edu.msu.cme.rdp.classifier.train

Class LineageSequenceParser

java.lang.Object

edu.msu.cme.rdp.classifier.train.LineageSequenceParser

public class LineageSequenceParser
extends java.lang.Object

A parser to parse a reader containing the raw sequences.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	delimiter

Constructor Summary

Constructors

Constructor and 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.

Method Summary

Modifier and Type	Method and Description
void	close() Closes the reader.
boolean	hasNext() Returns true if there is a parsed sequence available.
LineageSequence	next() Returns the next parsed sequence.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

delimiter

public static final java.lang.String delimiter

See Also:

Constant Field Values

Constructor Detail

LineageSequenceParser

public LineageSequenceParser(java.io.File inFile)
                      throws java.io.IOException

Creates new RawSequenceParser to parse the input fasta file.

Throws:

java.io.IOException

LineageSequenceParser

public LineageSequenceParser(java.io.InputStream is)
                      throws java.io.IOException

Creates new RawSequenceParser to parse the input fasta file.

Throws:

java.io.IOException

Method Detail

close

public void close()
           throws java.io.IOException

Closes the reader.

Throws:

java.io.IOException

hasNext

public boolean hasNext()
                throws java.io.IOException

Returns true if there is a parsed sequence available.

Throws:

java.io.IOException

next

public LineageSequence next()
                     throws java.util.NoSuchElementException,
                            java.io.IOException

Returns the next parsed sequence.

Throws:

java.util.NoSuchElementException

java.io.IOException