X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FPhylipFile.java;h=539826ffb31d811c2a6e3e39a7219386ca7524cd;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=ce65eea1486deb4d83e5f4924c1866896583859e;hpb=77abb3fac2965a8966410cd77cd749c7c1dc6453;p=jalview.git
diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index ce65eea..539826f 100644
--- a/src/jalview/io/PhylipFile.java
+++ b/src/jalview/io/PhylipFile.java
@@ -1,9 +1,25 @@
-/**
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import jalview.datamodel.Alignment;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
@@ -11,9 +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).
*
@@ -22,7 +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
@@ -43,9 +60,6 @@ import java.io.IOException;
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";
/**
@@ -69,13 +83,14 @@ public class PhylipFile extends AlignFile
/**
* @param inFile
- * @param type
+ * @param sourceType
* @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);
}
/**
@@ -98,8 +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)
{
@@ -130,8 +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)));
}
@@ -171,13 +186,6 @@ public class PhylipFile extends AlignFile
seqs.add(sequenceElements[i]);
}
- // create an alignment based on the sequences
- Alignment a = new Alignment(sequenceElements);
- // add annotations - although comments say addAnnotations
- // is used by AppletFormatAdapter, it doesn't say other
- // classes should/can not use it
- addAnnotations(a);
-
} catch (IOException e)
{
System.err.println("Exception parsing PHYLIP file " + e);
@@ -209,14 +217,14 @@ public class PhylipFile extends AlignFile
*/
private String validateName(String name) throws IOException
{
- char[] invalidCharacters = new char[]
- { '(', ')', '[', ']', ':', ';', ',' };
+ char[] invalidCharacters = new char[] { '(', ')', '[', ']', ':', ';',
+ ',' };
for (char c : invalidCharacters)
{
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;
@@ -233,15 +241,15 @@ public class PhylipFile extends AlignFile
* @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(
- (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
@@ -253,7 +261,7 @@ public class PhylipFile extends AlignFile
int numInterleavedColumns = 60;
int sequenceLength = 0;
- for (SequenceI s : seqs)
+ for (SequenceI s : sqs)
{
// ensure name is only 10 characters
@@ -272,13 +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,
@@ -304,11 +312,10 @@ public class PhylipFile extends AlignFile
// 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
- + numInterleavedColumns, sequenceLength)))
+ sb.append(s.getSequence(start,
+ Math.min(start + numInterleavedColumns, sequenceLength)))
.append(newline);
}
}
@@ -317,4 +324,4 @@ public class PhylipFile extends AlignFile
return sb.toString();
}
-}
\ No newline at end of file
+}