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ContigNotFoundException - Exception in pro.parseq.GenomeExplorer.exceptions

ContigNotFoundException(String, String) - Constructor for exception pro.parseq.GenomeExplorer.exceptions.ContigNotFoundException

E

Explorer - Class in pro.parseq.GenomeExplorer

Reference genome sequences explorer class It wraps samtools functionality to provide it over your references References should be located in separate folders inside the "parent" references folder Each reference's folder should include 3 files: - reference fasta file - reference index file - reference dictionary file

Explorer(String) - Constructor for class pro.parseq.GenomeExplorer.Explorer

Instantiates Explorer class Finds all references inside the "parent" folder specified

G

getContig() - Method in exception pro.parseq.GenomeExplorer.exceptions.ContigNotFoundException

getContigLength(String, String) - Method in class pro.parseq.GenomeExplorer.Explorer

Get reference's contig length

getPath() - Method in exception pro.parseq.GenomeExplorer.exceptions.IllegalReferencesFolderPathException

getReference() - Method in exception pro.parseq.GenomeExplorer.exceptions.ContigNotFoundException

getReference() - Method in exception pro.parseq.GenomeExplorer.exceptions.NoSuchReferenceException

getReferenceContigsList(String) - Method in class pro.parseq.GenomeExplorer.Explorer

Get contigs list for reference specified

getReferenceGenomesList() - Method in class pro.parseq.GenomeExplorer.Explorer

Get available references

getReferenceSequence(String, String, long, long, ReferenceSequenceCase) - Method in class pro.parseq.GenomeExplorer.Explorer

Get reference genome sequence for parameters specified

getReferenceSequencesList(String) - Method in class pro.parseq.GenomeExplorer.Explorer

Get references sequences for reference specified

H

hasContig(String, String) - Method in class pro.parseq.GenomeExplorer.Explorer

Returns true if reference's contig list contains contig of specified name

hasReference(String) - Method in class pro.parseq.GenomeExplorer.Explorer

Returns true if references dictionary contains mapping for specified reference name

I

IllegalReferencesFolderPathException - Exception in pro.parseq.GenomeExplorer.exceptions

Represents situation when "parent" references folder is not a directory

IllegalReferencesFolderPathException(String) - Constructor for exception pro.parseq.GenomeExplorer.exceptions.IllegalReferencesFolderPathException

N

NoSuchReferenceException - Exception in pro.parseq.GenomeExplorer.exceptions

NoSuchReferenceException(String) - Constructor for exception pro.parseq.GenomeExplorer.exceptions.NoSuchReferenceException

P

pro.parseq.GenomeExplorer - package pro.parseq.GenomeExplorer

pro.parseq.GenomeExplorer.exceptions - package pro.parseq.GenomeExplorer.exceptions

R

ReferenceSequenceCase - Enum in pro.parseq.GenomeExplorer

Enumeration for preferred reference sequence case

V

valueOf(String) - Static method in enum pro.parseq.GenomeExplorer.ReferenceSequenceCase

Returns the enum constant of this type with the specified name.

values() - Static method in enum pro.parseq.GenomeExplorer.ReferenceSequenceCase

Returns an array containing the constants of this enum type, in the order they are declared.

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