/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.io;
* Creates a new FastaFile object.
*
* @param inFile
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public FastaFile(String inFile, String type) throws IOException
{
* DOCUMENT ME!
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void parse() throws IOException
{
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param len
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param gaps
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param displayId
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
out.append(" " + s[i].getDescription());
}
- out.append("\n");
+ out.append(newline);
int nochunks = (s[i].getLength() / len) + 1;
if (end < s[i].getLength())
{
- out.append(s[i].getSequenceAsString(start, end) + "\n");
+ out.append(s[i].getSequenceAsString(start, end) + newline);
}
else if (start < s[i].getLength())
{
out.append(s[i].getSequenceAsString(start, s[i].getLength())
- + "\n");
+ + newline);
}
}