edu.msu.cme.rdp.classifier.train
Class RawSequenceParser

java.lang.Object
  edu.msu.cme.rdp.classifier.train.RawSequenceParser

public class RawSequenceParser
extends java.lang.Object

A parser to parse a reader containing the raw sequences.

Field Summary

private ParsedRawSequence	curSeq
static java.lang.String	delimiter
private java.util.regex.Matcher	matcher
private ParsedRawSequence	onDeck
private java.util.regex.Pattern	pattern
private java.io.BufferedReader	reader
private java.lang.String	regexFasta

Constructor Summary

RawSequenceParser(java.io.Reader in)
Creates new RawSequenceParser to parse the input fasta file.

Method Summary

void	close() Closes the reader.
private java.util.List	decomposeHeader(java.lang.String s) Takes two different formats: the old format is a string of sequence header( ancestors seperated by delimiter, such as ";" in our case).
private ParsedRawSequence	getNextElement() Reads from the input stream and returns a parsed sequence.
boolean	hasNext() Returns true if there is a parsed sequence available.
private java.lang.String	modifySequence(java.lang.String s) Modifies the sequence.
ParsedRawSequence	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

pattern

private java.util.regex.Pattern pattern

matcher

private java.util.regex.Matcher matcher

regexFasta

private java.lang.String regexFasta

reader

private java.io.BufferedReader reader

onDeck

private ParsedRawSequence onDeck

curSeq

private ParsedRawSequence curSeq

Constructor Detail

RawSequenceParser

public RawSequenceParser(java.io.Reader in)

Creates new RawSequenceParser to parse the input fasta file.

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 ParsedRawSequence next()
                       throws java.util.NoSuchElementException,
                              java.io.IOException

Returns the next parsed sequence.

Throws:

java.util.NoSuchElementException

java.io.IOException

getNextElement

private ParsedRawSequence getNextElement()
                                  throws java.io.IOException

Reads from the input stream and returns a parsed sequence. Header format: seqID followed by a tab, followed by a list of ancestor nodes Reads one line for the header and decompose the header into a list of ancestors. Then reads the following lines for the sequence string and modifies the sequence string.

Throws:

java.io.IOException

decomposeHeader

private java.util.List decomposeHeader(java.lang.String s)

Takes two different formats: the old format is a string of sequence header( ancestors seperated by delimiter, such as ";" in our case). new format: the taxid of the immediate parent taxon It returns an array of ancestors with root ancestor first.

modifySequence

private java.lang.String modifySequence(java.lang.String s)

Modifies the sequence. Removes - and ~. It returns a string.