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Merge branch 'features/JAL-2393customMatrices' into develop
[jalview.git]
/
src
/
jalview
/
io
/
PhylipFile.java
diff --git
a/src/jalview/io/PhylipFile.java
b/src/jalview/io/PhylipFile.java
index
2c8beae
..
e8fe7e9
100644
(file)
--- a/
src/jalview/io/PhylipFile.java
+++ b/
src/jalview/io/PhylipFile.java
@@
-240,15
+240,15
@@
public class PhylipFile extends AlignFile
* @see {@link AlignFile#print()}
*/
@Override
* @see {@link AlignFile#print()}
*/
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
{
- StringBuffer sb = new StringBuffer(Integer.toString(seqs.size()));
+ StringBuffer sb = new StringBuffer(Integer.toString(sqs.length));
sb.append(" ");
// if there are no sequences, then define the number of characters as 0
sb.append(
sb.append(" ");
// if there are no sequences, then define the number of characters as 0
sb.append(
- (seqs.size() > 0) ? Integer
- .toString(seqs.get(0).getSequence().length) : "0")
+ (sqs.length > 0) ? Integer.toString(sqs[0].getSequence().length)
+ : "0")
.append(newline);
// Due to how IO is handled, there doesn't appear to be a way to store
.append(newline);
// Due to how IO is handled, there doesn't appear to be a way to store
@@
-260,7
+260,7
@@
public class PhylipFile extends AlignFile
int numInterleavedColumns = 60;
int sequenceLength = 0;
int numInterleavedColumns = 60;
int sequenceLength = 0;
- for (SequenceI s : seqs)
+ for (SequenceI s : sqs)
{
// ensure name is only 10 characters
{
// ensure name is only 10 characters
@@
-311,7
+311,7
@@
public class PhylipFile extends AlignFile
// add blank line to separate this matrix from previous
sb.append(newline);
int start = i * numInterleavedColumns;
// add blank line to separate this matrix from previous
sb.append(newline);
int start = i * numInterleavedColumns;
- for (SequenceI s : seqs)
+ for (SequenceI s : sqs)
{
sb.append(
s.getSequence(start, Math.min(start
{
sb.append(
s.getSequence(start, Math.min(start