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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git]
/
src
/
jalview
/
io
/
PileUpfile.java
diff --git
a/src/jalview/io/PileUpfile.java
b/src/jalview/io/PileUpfile.java
index
d120ac3
..
e826687
100755
(executable)
--- a/
src/jalview/io/PileUpfile.java
+++ b/
src/jalview/io/PileUpfile.java
@@
-1,19
+1,22
@@
/*
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*
* This file is part of Jalview.
*
* 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.
- *
+ * 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.
*
* 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
*/
package jalview.io;
@@
-32,18
+35,10
@@
package jalview.io;
* found in Emboss (thanks David Martin!)
*
*/
* found in Emboss (thanks David Martin!)
*
*/
-import java.io.*;
-
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
public class PileUpfile extends MSFfile
{
public class PileUpfile extends MSFfile
{
@@
-65,19
+60,13
@@
public class PileUpfile extends MSFfile
*
* @throws IOException
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
*/
*/
- public PileUpfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PileUpfile(String inFile, String type) throws IOException
{
super(inFile, type);
}
{
super(inFile, type);
}
- public PileUpfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PileUpfile(FileParse source) throws IOException
{
super(source);
}
{
super(source);
}
@@
-97,7
+86,7
@@
public class PileUpfile extends MSFfile
StringBuffer out = new StringBuffer("PileUp");
out.append(newline);
out.append(newline);
StringBuffer out = new StringBuffer("PileUp");
out.append(newline);
out.append(newline);
-
+
int max = 0;
int maxid = 0;
int max = 0;
int maxid = 0;
@@
-112,8
+101,7
@@
public class PileUpfile extends MSFfile
}
out.append(" MSF: " + s[0].getSequence().length
}
out.append(" MSF: " + s[0].getSequence().length
- + " Type: P Check: " + bigChecksum % 10000
- + " ..");
+ + " Type: P Check: " + bigChecksum % 10000 + " ..");
out.append(newline);
out.append(newline);
out.append(newline);
out.append(newline);
out.append(newline);
out.append(newline);
@@
-145,8
+133,11
@@
public class PileUpfile extends MSFfile
}
maxid++;
}
maxid++;
- out.append(newline);out.append(newline);out.append("//");
- out.append(newline);out.append(newline);
+ out.append(newline);
+ out.append(newline);
+ out.append("//");
+ out.append(newline);
+ out.append(newline);
int len = 50;
int len = 50;