/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
*
- * 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.
*
- * 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
+ * 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/>.
*/
package jalview.io;
* Creates a new MSFfile object.
*
* @param inFile
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public PileUpfile(String inFile, String type) throws IOException
{
public String print(SequenceI[] s)
{
- StringBuffer out = new StringBuffer("PileUp\n\n");
-
+ StringBuffer out = new StringBuffer("PileUp");
+ out.append(newline);
+ out.append(newline);
+
int max = 0;
int maxid = 0;
out.append(" MSF: " + s[0].getSequence().length
+ " Type: P Check: " + bigChecksum % 10000
- + " ..\n\n\n");
+ + " ..");
+ out.append(newline);
+ out.append(newline);
+ out.append(newline);
i = 0;
while ((i < s.length) && (s[i] != null))
{
String seq = s[i].getSequenceAsString();
out.append(" Name: " + printId(s[i]) + " oo Len: " + seq.length()
- + " Check: " + checksums[i] + " Weight: 1.00\n");
+ + " Check: " + checksums[i] + " Weight: 1.00");
+ out.append(newline);
if (seq.length() > max)
{
}
maxid++;
- out.append("\n\n//\n\n");
+ out.append(newline);out.append(newline);out.append("//");
+ out.append(newline);out.append(newline);
int len = 50;
}
else
{
- out.append("\n");
+ out.append(newline);
}
}
else
if (start < s[j].getSequence().length)
{
out.append(s[j].getSequenceAsString().substring(start));
- out.append("\n");
+ out.append(newline);
}
else
{
if (k == 0)
{
- out.append("\n");
+ out.append(newline);
}
}
}
j++;
}
- out.append("\n");
+ out.append(newline);
}
return out.toString();