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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
8402d24
..
d9ed516
100755
(executable)
--- a/
src/jalview/io/PIRFile.java
+++ b/
src/jalview/io/PIRFile.java
@@
-22,6
+22,7
@@
package jalview.io;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.io.IOException;
import java.util.Vector;
import java.io.IOException;
import java.util.Vector;
@@
-103,14
+104,9
@@
public class PIRFile extends AlignFile
}
@Override
}
@Override
- public String print()
+ 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;
@@
-162,7
+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)
{