All Classes and Interfaces

Class	Description
App	Hello world!
BlastHomologyHits
BlastXMLQuery
ChromosomeMappingTools	A class that can map chromosomal positions to mRNA (coding sequence) positions.
ChromPos	Created by ap3 on 27/10/2014.
Cytoband
CytobandParser	Parses the cytoband (karyotype) file from UCSC.
Fastq	FASTQ formatted sequence.
FastqBuilder	Fluent builder API for creating FASTQ formatted sequences.
FastqReader	Reader for FASTQ formatted sequences.
FastqTools	Utility methods for FASTQ formatted sequences.
FastqVariant	FASTQ sequence format variant.
FastqWriter	Writer for FASTQ formatted sequences.
Feature	A Feature corresponds to a single row in a GFF file.
FeatureHelper
FeatureI	A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.
FeatureList	A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
GCStats
GeneChromosomePosition
GeneChromosomePositionParser	A parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positions
GeneFeatureHelper
GeneIDGFF2Reader	http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneIDXMLReader
GeneMarkGTFReader	http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneName	A simple bean that contains gene name information as available from www.genenames.org
GeneNamesParser	Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
GFF3FromUniprotBlastHits
GFF3Reader	http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GFF3Writer
IlluminaFastqReader	Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqWriter	Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.
Location	A location on a sequence.
LocIterator	Move a sliding window over a Location.
OutputHitsGFF
ParseListener	Low-level event based parser callback.
ProteinMappingTools
SangerFastqReader	Reader for FastqVariant.FASTQ_SANGER formatted sequences.
SangerFastqWriter	Writer for FastqVariant.FASTQ_SANGER formatted sequences.
SolexaFastqReader	Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.
SolexaFastqWriter	Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.
SplitFasta	Utility to write each Fasta entry to a unique file
StainType
StreamListener	Event based parser callback.
TwoBitFacade	A facade that makes it easier to work with a 2bit file.
TwoBitParser	downloaded from http://storage.bioinf.fbb.msu.ru/~roman/TwoBitParser.java Class is a parser of UCSC Genome Browser file format .2bit used to store nucleotide sequence information.
UniprotToFasta