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- -compbio.data.sequence -
-Class FastaReader

-
-java.lang.Object
-  extended by compbio.data.sequence.FastaReader
-
-
-
All Implemented Interfaces:
Iterator<FastaSequence>
-
-
-
-
public class FastaReader
extends Object
implements 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
-
-
- -

- - - - - - - - - - - - - - -
-Constructor Summary
FastaReader(InputStream inputStream) - -
-          This class will not close the incoming stream! So the client should do - so.
FastaReader(String inputFile) - -
-          Header data can contain non-ASCII symbols and read in UTF8
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- voidclose() - -
-          Call this method to close the connection to the input file if you want to - free up the resources.
- booleanhasNext() - -
-          
- FastaSequencenext() - -
-          Reads the next FastaSequence from the input
- voidremove() - -
-          Not implemented
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-FastaReader

-
-public FastaReader(String inputFile)
-            throws 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: -
FileNotFoundException - if the input file is not found -
IllegalStateException - if the close method was called on this instance
-
-
- -

-FastaReader

-
-public FastaReader(InputStream inputStream)
-            throws FileNotFoundException
-
-
This class will not close the incoming stream! So the client should do - so. -

-

-
Parameters:
inputStream - -
Throws: -
FileNotFoundException
-
- - - - - - - - -
-Method Detail
- -

-hasNext

-
-public boolean hasNext()
-
-
-

-

-
Specified by:
hasNext in interface Iterator<FastaSequence>
-
-
- -
Throws: -
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 Iterator<FastaSequence>
-
-
- -
Throws: -
AssertionError - if the header or the sequence is missing -
IllegalStateException - if the close method was called on this instance
-
-
-
- -

-remove

-
-public void remove()
-
-
Not implemented -

-

-
Specified by:
remove in interface 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. -

-

-
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
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