/*
- * 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
package jalview.io;
/**
- * <p>Title: </p>
- * PileUpfile
- * <p>Description: </p>
- *
- * Read and write PileUp style MSF Files.
- * This used to be the MSFFile class, and was written according to the EBI's idea
- * of a subset of the MSF alignment format. But, that was updated to reflect current
- * GCG style IO fashion, as found in Emboss (thanks David Martin!)
- *
- **/
+ * <p>
+ * Title:
+ * </p>
+ * PileUpfile
+ * <p>
+ * Description:
+ * </p>
+ *
+ * Read and write PileUp style MSF Files. This used to be the MSFFile class, and
+ * was written according to the EBI's idea of a subset of the MSF alignment
+ * format. But, that was updated to reflect current GCG style IO fashion, as
+ * found in Emboss (thanks David Martin!)
+ *
+ */
import java.io.*;
import jalview.datamodel.*;
import jalview.util.*;
-public class PileUpfile
- extends MSFfile
+public class PileUpfile extends MSFfile
{
/**
/**
* Creates a new MSFfile object.
- *
- * @param inFile DOCUMENT ME!
- * @param type DOCUMENT ME!
- *
- * @throws IOException DOCUMENT ME!
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
*/
- public PileUpfile(String inFile, String type)
- throws IOException
+ public PileUpfile(String inFile, String type) throws IOException
{
super(inFile, type);
}
+
public PileUpfile(FileParse source) throws IOException
{
super(source);
}
+
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String print()
i++;
}
- out.append(" MSF: " + s[0].getSequence().length +
- " Type: P Check: " + bigChecksum % 10000 + " ..\n\n\n");
+ out.append(" MSF: " + s[0].getSequence().length
+ + " Type: P Check: " + bigChecksum % 10000
+ + " ..\n\n\n");
i = 0;
- while ( (i < s.length) && (s[i] != null))
+ 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");
+ out.append(" Name: " + printId(s[i]) + " oo Len: " + seq.length()
+ + " Check: " + checksums[i] + " Weight: 1.00\n");
if (seq.length() > max)
{
int nochunks = (max / len) + 1;
- if ( (max % len) == 0)
+ if ((max % len) == 0)
{
nochunks--;
}
{
int j = 0;
- while ( (j < s.length) && (s[j] != null))
+ while ((j < s.length) && (s[j] != null))
{
String name = printId(s[j]);
int start = (i * 50) + (k * 10);
int end = start + 10;
- if ( (end < s[j].getSequence().length) &&
- (start < s[j].getSequence().length))
+ if ((end < s[j].getSequence().length)
+ && (start < s[j].getSequence().length))
{
out.append(s[j].getSequence(start, end));