidden));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();