X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPhylipFile.java;h=539826ffb31d811c2a6e3e39a7219386ca7524cd;hb=c6018dc0dc12720e13b75850a5303279ac7094b7;hp=e8fe7e94b9a371b5cdb0b4778246585211a065b9;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git
diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index e8fe7e9..539826f 100644
--- a/src/jalview/io/PhylipFile.java
+++ b/src/jalview/io/PhylipFile.java
@@ -27,9 +27,9 @@ import java.io.IOException;
/**
*
- * Parser and exporter for PHYLIP file format, as defined in the
- * documentation. The parser imports PHYLIP files in both sequential and
+ * Parser and exporter for PHYLIP file format, as defined
+ * in
+ * the documentation. The parser imports PHYLIP files in both sequential and
* interleaved format, and (currently) exports in interleaved format (using 60
* characters per matrix for the sequence).
*
@@ -38,7 +38,8 @@ import java.io.IOException;
* The following assumptions have been made for input
*
* - Sequences are expressed as letters, not real numbers with decimal points
- * separated by blanks (which is a valid option according to the specification)
+ * separated by blanks (which is a valid option according to the
+ * specification)
*
*
* The following assumptions have been made for output
@@ -112,8 +113,8 @@ public class PhylipFile extends AlignFile
"First line must contain the number of specifies and number of characters");
}
- int numberSpecies = Integer.parseInt(lineElements[0]), numberCharacters = Integer
- .parseInt(lineElements[1]);
+ int numberSpecies = Integer.parseInt(lineElements[0]),
+ numberCharacters = Integer.parseInt(lineElements[1]);
if (numberSpecies <= 0)
{
@@ -144,8 +145,8 @@ public class PhylipFile extends AlignFile
}
else
{
- sequenceElements[i] = parseId(validateName(potentialName
- .substring(0, tabIndex)));
+ sequenceElements[i] = parseId(
+ validateName(potentialName.substring(0, tabIndex)));
sequences[i] = new StringBuffer(
removeWhitespace(line.substring(tabIndex)));
}
@@ -222,8 +223,8 @@ public class PhylipFile extends AlignFile
{
if (name.indexOf(c) > -1)
{
- throw new IOException("Species name contains illegal character "
- + c);
+ throw new IOException(
+ "Species name contains illegal character " + c);
}
}
return name;
@@ -247,7 +248,7 @@ public class PhylipFile extends AlignFile
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)
+(sqs.length > 0) ? Integer.toString(sqs[0].getLength())
: "0")
.append(newline);
@@ -279,13 +280,13 @@ public class PhylipFile extends AlignFile
// 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
- sequenceLength = s.getSequence().length;
+ sequenceLength = s.getLength();
// interleaved breaks the sequence into chunks for
// interleavedColumns characters
sb.append(s.getSequence(0,
@@ -313,9 +314,8 @@ public class PhylipFile extends AlignFile
int start = i * numInterleavedColumns;
for (SequenceI s : sqs)
{
- sb.append(
- s.getSequence(start, Math.min(start
- + numInterleavedColumns, sequenceLength)))
+ sb.append(s.getSequence(start,
+ Math.min(start + numInterleavedColumns, sequenceLength)))
.append(newline);
}
}