/*
- * 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 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
- * 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
/**
* DOCUMENT ME!
* Creates a new MSFfile object.
*
* @param inFile
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public MSFfile(String inFile, String type) throws IOException
{
super(source);
}
- {
- // TODO Auto-generated constructor stub
- }
-
/**
* DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param is_NA
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
SequenceI[] s = new SequenceI[seqs.length];
StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
- + "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't
- // remember NA or AA yet.
-
+ + "_MULTIPLE_ALIGNMENT 1.0");
+ // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+ out.append(newline);
+ out.append(newline);
int max = 0;
int maxid = 0;
int i = 0;
{
// Replace all internal gaps with . and external spaces with ~
s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
- .replace('-', '.'));
+ .replace('-', '.'), seqs[i].getStart(), seqs[i].getEnd());
StringBuffer sb = new StringBuffer();
sb.append(s[i].getSequence());
long maxNB = 0;
out.append(" MSF: " + s[0].getSequence().length + " Type: "
+ (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000)
- + " ..\n\n\n");
+ + " ..");
+ out.append(newline);
+ out.append(newline);
+ out.append(newline);
String[] nameBlock = new String[s.length];
String[] idBlock = new String[s.length];
idBlock[i] = new String("Len: "
+ maxLenpad.form(s[i].getSequence().length) + " Check: "
- + maxChkpad.form(checksums[i]) + " Weight: 1.00\n");
+ + maxChkpad.form(checksums[i]) + " Weight: 1.00" + newline);
if (s[i].getName().length() > maxid)
{
}
maxid++;
- out.append("\n\n//\n\n");
-
+ out.append(newline);
+ out.append(newline);
+ out.append("//");
+ out.append(newline);
+ out.append(newline);
int len = 50;
int nochunks = (max / len) + 1;
}
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();