-/**
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import jalview.datamodel.Alignment;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
seqs.add(sequenceElements[i]);
}
- // create an alignment based on the sequences
- Alignment a = new Alignment(sequenceElements);
- // add annotations - although comments say addAnnotations
- // is used by AppletFormatAdapter, it doesn't say other
- // classes should/can not use it
- addAnnotations(a);
-
} catch (IOException e)
{
System.err.println("Exception parsing PHYLIP file " + e);
*/
private String validateName(String name) throws IOException
{
- char[] invalidCharacters = new char[]
- { '(', ')', '[', ']', ':', ';', ',' };
+ char[] invalidCharacters = new char[] { '(', ')', '[', ']', ':', ';',
+ ',' };
for (char c : invalidCharacters)
{
if (name.indexOf(c) > -1)
return sb.toString();
}
-}
\ No newline at end of file
+}