Uses of Class
org.helm.notation2.exception.NucleotideLoadingException

Packages that use NucleotideLoadingException

Package	Description
org.helm.notation2
org.helm.notation2.tools

Uses of NucleotideLoadingException in org.helm.notation2

Methods in org.helm.notation2 that throw NucleotideLoadingException

Modifier and Type	Method and Description
static NucleotideFactory	NucleotideFactory.getInstance()
static void	NucleotideFactory.initializeNucleotideTemplatesFromWebService()

Uses of NucleotideLoadingException in org.helm.notation2.tools

Methods in org.helm.notation2.tools that throw NucleotideLoadingException

Modifier and Type	Method and Description
static boolean	RNAUtils.areAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation polymerOne, org.helm.notation2.parser.notation.polymer.PolymerNotation polymerTwo) method to check if two given polymers are complement to each other
static Nucleotide	NucleotideParser.convertToNucleotide(String id, boolean last) method to convert an string to an nucleotide
protected static org.helm.notation2.parser.notation.polymer.PolymerListElements	FastaFormat.generateElementsforRNA(String sequence, org.helm.notation2.parser.notation.polymer.HELMEntity entity) method to fill a rna polymer with its elements (MonomerNotationUnits)
String	WebService.generateHELMFromFastaNucleotide(String notation) method to generate HELM from a FASTA containing rna/dna sequences
static org.helm.notation2.parser.notation.HELM2Notation	FastaFormat.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 org.helm.notation2.parser.notation.polymer.PolymerNotation	RNAUtils.getAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the antiparallel polymer for a rna/dna polymer
static org.helm.notation2.parser.notation.polymer.PolymerNotation	RNAUtils.getComplement(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the normal complement polymer for a given rna/dna polymer
static org.helm.notation2.parser.notation.polymer.PolymerNotation	RNAUtils.getInverse(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the polymer with the inverse sequence of the current polymer
static String	RNAUtils.getNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the nucleotide sequence for the polymer
static String	SequenceConverter.getNucleotideSequenceFromNotation(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to get for all rna/dnas the nucleotide sequence form an HELM2Notation
static org.helm.notation2.parser.notation.polymer.PolymerNotation	RNAUtils.getReverseComplement(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the polymer with the reverse complement sequence of the current polymer
static org.helm.notation2.parser.notation.HELM2Notation	SiRNANotation.getSiRNANotation(String senseSeq, String antiSenseSeq) this method converts nucleotide sequences into HELM2Notation
static org.helm.notation2.parser.notation.HELM2Notation	SiRNANotation.getSirnaNotation(String senseSeq, String antiSenseSeq, String rnaDesignType) this method converts nucleotide sequences into HELM notation based on design pattern
static List<org.helm.notation2.parser.notation.connection.ConnectionNotation>	RNAUtils.hybridizeAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation one, org.helm.notation2.parser.notation.polymer.PolymerNotation two) method to hybridize two PolymerNotations together if they are antiparallel
String	WebService.readRNA(String rna) method to read a single rna sequence and generates HELM
static org.helm.notation2.parser.notation.HELM2Notation	SequenceConverter.readRNA(String notation) method to read a rna/dna sequence and generate a HELM2Notation object of it