edu.msu.cme.rdp.classifier.readseqwrapper
Class SequenceParser

java.lang.Object
  edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser

public class SequenceParser
extends java.lang.Object

A class whick parses the input sequences and creates Sequence objects.

Field Summary

private static char[]	charLookup
private ParsedSequence	curSeq
private java.lang.String	emblErrorMsg
private java.lang.String	fastaErrorMsg
private java.lang.String	format
private java.lang.String	formatError
private java.lang.String	genbankErrorMsg
(package private) java.util.regex.Matcher	matcher
private static int	MAX_ASCII
(package private) java.util.regex.Pattern	pattern
(package private) java.io.BufferedReader	reader
(package private) java.lang.String	regexEmbl
(package private) java.lang.String	regexFasta
(package private) java.lang.String	regexGenbank
private static java.lang.String	TEXT_FORMAT
(package private) static java.lang.String	UNKNOWN_SEQ

Constructor Summary

SequenceParser(java.io.InputStream inStream)
Creates new SequenceParser to parse the sequences from an InputStream.

SequenceParser(java.io.Reader rhs)
Creates new SequenceParser to parse the sequences from a Reader.

Method Summary

void	close() Closes the reader.
ParsedSequence	getNextSequence() Returns the next available ParsedSequence from input.
private void	init() Checks the format of the input.
private java.lang.String	modifySequence(java.lang.String s) Modifies the sequence string.
private void	setSequenceFormat() Checks the format of the first input sequence.

Methods inherited from class java.lang.Object

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

Field Detail

reader

java.io.BufferedReader reader

pattern

java.util.regex.Pattern pattern

matcher

java.util.regex.Matcher matcher

regexFasta

java.lang.String regexFasta

regexGenbank

java.lang.String regexGenbank

regexEmbl

java.lang.String regexEmbl

TEXT_FORMAT

private static final java.lang.String TEXT_FORMAT

See Also:

Constant Field Values

UNKNOWN_SEQ

static final java.lang.String UNKNOWN_SEQ

See Also:

Constant Field Values

curSeq

private ParsedSequence curSeq

formatError

private java.lang.String formatError

format

private java.lang.String format

fastaErrorMsg

private java.lang.String fastaErrorMsg

genbankErrorMsg

private java.lang.String genbankErrorMsg

emblErrorMsg

private java.lang.String emblErrorMsg

MAX_ASCII

private static final int MAX_ASCII

See Also:

Constant Field Values

charLookup

private static char[] charLookup

Constructor Detail

SequenceParser

public SequenceParser(java.io.InputStream inStream)
               throws java.io.IOException,
                      SequenceParserException

Creates new SequenceParser to parse the sequences from an InputStream. supported formats: Fasta, Genbank, EMBL or free text for single sequence.

Throws:

java.io.IOException

SequenceParserException

SequenceParser

public SequenceParser(java.io.Reader rhs)
               throws java.io.IOException,
                      SequenceParserException

Creates new SequenceParser to parse the sequences from a Reader. supported formats: Fasta, Genbank, EMBL or free text for single sequence.

Throws:

java.io.IOException

SequenceParserException

Method Detail

init

private void init()
           throws java.io.IOException,
                  SequenceParserException

Checks the format of the input.

Throws:

exception - if the format is not one of the supported formats: Fasta, Genbank, EMBL or free text for single sequence.

java.io.IOException

SequenceParserException

setSequenceFormat

private void setSequenceFormat()
                        throws java.io.IOException,
                               SequenceParserException

Checks the format of the first input sequence. It assumes that all the sequences from the input share the same format.

Throws:

java.io.IOException

SequenceParserException

getNextSequence

public ParsedSequence getNextSequence()
                               throws java.io.IOException,
                                      SequenceParserException

Returns the next available ParsedSequence from input. If no sequence is available, then null is returned.

Throws:

java.io.IOException

SequenceParserException

close

public void close()
           throws java.io.IOException

Closes the reader.

Throws:

java.io.IOException

modifySequence

private java.lang.String modifySequence(java.lang.String s)
                                 throws java.io.IOException

Modifies the sequence string. Removes -, ~ and digits. Returns a string.

Throws:

java.io.IOException