org.helm.notation2.tools

Class FastaFormat

java.lang.Object

org.helm.notation2.tools.FastaFormat

public final class FastaFormat
extends Object

FastaFormat, class to convert FastaFiles to HELMNotation and vice versa

Author:

hecht

Method Summary

Methods

Modifier and Type	Method and Description
static org.helm.notation2.parser.notation.HELM2Notation	convertIntoAnalogSequence(org.helm.notation2.parser.notation.HELM2Notation helm2Notation) method to convert all Peptides and RNAs into the natural analogue sequence and generates HELM2Notation
protected static org.helm.notation2.parser.notation.polymer.PolymerListElements	generateElementsforRNA(String sequence, org.helm.notation2.parser.notation.polymer.HELMEntity entity) method to fill a rna polymer with its elements (MonomerNotationUnits)
protected static org.helm.notation2.parser.notation.polymer.PolymerListElements	generateElementsOfPeptide(String sequence, org.helm.notation2.parser.notation.polymer.HELMEntity entity) method to fill a peptide polymer with its elements (MonomerNotationUnits)
static String	generateFasta(org.helm.notation2.parser.notation.HELM2Notation helm2Notation2) method to generate for the whole HELM2Notation fasta-files, it contains fasta for all rna and peptides
protected static String	generateFastaFromPeptide(List<Monomer> monomers) method to generate Fasta for a list of peptide monomers
static String	generateFastaFromPeptidePolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) method to generate Fasta for peptide polymers
protected static String	generateFastaFromRNA(List<Monomer> monomers) method to generate Fasta for a list of rna monomers
static String	generateFastaFromRNAPolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) method to generate Fasta for rna polymers
static org.helm.notation2.parser.notation.HELM2Notation	generatePeptidePolymersFromFASTAFormatHELM1(String fasta) method to read the information from a FastaFile-Format + generate peptide polymers, be careful, it produces only polymers in the HELM1 standard, no ambiguity
static org.helm.notation2.parser.notation.HELM2Notation	generateRNAPolymersFromFastaFormatHELM1(String fasta) method to read the information from a FastaFile-Format + generate RNA Polymers be careful, it produces only polymers in the HELM1 standard, no ambiguity
static boolean	isNormalDirection(String sequence) method to check if the sequence is in normal direction 5' to 3'

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

generatePeptidePolymersFromFASTAFormatHELM1

public static org.helm.notation2.parser.notation.HELM2Notation generatePeptidePolymersFromFASTAFormatHELM1(String fasta)
                                                                                                    throws FastaFormatException,
                                                                                                           ChemistryException

method to read the information from a FastaFile-Format + generate peptide polymers, be careful, it produces only polymers in the HELM1 standard, no ambiguity

Parameters:

fasta - FastaFile in string format

Returns:

HELM2Notation generated HELM2Notation

Throws:

FastaFormatException - if the input is not correct

ChemistryException - if chemistry engine can not be initialized

generateRNAPolymersFromFastaFormatHELM1

public static org.helm.notation2.parser.notation.HELM2Notation generateRNAPolymersFromFastaFormatHELM1(String fasta)
                                                                                                throws FastaFormatException,
                                                                                                       org.helm.notation2.parser.exceptionparser.NotationException,
                                                                                                       ChemistryException,
                                                                                                       NucleotideLoadingException

method to read the information from a FastaFile-Format + generate RNA Polymers be careful, it produces only polymers in the HELM1 standard, no ambiguity

Parameters:

fasta - FastaFile in string format

Returns:

HELM2Notation generated HELM2Notation

Throws:

FastaFormatException - if the input is not correct

org.helm.notation2.parser.exceptionparser.NotationException - if notation is not valid

ChemistryException - if chemistry engine can not be initialized

NucleotideLoadingException - if nucleotides can not be loaded

generateElementsOfPeptide

protected static org.helm.notation2.parser.notation.polymer.PolymerListElements generateElementsOfPeptide(String sequence,
                                                                                       org.helm.notation2.parser.notation.polymer.HELMEntity entity)
                                                                                                   throws FastaFormatException,
                                                                                                          ChemistryException

method to fill a peptide polymer with its elements (MonomerNotationUnits)

Parameters:

sequence - peptide sequence

entity - HELMEntity

Returns:

PolymerListElements

Throws:

FastaFormatException - if the input sequence is not correct

ChemistryException - if chemistry engine can not be initialized

generateElementsforRNA

protected static org.helm.notation2.parser.notation.polymer.PolymerListElements generateElementsforRNA(String sequence,
                                                                                    org.helm.notation2.parser.notation.polymer.HELMEntity entity)
                                                                                                throws FastaFormatException,
                                                                                                       org.helm.notation2.parser.exceptionparser.NotationException,
                                                                                                       ChemistryException,
                                                                                                       NucleotideLoadingException

method to fill a rna polymer with its elements (MonomerNotationUnits)

Parameters:

sequence - rna sequence

entity - HELMEntity

Returns:

PolymerListElements

Throws:

FastaFormatException - if the input sequence is not correct

org.helm.notation2.parser.exceptionparser.NotationException - if notation is not valid

ChemistryException - if chemistry engine can not be initialized

NucleotideLoadingException - if nucleotides can not be loaded

generateFastaFromPeptidePolymer

public static String generateFastaFromPeptidePolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)
                                              throws FastaFormatException,
                                                     ChemistryException

method to generate Fasta for peptide polymers

Parameters:

polymers - List of peptide PolymerNotation

Returns:

generated FASTA

Throws:

FastaFormatException - if the peptides can not be transformed to FASTA

ChemistryException - if the Chemistry Engine can not be initialized

generateFastaFromPeptide

protected static String generateFastaFromPeptide(List<Monomer> monomers)

method to generate Fasta for a list of peptide monomers

Parameters:

monomers - peptide monomers

Returns:

Fasta sequence

generateFastaFromRNAPolymer

public static String generateFastaFromRNAPolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)
                                          throws FastaFormatException,
                                                 ChemistryException

method to generate Fasta for rna polymers

Parameters:

polymers - list of rna PolymerNotation

Returns:

Fasta

Throws:

FastaFormatException - if the polymers can not be transformed into FASTA

ChemistryException - if the Chemistry Engine can not be initialized

generateFastaFromRNA

protected static String generateFastaFromRNA(List<Monomer> monomers)

method to generate Fasta for a list of rna monomers

Parameters:

monomers - list of monomers

Returns:

sequence

generateFasta

public static String generateFasta(org.helm.notation2.parser.notation.HELM2Notation helm2Notation2)
                            throws FastaFormatException,
                                   ChemistryException

method to generate for the whole HELM2Notation fasta-files, it contains fasta for all rna and peptides

Parameters:

helm2Notation2 - HELM2Notation

Returns:

FASTA-File-Format

Throws:

FastaFormatException - if the HELM2Notation can not be transformed to FASTA

ChemistryException - if the Chemistry Engine can not be initialized

convertIntoAnalogSequence

public static org.helm.notation2.parser.notation.HELM2Notation convertIntoAnalogSequence(org.helm.notation2.parser.notation.HELM2Notation helm2Notation)
                                                                                  throws FastaFormatException,
                                                                                         AnalogSequenceException,
                                                                                         ChemistryException,
                                                                                         org.helm.chemtoolkit.CTKException

method to convert all Peptides and RNAs into the natural analogue sequence and generates HELM2Notation

Parameters:

helm2Notation - HELM2Notation

Returns:

analog helm2notation

Throws:

FastaFormatException - if it can not be converted to analog sequence

AnalogSequenceException - if the natural analogue sequence can not be produced

ChemistryException - if chemistry engine can not be initialized

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

isNormalDirection

public static boolean isNormalDirection(String sequence)

method to check if the sequence is in normal direction 5' to 3'

Parameters:

sequence - rna sequence

Returns:

true, if the sequence is in normal direction, false otherwise