Package org.biojavax.bio.phylo.io.nexus
Class NexusFileFormat
- java.lang.Object
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- org.biojavax.bio.phylo.io.nexus.NexusFileFormat
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public class NexusFileFormat extends java.lang.Object
Reads/writes Nexus files and fires events at a NexusFileListener object. Blocks are parsed using NexusBlockParser objects provided at runtime. Each of those objects should probably have a NexusBlockListener object associated with them that receives events generated from the processed data in the block.- Since:
- 1.6
- Author:
- Richard Holland, Tobias Thierer, Jim Balhoff
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
NEW_LINE
New-line symbol.
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
parseFile(NexusFileListener listener, java.io.File inputFile)
Parse a file and send events to the given listener.static void
parseInputStream(NexusFileListener listener, java.io.InputStream inputStream)
Parse a stream and send events to the given listener.static void
parseReader(NexusFileListener listener, java.io.Reader inputReader)
Parse a reader and send events to the given listener.static void
writeFile(java.io.File file, NexusFile nexusFile)
Writes the given Nexus output to a file.static void
writeStream(java.io.OutputStream os, NexusFile nexusFile)
Writes the given Nexus output to a stream.static void
writeWriter(java.io.Writer writer, NexusFile nexusFile)
Writes the given Nexus output to a writer.
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Field Detail
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NEW_LINE
public static final java.lang.String NEW_LINE
New-line symbol.
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Method Detail
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parseFile
public static void parseFile(NexusFileListener listener, java.io.File inputFile) throws java.io.IOException, ParseException
Parse a file and send events to the given listener.- Parameters:
listener
- the listener that will receive events.inputFile
- the file to parse.- Throws:
java.io.IOException
- if anything goes wrong with reading the file.ParseException
- if the file format is incorrect.
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parseInputStream
public static void parseInputStream(NexusFileListener listener, java.io.InputStream inputStream) throws java.io.IOException, ParseException
Parse a stream and send events to the given listener.- Parameters:
listener
- the listener that will receive events.inputStream
- the stream to parse.- Throws:
java.io.IOException
- if anything goes wrong with reading the stream.ParseException
- if the stream format is incorrect.
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parseReader
public static void parseReader(NexusFileListener listener, java.io.Reader inputReader) throws java.io.IOException, ParseException
Parse a reader and send events to the given listener.- Parameters:
listener
- the listener that will receive events.inputReader
- the file to parse.- Throws:
java.io.IOException
- if anything goes wrong with reading the reader.ParseException
- if the reader format is incorrect.
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writeFile
public static void writeFile(java.io.File file, NexusFile nexusFile) throws java.io.IOException
Writes the given Nexus output to a file.- Parameters:
file
- the file to write to.nexusFile
- the Nexus output to write.- Throws:
java.io.IOException
- if there is a problem during writing.
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writeStream
public static void writeStream(java.io.OutputStream os, NexusFile nexusFile) throws java.io.IOException
Writes the given Nexus output to a stream.- Parameters:
os
- the stream to write to.nexusFile
- the Nexus output to write.- Throws:
java.io.IOException
- if there is a problem during writing.
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writeWriter
public static void writeWriter(java.io.Writer writer, NexusFile nexusFile) throws java.io.IOException
Writes the given Nexus output to a writer.- Parameters:
writer
- the writer to write to.nexusFile
- the Nexus output to write.- Throws:
java.io.IOException
- if there is a problem during writing.
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