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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git]
/
src
/
jalview
/
io
/
FastaFile.java
diff --git
a/src/jalview/io/FastaFile.java
b/src/jalview/io/FastaFile.java
index
6e5de81
..
ec1c82e
100755
(executable)
--- a/
src/jalview/io/FastaFile.java
+++ b/
src/jalview/io/FastaFile.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.
*
@@
-20,9
+20,13
@@
*/
package jalview.io;
*/
package jalview.io;
-import java.io.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-73,6
+77,7
@@
public class FastaFile extends AlignFile
* @throws IOException
* DOCUMENT ME!
*/
* @throws IOException
* DOCUMENT ME!
*/
+ @Override
public void parse() throws IOException
{
StringBuffer sb = new StringBuffer();
public void parse() throws IOException
{
StringBuffer sb = new StringBuffer();
@@
-169,8
+174,7
@@
public class FastaFile extends AlignFile
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
- AlignmentAnnotation aa = (AlignmentAnnotation) annotations
- .elementAt(i);
+ AlignmentAnnotation aa = annotations.elementAt(i);
aa.setPadGaps(true, al.getGapCharacter());
al.addAnnotation(aa);
}
aa.setPadGaps(true, al.getGapCharacter());
al.addAnnotation(aa);
}
@@
-205,7
+209,8
@@
public class FastaFile extends AlignFile
out.append(newline);
out.append(newline);
- int nochunks = (s[i].getLength() / len) + 1;
+ int nochunks = (s[i].getLength() / len)
+ + (s[i].getLength() % len > 0 ? 1 : 0);
for (int j = 0; j < nochunks; j++)
{
for (int j = 0; j < nochunks; j++)
{
@@
-234,6
+239,7
@@
public class FastaFile extends AlignFile
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
+ @Override
public String print()
{
return print(getSeqsAsArray());
public String print()
{
return print(getSeqsAsArray());