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java.lang.Objectorg.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat
public class PHYLIPFileFormat
Reads PHYLIP interleaved alignment files and fires events at a PHYLIPFileListener object.
Method Summary | |
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static void |
parse(PHYLIPFileListener listener,
BufferedReader reader)
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static void |
parseFile(PHYLIPFileListener listener,
File inputFile)
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static void |
parseInputStream(PHYLIPFileListener listener,
InputStream inputStream)
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static void |
parseReader(PHYLIPFileListener listener,
Reader inputReader)
|
static void |
writeFile(File file,
Alignment alignment)
Writes the given Alignment in PHYLIP format to a file. |
static void |
writeStream(OutputStream os,
Alignment alignment)
Writes the given Alignment in PHYLIP format to a stream. |
static void |
writeWriter(Writer writer,
Alignment alignment)
Writes the given Alignment in PHYLIP format to a writer. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static void parseFile(PHYLIPFileListener listener, File inputFile) throws IOException, ParseException
IOException
ParseException
public static void parseInputStream(PHYLIPFileListener listener, InputStream inputStream) throws IOException, ParseException
IOException
ParseException
public static void parseReader(PHYLIPFileListener listener, Reader inputReader) throws IOException, ParseException
IOException
ParseException
public static void parse(PHYLIPFileListener listener, BufferedReader reader) throws IOException, ParseException
IOException
ParseException
public static void writeFile(File file, Alignment alignment) throws IOException
file
- the file to write to.alignment
- the Alignment object to write.
IOException
- if there is a problem during writing.public static void writeStream(OutputStream os, Alignment alignment) throws IOException
os
- the stream to write to.alignment
- the Alignment object to write.
IOException
- if there is a problem during writing.public static void writeWriter(Writer writer, Alignment alignment) throws IOException
writer
- the writer to write to.alignment
- the Alignment object to write.
IOException
- if there is a problem during writing.
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