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Merge branch 'features/JAL-2446NCList' into features/JAL-2609fastPaintWrapped
[jalview.git]
/
src
/
jalview
/
io
/
PhylipFile.java
diff --git
a/src/jalview/io/PhylipFile.java
b/src/jalview/io/PhylipFile.java
index
f48f1c6
..
e1d82ee
100644
(file)
--- a/
src/jalview/io/PhylipFile.java
+++ b/
src/jalview/io/PhylipFile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 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.
*
@@
-59,9
+59,6
@@
import java.io.IOException;
public class PhylipFile extends AlignFile
{
public class PhylipFile extends AlignFile
{
- // Define file extension and description to save repeating it elsewhere
- public static final String FILE_EXT = "phy";
-
public static final String FILE_DESC = "PHYLIP";
/**
public static final String FILE_DESC = "PHYLIP";
/**
@@
-85,13
+82,14
@@
public class PhylipFile extends AlignFile
/**
* @param inFile
/**
* @param inFile
- * @param type
+ * @param sourceType
* @throws IOException
* @see {@link AlignFile#AlignFile(FileParse)}
*/
* @throws IOException
* @see {@link AlignFile#AlignFile(FileParse)}
*/
- public PhylipFile(String inFile, String type) throws IOException
+ public PhylipFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
/**
}
/**
@@
-242,15
+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].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
@@
-262,7
+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
@@
-281,13
+279,13
@@
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,
@@
-313,7
+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