Package org.helm.notation2.tools

Class SequenceConverter

java.lang.Object

org.helm.notation2.tools.SequenceConverter

public final class SequenceConverter
extends Object

SequenceConverter class to convert sequence into the HELM2Notation object and vice versa

Author:

hecht

Method Summary

Modifier and Type	Method	Description
static String	getNucleotideNaturalAnalogSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2Notation)	method to generate for all rna polymers the natural analogue sequence
static String	getNucleotideSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2notation)	method to get for all rna/dnas the nucleotide sequence form an HELM2Notation
static String	getPeptideNaturalAnalogSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2Notation)	method to generate for all peptide polymers the natural analogue sequence
static String	getPeptideSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2notation)	method to get for all peptides the sequence
static org.helm.notation2.parser.notation.HELM2Notation	readPeptide(String notation)	method to read a peptide sequence and generate a HELM2Notation object of it
static org.helm.notation2.parser.notation.HELM2Notation	readRNA(String notation)	method to read a rna/dna sequence and generate a HELM2Notation object of it

Methods inherited from class java.lang.Object

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

Method Details

readPeptide

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

method to read a peptide sequence and generate a HELM2Notation object of it

Parameters:

notation - peptide sequence

Returns:

HELM2Notation object

Throws:

FastaFormatException - if the peptide sequence is not in the right format

org.helm.notation2.parser.exceptionparser.NotationException - if the notation object can not be built

ChemistryException - if chemistry engine can not be initialized

readRNA

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

method to read a rna/dna sequence and generate a HELM2Notation object of it

Parameters:

notation - rna/dna sequence

Returns:

HELM2Notation object

Throws:

FastaFormatException - if the rna/dna sequence is not in the right format

org.helm.notation2.parser.exceptionparser.NotationException - if the notation object can not be built

ChemistryException - if chemistry engine can not be initialized

NucleotideLoadingException - if nucleotides can not be loaded

getNucleotideSequenceFromNotation

public static String getNucleotideSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2notation) throws org.helm.notation2.parser.exceptionparser.NotationException, NucleotideLoadingException, HELM2HandledException, ChemistryException

method to get for all rna/dnas the nucleotide sequence form an HELM2Notation

Parameters:

helm2notation - input HELM2Notation

Returns:

rna/dna nucleotide sequences divided with white space

Throws:

NucleotideLoadingException - if nucleotides can not be loaded

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

HELM2HandledException - if HELM2 features are involved

ChemistryException - if chemistry engine can not be initialized

getPeptideSequenceFromNotation

public static String getPeptideSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2notation) throws HELM2HandledException, PeptideUtilsException, NotationException, ChemistryException

method to get for all peptides the sequence

Parameters:

helm2notation - HELM2Notation

Returns:

rna sequences divided by white space

Throws:

HELM2HandledException - if the polymer contains HELM2 features

PeptideUtilsException - if the polymer is not a peptide

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

getNucleotideNaturalAnalogSequenceFromNotation

public static String getNucleotideNaturalAnalogSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2Notation) throws org.helm.notation2.parser.exceptionparser.NotationException, HELM2HandledException, ChemistryException

method to generate for all rna polymers the natural analogue sequence

Parameters:

helm2Notation - input HELm2Notation

Returns:

natural analogue sequence(s)

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if the input complex notation contains non-nucleid acid polymer(s)

HELM2HandledException - if the polymer(s) contain(s) HELM2 features

ChemistryException - if the Chemistry Engine can not be initialized

getPeptideNaturalAnalogSequenceFromNotation

public static String getPeptideNaturalAnalogSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2Notation) throws HELM2HandledException, PeptideUtilsException, org.helm.notation2.parser.exceptionparser.NotationException, ChemistryException

method to generate for all peptide polymers the natural analogue sequence

Parameters:

helm2Notation - input HELM2Notation

Returns:

natural analogue sequence(s)

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if the input complex notation contains non-peptide polymer(s)

HELM2HandledException - if the polymer(s) contain(s) HELM2 features

PeptideUtilsException - if the polymer is not a peptide

ChemistryException - if the Chemistry Engine can not be initialized