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3253 reconciled with develop
[jalview.git]
/
src
/
jalview
/
io
/
PIRFile.java
diff --git
a/src/jalview/io/PIRFile.java
b/src/jalview/io/PIRFile.java
index
28f553a
..
d9ed516
100755
(executable)
--- a/
src/jalview/io/PIRFile.java
+++ b/
src/jalview/io/PIRFile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,10
+20,12
@@
*/
package jalview.io;
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
public class PIRFile extends AlignFile
{
public class PIRFile extends AlignFile
{
@@
-35,9
+37,10
@@
public class PIRFile extends AlignFile
{
}
{
}
- public PIRFile(String inFile, String type) throws IOException
+ public PIRFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public PIRFile(FileParse source) throws IOException
}
public PIRFile(FileParse source) throws IOException
@@
-45,6
+48,7
@@
public class PIRFile extends AlignFile
super(source);
}
super(source);
}
+ @Override
public void parse() throws IOException
{
StringBuffer sequence;
public void parse() throws IOException
{
StringBuffer sequence;
@@
-99,14
+103,10
@@
public class PIRFile extends AlignFile
}
}
}
}
- public String print()
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
{
- return print(getSeqsAsArray());
- }
-
- public String print(SequenceI[] s)
- {
- boolean is_NA = jalview.util.Comparison.isNucleotide(s);
+ boolean is_NA = Comparison.isNucleotide(s);
int len = 72;
StringBuffer out = new StringBuffer();
int i = 0;
int len = 72;
StringBuffer out = new StringBuffer();
int i = 0;
@@
-158,7
+158,7
@@
public class PIRFile extends AlignFile
}
else
{
}
else
{
- out.append(">P1;" + printId(s[i]));
+ out.append(">P1;" + printId(s[i], jvsuffix));
out.append(newline);
if (s[i].getDescription() != null)
{
out.append(newline);
if (s[i].getDescription() != null)
{
@@
-173,7
+173,8
@@
public class PIRFile extends AlignFile
}
}
}
}
}
}
- int nochunks = (seq.length() / len) + 1;
+ int nochunks = (seq.length() / len)
+ + (seq.length() % len > 0 ? 1 : 0);
for (int j = 0; j < nochunks; j++)
{
for (int j = 0; j < nochunks; j++)
{