X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2FFastaReader.html;fp=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2FFastaReader.html;h=f70765236212956dcaedd7a804aa87b5c4af8389;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/data/sequence/FastaReader.html b/website/full_javadoc/compbio/data/sequence/FastaReader.html new file mode 100644 index 0000000..f707652 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/FastaReader.html @@ -0,0 +1,415 @@ + + + + + + +FastaReader + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
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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 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
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+ + + +
+ + +