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JAL-4001 Check --nousagestats before doing analytics in headless mode
[jalview.git]
/
src
/
jalview
/
io
/
PhylipFile.java
diff --git
a/src/jalview/io/PhylipFile.java
b/src/jalview/io/PhylipFile.java
index
2a961a2
..
12e87a6
100644
(file)
--- a/
src/jalview/io/PhylipFile.java
+++ b/
src/jalview/io/PhylipFile.java
@@
-247,9
+247,7
@@
public class PhylipFile extends AlignFile
StringBuffer sb = new StringBuffer(Integer.toString(sqs.length));
sb.append(" ");
// if there are no sequences, then define the number of characters as 0
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(
- (sqs.length > 0) ? Integer.toString(sqs[0].getSequence().length)
- : "0")
+ sb.append((sqs.length > 0) ? Integer.toString(sqs[0].getLength()) : "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
@@
-280,13
+278,13
@@
public class PhylipFile extends AlignFile
// sequential has the entire sequence following the name
if (sequential)
{
// sequential has the entire sequence following the name
if (sequential)
{
- sb.append(s.getSequence());
+ sb.append(s.getSequenceAsString());
}
else
{
// Jalview ensures all sequences are of same length so no need
// to keep track of min/max length
}
else
{
// Jalview ensures all sequences are of same length so no need
// to keep track of min/max length
- sequenceLength = s.getSequence().length;
+ sequenceLength = s.getLength();
// interleaved breaks the sequence into chunks for
// interleavedColumns characters
sb.append(s.getSequence(0,
// interleaved breaks the sequence into chunks for
// interleavedColumns characters
sb.append(s.getSequence(0,