/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, 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 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.
- *
+ *
* 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
import jalview.datamodel.*;
-public class PIRFile
- extends AlignFile
+public class PIRFile extends AlignFile
{
public static boolean useModellerOutput = false;
- Vector words = new Vector(); //Stores the words in a line after splitting
+ Vector words = new Vector(); // Stores the words in a line after splitting
public PIRFile()
{
}
- public PIRFile(String inFile, String type)
- throws IOException
+ public PIRFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
+
public PIRFile(FileParse source) throws IOException
{
super(source);
}
- public void parse()
- throws IOException
+
+ public void parse() throws IOException
{
StringBuffer sequence;
String line = null;
ModellerDescription md;
- while ( (line = nextLine()) != null)
+ while ((line = nextLine()) != null)
{
if (line.length() == 0)
{
- //System.out.println("blank line");
+ // System.out.println("blank line");
continue;
}
if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
seqs.addElement(newSeq);
- md = new ModellerDescription(newSeq.
- getDescription());
+ md = new ModellerDescription(newSeq.getDescription());
md.updateSequenceI(newSeq);
}
}
int i = 0;
ModellerDescription md;
- while ( (i < s.length) && (s[i] != null))
+ while ((i < s.length) && (s[i] != null))
{
String seq = s[i].getSequenceAsString();
seq = seq + "*";
out.append(">N1;" + s[i].getName() + "\n");
if (s[i].getDescription() == null)
{
- out.append(s[i].getName() + " " +
- (s[i].getEnd() - s[i].getStart() + 1));
+ out.append(s[i].getName() + " "
+ + (s[i].getEnd() - s[i].getStart() + 1));
out.append(is_NA ? " bases\n" : " residues\n");
}
else
}
else
{
- out.append(s[i].getName() + " "
- + (s[i].getEnd() - s[i].getStart() + 1)
- + " residues\n");
+ out
+ .append(s[i].getName() + " "
+ + (s[i].getEnd() - s[i].getStart() + 1)
+ + " residues\n");
}
}
}