Squil API squil-98 (20130530172026)
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E

edu.cornell.med.icb.parsers - package edu.cornell.med.icb.parsers
Classes in this package provide support for parsing protein sequence files such as FASTA.

F

FastaParser - Class in edu.cornell.med.icb.parsers
Parse a FASTA file.
FastaParser(Reader) - Constructor for class edu.cornell.med.icb.parsers.FastaParser
Create a parser to read sequences.
FastaParser() - Constructor for class edu.cornell.med.icb.parsers.FastaParser
Create a parser to read sequences.
filterProteinResidues(CharSequence, MutableString) - Static method in class edu.cornell.med.icb.parsers.FastaParser
Filter a string to keep only protein residues.

G

getBaseReader() - Method in class edu.cornell.med.icb.parsers.ReaderFastaParser
 
guessAccessionCode(CharSequence, MutableString) - Static method in class edu.cornell.med.icb.parsers.FastaParser
Try to extract an accession code from a FASTA description line.
guessAccessionCode(CharSequence, MutableString) - Static method in class edu.cornell.med.icb.parsers.ReaderFastaParser
Try to extract an accession code from a FASTA description line.

H

hasNext() - Method in class edu.cornell.med.icb.parsers.FastaParser
Returns true if the reader has at least one more sequence.
hasNextSequence() - Method in class edu.cornell.med.icb.parsers.ReaderFastaParser
Returns true if the reader has at least one more sequence.

N

next(MutableString, MutableString) - Method in class edu.cornell.med.icb.parsers.FastaParser
Obtain the next sequence from the reader over the FASTA formatted content.
nextSequence(MutableString) - Method in class edu.cornell.med.icb.parsers.ReaderFastaParser
Obtain the next sequence from the reader over the FASTA formatted content.

R

ReaderFastaParser - Class in edu.cornell.med.icb.parsers
A parser for fasta files which supports reading sequences one character at a time.
ReaderFastaParser(Reader) - Constructor for class edu.cornell.med.icb.parsers.ReaderFastaParser
Create a parser to read sequences.
ReaderFastaParser() - Constructor for class edu.cornell.med.icb.parsers.ReaderFastaParser
Create a parser to read sequences.

S

setReader(Reader) - Method in class edu.cornell.med.icb.parsers.FastaParser
Repositions this reader on a different file/data content.
setReader(Reader) - Method in class edu.cornell.med.icb.parsers.ReaderFastaParser
Repositions this reader on a different file/data content.

E F G H N R S
Squil API squil-98 (20130530172026)

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