Package edu.msu.cme.rdp.classifier.train
Class LineageSequenceParser
- java.lang.Object
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- edu.msu.cme.rdp.classifier.train.LineageSequenceParser
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public class LineageSequenceParser extends java.lang.Object
A parser to parse a reader containing the raw sequences.
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
delimiter
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Constructor Summary
Constructors Constructor Description LineageSequenceParser(java.io.File inFile)
Creates new RawSequenceParser to parse the input fasta file.LineageSequenceParser(java.io.InputStream is)
Creates new RawSequenceParser to parse the input fasta file.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
Closes the reader.boolean
hasNext()
Returns true if there is a parsed sequence available.LineageSequence
next()
Returns the next parsed sequence.
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Field Detail
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delimiter
public static final java.lang.String delimiter
- See Also:
- Constant Field Values
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Constructor Detail
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LineageSequenceParser
public LineageSequenceParser(java.io.File inFile) throws java.io.IOException
Creates new RawSequenceParser to parse the input fasta file.- Throws:
java.io.IOException
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LineageSequenceParser
public LineageSequenceParser(java.io.InputStream is) throws java.io.IOException
Creates new RawSequenceParser to parse the input fasta file.- Throws:
java.io.IOException
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Method Detail
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close
public void close() throws java.io.IOException
Closes the reader.- Throws:
java.io.IOException
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hasNext
public boolean hasNext() throws java.io.IOException
Returns true if there is a parsed sequence available.- Throws:
java.io.IOException
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next
public LineageSequence next() throws java.util.NoSuchElementException, java.io.IOException
Returns the next parsed sequence.- Throws:
java.util.NoSuchElementException
java.io.IOException
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