X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPhylipFile.java;h=754288422ed37a68ba6abd8e31ff0227d16cea9c;hb=refs%2Fheads%2Fbug%2FJAL-4290_headless_alignment_figure_with_sse;hp=e1d82ee0303c7ee63640af9e87a581e61f6f8c6e;hpb=ff450fad8709ae81919af7a15ea382af7292794c;p=jalview.git
diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index e1d82ee..7542884 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)));
}
@@ -187,7 +188,7 @@ public class PhylipFile extends AlignFile
} catch (IOException e)
{
- System.err.println("Exception parsing PHYLIP file " + e);
+ jalview.bin.Console.errPrintln("Exception parsing PHYLIP file " + e);
e.printStackTrace(System.err);
throw e;
}
@@ -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;
@@ -246,9 +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
- sb.append(
-(sqs.length > 0) ? Integer.toString(sqs[0].getLength())
- : "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
@@ -313,9 +312,8 @@ 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);
}
}