org.helm.notation2.tools

Class SiRNANotation

java.lang.Object

org.helm.notation2.tools.SiRNANotation

public class SiRNANotation
extends Object

SiRNANotation, class to generate SirnaNotation

Author:

hecht

Field Summary

Fields

Modifier and Type	Field and Description
static Map<String,String>	complementMap

Constructor Summary

Constructors

Constructor and Description
SiRNANotation()

Method Summary

Modifier and Type	Method and Description
static org.helm.notation2.parser.notation.HELM2Notation	getSiRNANotation(String senseSeq, String antiSenseSeq) this method converts nucleotide sequences into HELM2Notation
static org.helm.notation2.parser.notation.HELM2Notation	getSirnaNotation(String senseSeq, String antiSenseSeq, String rnaDesignType) this method converts nucleotide sequences into HELM notation based on design pattern

Methods inherited from class java.lang.Object

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

Field Detail

complementMap

public static Map<String,String> complementMap

Constructor Detail

SiRNANotation

public SiRNANotation()

Method Detail

getSiRNANotation

public static org.helm.notation2.parser.notation.HELM2Notation getSiRNANotation(String senseSeq,
                                                                                String antiSenseSeq)
                                                                         throws org.helm.notation2.parser.exceptionparser.NotationException,
                                                                                FastaFormatException,
                                                                                HELM2HandledException,
                                                                                RNAUtilsException,
                                                                                NotationException,
                                                                                ChemistryException,
                                                                                org.helm.chemtoolkit.CTKException,
                                                                                NucleotideLoadingException

this method converts nucleotide sequences into HELM2Notation

Parameters:

senseSeq - 5-3 nucleotide sequence for default notation

antiSenseSeq - 3-5 nucleotide sequence for default notation

Returns:

HELM2Notation for siRNA

Throws:

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

FastaFormatException - if the fasta input is not valid

HELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 Format

RNAUtilsException - if the polymer is not a RNA/DNA

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

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

NucleotideLoadingException - if nucleotides can not be loaded

getSirnaNotation

public static org.helm.notation2.parser.notation.HELM2Notation getSirnaNotation(String senseSeq,
                                                                                String antiSenseSeq,
                                                                                String rnaDesignType)
                                                                         throws org.helm.notation2.parser.exceptionparser.NotationException,
                                                                                FastaFormatException,
                                                                                HELM2HandledException,
                                                                                RNAUtilsException,
                                                                                NotationException,
                                                                                ChemistryException,
                                                                                org.helm.chemtoolkit.CTKException,
                                                                                NucleotideLoadingException

this method converts nucleotide sequences into HELM notation based on design pattern

Parameters:

senseSeq - 5-3 nucleotide sequence

antiSenseSeq - 3-5 nucleotide sequence

rnaDesignType - given design pattern

Returns:

HELM2Notation for siRNA

Throws:

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

FastaFormatException - if the fasta input is not valid

HELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 Format

RNAUtilsException - if the polymer is not a RNA/DNA

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

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

NucleotideLoadingException - if nucleotides can not be loaded