compbio.data.sequence

Class FastaReader

java.lang.Object

compbio.data.sequence.FastaReader

All Implemented Interfaces:

java.util.Iterator<FastaSequence>

public class FastaReader
extends java.lang.Object
implements java.util.Iterator<FastaSequence>

Reads files with FASTA formatted sequences. All the information in the FASTA header is preserved including trailing white spaces. All the white spaces are removed from the sequence. Examples of the correct input:

 
 >zedpshvyzg
 GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
 
 >xovkactesa
 CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
 FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
 FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
 DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
 
 >ntazzewyvv
 CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
 EASINM AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG      
 EFITEA WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW 
   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
 
    > 12 d t y wi               k       jbke    
   KLSHHDCD
    N
     H
     HSKCTEPHCGNSHQMLHRDP
     CCDQCQSWEAENWCASMRKAILF
 
 

Version:

1.0 April 2011

Author:

Peter Troshin

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	DELIM Delimiter for the scanner
private java.util.Scanner	input

Constructor Summary

Constructors

Constructor and Description
FastaReader(java.io.InputStream inputStream) This class will not close the incoming stream! So the client should do so.
FastaReader(java.lang.String inputFile) Header data can contain non-ASCII symbols and read in UTF8

Method Summary

Modifier and Type	Method and Description
void	close() Call this method to close the connection to the input file if you want to free up the resources.
boolean	hasNext()
FastaSequence	next() Reads the next FastaSequence from the input
void	remove() Not implemented
private static FastaSequence	toFastaSequence(java.lang.String singleFastaEntry)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

input

private final java.util.Scanner input

DELIM

private final java.lang.String DELIM

Delimiter for the scanner

See Also:

Constant Field Values

Constructor Detail

FastaReader

public FastaReader(java.lang.String inputFile)
            throws java.io.FileNotFoundException

Header data can contain non-ASCII symbols and read in UTF8

Parameters:

inputFile - the file containing the list of FASTA formatted sequences to read from

Throws:

java.io.FileNotFoundException - if the input file is not found

java.lang.IllegalStateException - if the close method was called on this instance

FastaReader

public FastaReader(java.io.InputStream inputStream)
            throws java.io.FileNotFoundException

This class will not close the incoming stream! So the client should do so.

Parameters:

inputStream -

Throws:

java.io.FileNotFoundException

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<FastaSequence>

Throws:

java.lang.IllegalStateException - if the close method was called on this instance

next

public FastaSequence next()

Reads the next FastaSequence from the input

Specified by:

next in interface java.util.Iterator<FastaSequence>

Throws:

java.lang.AssertionError - if the header or the sequence is missing

java.lang.IllegalStateException - if the close method was called on this instance

MismatchException - - if there were no more FastaSequence's.

remove

public void remove()

Not implemented

Specified by:

remove in interface java.util.Iterator<FastaSequence>

close

public void close()

Call this method to close the connection to the input file if you want to free up the resources. The connection will be closed on the JVM shutdown if this method was not called explicitly. No further reading on this instance of the FastaReader will be possible after calling this method.

toFastaSequence

private static FastaSequence toFastaSequence(java.lang.String singleFastaEntry)