- generateCanSMILESForHELM2(String) - Method in class org.helm.notation2.tools.WebService
-
method to generate a SMILES representation for a whole HELM2 input
- generateElementsforRNA(String, HELMEntity) - Static method in class org.helm.notation2.tools.FastaFormat
-
method to fill a rna polymer with its elements (MonomerNotationUnits)
- generateElementsOfPeptide(String, HELMEntity) - Static method in class org.helm.notation2.tools.FastaFormat
-
method to fill a peptide polymer with its elements (MonomerNotationUnits)
- generateFasta(HELM2Notation) - Static method in class org.helm.notation2.tools.FastaFormat
-
method to generate for the whole HELM2Notation fasta-files, it contains
fasta for all rna and peptides
- generateFasta(String) - Method in class org.helm.notation2.tools.WebService
-
method to generate FASTA-Formats for all rna and peptide sequences from
an HELM input
- generateFastaFromPeptide(List<Monomer>) - Static method in class org.helm.notation2.tools.FastaFormat
-
method to generate Fasta for a list of peptide monomers
- generateFastaFromPeptidePolymer(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.FastaFormat
-
method to generate Fasta for peptide polymers
- generateFastaFromRNA(List<Monomer>) - Static method in class org.helm.notation2.tools.FastaFormat
-
method to generate Fasta for a list of rna monomers
- generateFastaFromRNAPolymer(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.FastaFormat
-
method to generate Fasta for rna polymers
- generateHELMFromFastaNucleotide(String) - Method in class org.helm.notation2.tools.WebService
-
method to generate HELM from a FASTA containing rna/dna sequences
- generateHELMFromFastaPeptide(String) - Method in class org.helm.notation2.tools.WebService
-
method to generate HELM from a FASTA containing peptide sequence(s)
- generateImageForHELMMolecule(String) - Method in class org.helm.notation2.tools.WebService
-
method to generate a HELM molecule
- generateImageForMonomer(Monomer, boolean) - Method in class org.helm.notation2.tools.WebService
-
method to generate an image for a monomer
- generateImageHELMMolecule(HELM2Notation) - Static method in class org.helm.notation2.tools.Images
-
method to generate an image of the HELM molecule
- generateImageofMonomer(Monomer, boolean) - Static method in class org.helm.notation2.tools.Images
-
generates an image of the atom/bond representation of monomer
- generateJSON(String) - Method in class org.helm.notation2.tools.WebService
-
method to generate JSON-Output for the HELM
- generateMDL(HELM2Notation) - Static method in class org.helm.notation2.tools.MDLUtils
-
method to generate MDL for a HELM molecule
- generateNaturalAnalogSequencePeptide(String) - Method in class org.helm.notation2.tools.WebService
-
method to generate the natural analogue sequence for all
peptide-sequences from an HELM input
- generateNaturalAnalogSequenceRNA(String) - Method in class org.helm.notation2.tools.WebService
-
method to generate the natural analogue sequence for all rna-sequences
from an HELM input
- generatePeptidePolymersFromFASTAFormatHELM1(String) - Static method in class org.helm.notation2.tools.FastaFormat
-
method to read the information from a FastaFile-Format + generate peptide
polymers, be careful, it produces only polymers in the HELM1 standard, no
ambiguity
- generateRNAPolymersFromFastaFormatHELM1(String) - Static method in class org.helm.notation2.tools.FastaFormat
-
method to read the information from a FastaFile-Format + generate RNA
Polymers be careful, it produces only polymers in the HELM1 standard, no
ambiguity
- generateSMILESForHELM2(String) - Method in class org.helm.notation2.tools.WebService
-
method to generate a SMILES representation for a whole HELM2 input
- generateTemporaryMonomer(String, String, String) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils
-
- getAllBasePairConnections(List<ConnectionNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
-
method to get all base pair connections of a given list of
ConnectionNotation
- getAllEdgeConnections(List<ConnectionNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
-
method to get all edge connections of a given List of ConnectionNotation
- getAllMonomers(MonomerNotation, int) - Static method in class org.helm.notation2.tools.Validation
-
method to get for one MonomerNotation all valid contained monomers
- getAllMonomersList() - Method in class org.helm.notation2.MonomerStore
-
This method returns all monomers of the store as list sorted by polymer
type
- getAllMonomersOnlyBase(MonomerNotation) - Static method in class org.helm.notation2.tools.Validation
-
method to get for one MonomerNotation all valid contained monomers.
- getAlternateId() - Method in class org.helm.notation2.Attachment
-
- getAlternateId() - Method in class org.helm.notation2.Monomer
-
- getAminoAcidList(String) - Static method in class org.helm.notation2.tools.AminoAcidParser
-
This method converts peptide sequence into a List of amino acid
- getAminoAcidList(String, String) - Static method in class org.helm.notation2.tools.AminoAcidParser
-
This method converts peptide sequence into a List of amino acid with
optional delimiter
- getAntiparallel(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to get the antiparallel polymer for a rna/dna polymer
- getAttachementElement(Attachment) - Static method in class org.helm.notation2.tools.MonomerParser
-
This method converts Attachment to ATTACHMENT XML element
- getAttachment(String) - Method in class org.helm.notation2.Monomer
-
get a specific attachment by passing in a label
- getAttachment(Element) - Static method in class org.helm.notation2.tools.MonomerParser
-
Convert ATTACHMENT element to Attachment object
- getAttachmentDB() - Method in class org.helm.notation2.MonomerCache
-
- getAttachmentDB() - Method in class org.helm.notation2.MonomerFactory
-
- getAttachmentLabelIDs() - Method in class org.helm.notation2.MonomerFactory
-
- getAttachmentList() - Method in class org.helm.notation2.Monomer
-
- getAttachmentListString() - Method in class org.helm.notation2.Monomer
-
- getBackgroundColor() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer
-
Returns the background color.
- getBaseMonomer() - Method in class org.helm.notation2.Nucleotide
-
get the base monomer, the return value could be null if this nucleotide
does not have a base
- getBaseMonomer(MonomerStore) - Method in class org.helm.notation2.Nucleotide
-
get the base monomer, the return value could be null if this nucleotide
does not have a base
- getBLOBPolymers(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
-
method to get all blob polymers given a list of PolymerNotation objects
- getCanonical(HELM2Notation) - Static method in class org.helm.notation2.tools.HELM1Utils
-
method to generate from a helm2notation a valid canonical HELM1
- getCanonicalSMILESForAll(HELM2Notation) - Static method in class org.helm.notation2.tools.SMILES
-
method to generate canonical smiles for the whole HELMNotation
- getCanonicalSMILESForPolymer(PolymerNotation) - Static method in class org.helm.notation2.tools.SMILES
-
method to generate canonical smiles for one single PolymerNotation
- getCanSMILES() - Method in class org.helm.notation2.Monomer
-
- getCapGroupName() - Method in class org.helm.notation2.Attachment
-
- getCapGroupSMILES() - Method in class org.helm.notation2.Attachment
-
- getCapMoleculeInfo(String) - Method in class org.helm.notation2.Monomer
-
This method returns the MoleculeInfo for the input R group label of this
monomer
- getCategory() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer
-
Returns the category.
- getChemistry() - Method in class org.helm.notation2.Chemistry
-
- getCHEMPolymers(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
-
method to get all chem polymers given a list of PolymerNotation objects
- getComplement(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to get the normal complement polymer for a given rna/dna polymer
- getComplexNotationString(Element) - Static method in class org.helm.notation2.tools.xHelmNotationParser
-
Extracts the complex notation string from the root node of the XHELM
document
- getConflictedMonomerMap(MonomerCache) - Method in class org.helm.notation2.MonomerFactory
-
- getDefaultUnit() - Method in class org.helm.notation2.calculation.ExtinctionCoefficient
-
- getDefaultUnitType() - Method in class org.helm.notation2.calculation.ExtinctionCoefficient
-
- getExactMass(HELM2Notation) - Static method in class org.helm.notation2.calculation.MoleculePropertyCalculator
-
method to get the ExactMass for the whole HELM
- getExactMass() - Method in class org.helm.notation2.MoleculeProperty
-
- getExternalMonomersPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
- getExternalNucleotidesPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
- getExtinctionCoefficient() - Method in class org.helm.notation2.MoleculeProperty
-
- getFontColor() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer
-
Returns the font color.
- getFormatedSirnaSequences(HELM2Notation) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
-
generate formated siRNA sequence with default padding char " " and
base-pair char "|"
- getFormatedSirnaSequences(HELM2Notation, String, String) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
-
- getHELMNotationString(Element) - Static method in class org.helm.notation2.tools.xHelmNotationParser
-
Extracts the HELM string from the root node of the XHELM document
- getId() - Method in class org.helm.notation2.Attachment
-
- getId() - Method in class org.helm.notation2.Monomer
-
- getInstance() - Static method in class org.helm.notation2.calculation.ExtinctionCoefficient
-
- getInstance() - Static method in class org.helm.notation2.Chemistry
-
method to get the singleton instance
- getInstance() - Static method in class org.helm.notation2.MonomerFactory
-
Initialize MonomerCache and returns the singleton Factory class
- getInstance() - Static method in class org.helm.notation2.NucleotideFactory
-
- getInstance() - Static method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Creates singleton instance of MonomerStoreConfiguration and returns
it.
- getInterConnections() - Method in class org.helm.notation2.InterConnections
-
- getInverse(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to get the polymer with the inverse sequence of the current
polymer
- getLabel() - Method in class org.helm.notation2.Attachment
-
- getLinkerNotation() - Method in class org.helm.notation2.Nucleotide
-
This method returns the HELM notation for nucleotide linker
- getListOfHandledMonomers(List<MonomerNotation>) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils
-
method to get all HELM1 valid MonomerNotations Only on these monomers
required HELM1 functions are performed
- getListOfHandledMonomersOnlyBase(List<MonomerNotation>) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils
-
method to get all HELM1 valid MonomerNotations Only on these monomers
required HELM1 functions are performed
- getListOfMonomer(List<MonomerNotation>) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils
-
method to get all monomers for all MonomerNotations
- getListOfMonomerNotation(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils
-
method to get all MonomerNotations for all given polymers
- getListOfPolymersSpecificType(String, List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
-
method to get all polymers for one specific polymer type
- getManipulator() - Method in class org.helm.notation2.Chemistry
-
method to get the Manipulator
- getMatchingBracketPosition(char[], int, char, char) - Static method in class org.helm.notation2.tools.NucleotideParser
-
- getMaxMatchFragment(String, String) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to get the largest matched fragment between two sequences, replace
T with U before Match
- getMaxMatchFragment(String, String, int) - Static method in class org.helm.notation2.tools.RNAUtils
-
This method returns the largest matched fragment between two sequences,
replace T with U before match
- getModifiedNucleotideSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to get the modifiedNucleotideSequence of the given PolymerNotation
- getMolecularFormula() - Method in class org.helm.notation2.MoleculeProperty
-
- getMolecularFormula(String) - Method in class org.helm.notation2.tools.WebService
-
method to calculate from a non-ambiguous HELM input the molecular formula
- getMolecularFormular(HELM2Notation) - Static method in class org.helm.notation2.calculation.MoleculePropertyCalculator
-
method to get the MolecularFormular for the whole HELM
- getMolecularProperties(String) - Method in class org.helm.notation2.tools.WebService
-
method to calculate froma non-ambiguous HELM input the molecular
properties: molecular formula, molecular weight, exact mass, extinction
coefficient
- getMolecularWeight(HELM2Notation) - Static method in class org.helm.notation2.calculation.MoleculePropertyCalculator
-
method to get the molecular weight for the whole HELM
- getMolecularWeight() - Method in class org.helm.notation2.MoleculeProperty
-
- getMolecule() - Method in class org.helm.notation2.RgroupStructure
-
- getMolecule(String) - Static method in class org.helm.notation2.tools.BuilderMolecule
-
- getMoleculeForMonomer(Monomer) - Static method in class org.helm.notation2.tools.BuilderMolecule
-
method to build a molecule for a given monomer
- getMoleculeProperties(HELM2Notation) - Static method in class org.helm.notation2.calculation.MoleculePropertyCalculator
-
method to get all molecule properties for one HELM2Notation
- getMolfile() - Method in class org.helm.notation2.Monomer
-
- getMonomer(String, String) - Method in class org.helm.notation2.MonomerStore
-
Returns the monomer specified by polymerType and alternatId
- getMonomer(String) - Method in class org.helm.notation2.MonomerStore
-
Returns the monomer by smiles string
- getMonomer(String, String, String) - Static method in class org.helm.notation2.tools.MethodsMonomerUtils
-
method to get the monomer from the database!
- getMonomer(Element) - Static method in class org.helm.notation2.tools.MonomerParser
-
Convert monomer element to Monomer object
- getMonomer(String) - Static method in class org.helm.notation2.tools.MonomerParser
-
- getMonomerCountForRNA(String) - Static method in class org.helm.notation2.tools.NucleotideParser
-
- getMonomerDB() - Method in class org.helm.notation2.MonomerCache
-
- getMonomerDB() - Method in class org.helm.notation2.MonomerFactory
-
retruns the monomer database
- getMonomerDB(boolean) - Method in class org.helm.notation2.MonomerFactory
-
returns the monomer database including monomers that where temporary marked
as new, else without those monomers
- getMonomerDB() - Method in class org.helm.notation2.MonomerStore
-
returns MonomerDB
- getMonomerElement(Monomer) - Static method in class org.helm.notation2.tools.MonomerParser
-
This method converts Monomer to MONOMER XML element
- getMonomerID() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer
-
Returns the monomer ID.
- getMonomerIDListFromNucleotide(String) - Static method in class org.helm.notation2.tools.NucleotideParser
-
- getMonomerList(String) - Static method in class org.helm.notation2.tools.MonomerParser
-
- getMonomerName() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer
-
Returns the monomer name.
- getMonomers(String) - Method in class org.helm.notation2.MonomerStore
-
Returns all monomers by polymerType
- getMonomerStore() - Method in class org.helm.notation2.MonomerFactory
-
create a MonomerStore instance based on MonomerFactory's monomerDB and
smilesMonomerDB
- getMonomerStore(Element) - Static method in class org.helm.notation2.tools.xHelmNotationParser
-
Generates the monomer store from a given XHELM document
- getMonomerType() - Method in class org.helm.notation2.Monomer
-
- getMonomerType() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer
-
Returns the monomer type.
- getMonomerTypes() - Method in class org.helm.notation2.MonomerFactory
-
- getName() - Method in class org.helm.notation2.Monomer
-
- getNaturalAnalog() - Method in class org.helm.notation2.Monomer
-
get the natural analog of this monomer.
- getNaturalAnalog() - Method in class org.helm.notation2.Nucleotide
-
return the natural analog of this nucleotide
- getNaturalAnalog(MonomerStore) - Method in class org.helm.notation2.Nucleotide
-
return the natural analog of this nucleotide
- getNaturalAnalogon() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer
-
Returns the natural analogon.
- getNaturalAnalogSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to generate the natural analogue sequence of a rna/dna of a given
polymer
- getNaturalAnalogueSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.PeptideUtils
-
method to produce for a peptide PolymerNotation the natural analogue
sequence
- getNotation() - Method in class org.helm.notation2.Nucleotide
-
- getNucleosideNotation() - Method in class org.helm.notation2.Nucleotide
-
This method returns the HELM notation for nucleoside
- getNucleotide(Element) - Static method in class org.helm.notation2.tools.NucleotideParser
-
- getNucleotide(String) - Static method in class org.helm.notation2.tools.NucleotideParser
-
- getNucleotideList(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to get all nucleotides for one polymer
- getNucleotideNaturalAnalogSequenceFromNotation(HELM2Notation) - Static method in class org.helm.notation2.tools.SequenceConverter
-
method to generate for all rna polymers the natural analogue sequence
- getNucleotideSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to get the nucleotide sequence for the polymer
- getNucleotideSequenceFromNotation(HELM2Notation) - Static method in class org.helm.notation2.tools.SequenceConverter
-
method to get for all rna/dnas the nucleotide sequence form an
HELM2Notation
- getNucleotideTemplates() - Method in class org.helm.notation2.NucleotideFactory
-
- getNucleotideTemplates(Element) - Static method in class org.helm.notation2.tools.NucleotideParser
-
- getNucleotideTemplatesXML(Map<String, Map<String, String>>) - Static method in class org.helm.notation2.tools.NucleotideParser
-
- getPeptideNaturalAnalogSequenceFromNotation(HELM2Notation) - Static method in class org.helm.notation2.tools.SequenceConverter
-
method to generate for all peptide polymers the natural analogue sequence
- getPeptidePolymers(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
-
method to get all peptide polymers given a list of PolymerNotation objects
- getPeptideSequenceFromNotation(HELM2Notation) - Static method in class org.helm.notation2.tools.SequenceConverter
-
method to get for all peptides the sequence
- getPeptideUnit() - Method in class org.helm.notation2.calculation.ExtinctionCoefficient
-
- getPhosphateMonomer() - Method in class org.helm.notation2.Nucleotide
-
return the phosphate monomer of this nucleotide
- getPhosphateMonomer(MonomerStore) - Method in class org.helm.notation2.Nucleotide
-
return the phosphate monomer of this nucleotide
- getPolymerType() - Method in class org.helm.notation2.Monomer
-
- getPolymerType() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer
-
Returns the polymer type.
- getPolymerTypes() - Method in class org.helm.notation2.MonomerFactory
-
- getPolymerTypeSet() - Method in class org.helm.notation2.MonomerStore
-
Returns the polymer type set
- getPositionType() - Method in class org.helm.notation2.Nucleotide
-
- getResource(String) - Static method in class org.helm.notation2.wsadapter.WSAdapterUtils
-
Call a GET routine on given resource URL.
- getReverseComplement(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to get the polymer with the reverse complement sequence of the
current polymer
- getReverseNucleotideTemplateMap() - Method in class org.helm.notation2.NucleotideFactory
-
- getReverseSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to generate the reverse rna/dna sequence of a given polymer
- getRgroupMap() - Method in class org.helm.notation2.RgroupStructure
-
- getRNAPolymers(List<PolymerNotation>) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
-
method to get all rna polymers given a List of PolymerNotation objects
- getRnaUnit() - Method in class org.helm.notation2.calculation.ExtinctionCoefficient
-
- getSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.PeptideUtils
-
method to produce for a peptide PolymerNotation the sequence
- getSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to get the rna sequence of the given PolymerNotation
- getShape() - Method in class org.helm.notation2.wsadapter.CategorizedMonomer
-
Returns the shape.
- getSiRNANotation(String, String) - Static method in class org.helm.notation2.tools.SiRNANotation
-
this method converts nucleotide sequences into HELM2Notation
- getSirnaNotation(String, String, String) - Static method in class org.helm.notation2.tools.SiRNANotation
-
this method converts nucleotide sequences into HELM notation based on
design pattern
- getSMILESForAll(HELM2Notation) - Static method in class org.helm.notation2.tools.SMILES
-
method to generate smiles for the whole HELMNotation
- getSMILESforPolymer(PolymerNotation) - Static method in class org.helm.notation2.tools.SMILES
-
method to generate smiles for one single PolymerNotation
- getSmilesMonomerDB() - Method in class org.helm.notation2.MonomerCache
-
- getSmilesMonomerDB() - Method in class org.helm.notation2.MonomerFactory
-
- getSmilesMonomerDB(boolean) - Method in class org.helm.notation2.MonomerFactory
-
- getSmilesMonomerDB() - Method in class org.helm.notation2.MonomerStore
-
returns SmilesMonomerDB
- getStandard(HELM2Notation) - Static method in class org.helm.notation2.tools.HELM1Utils
-
method to reproduce a standard HELM in HELM1 - Format
- getSugarMonomer() - Method in class org.helm.notation2.Nucleotide
-
get the sugar monomer, the return value could be null if the "nucleotide"
does not has a sugar
- getSugarMonomer(MonomerStore) - Method in class org.helm.notation2.Nucleotide
-
get the sugar monomer, the return value could be null if the "nucleotide"
does not has a sugar
- getSymbol() - Method in class org.helm.notation2.Nucleotide
-
- getTotalMonomerCount(HELM2Notation) - Static method in class org.helm.notation2.tools.HELM2NotationUtils
-
method to get the total number of MonomerNotationUnits in a HELMNotation
object
- getTotalMonomerCount(PolymerNotation) - Static method in class org.helm.notation2.tools.PolymerUtils
-
method to get the total monomer count of one PolymerNotation
- getTrimmedNucleotideSequence(PolymerNotation) - Static method in class org.helm.notation2.tools.RNAUtils
-
method to get the trimmed nucleotide sequence
- getUniqueExtendedSMILES(String) - Static method in class org.helm.notation2.tools.SMILES
-
- getUnit(int) - Method in class org.helm.notation2.calculation.ExtinctionCoefficient
-
- getWebserviceEditorCategorizationFullURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns URL and Path to monomer categorization resource combined.
- getWebserviceEditorCategorizationPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns path to monomer categorization resource.
- getWebserviceEditorCategorizationURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns URL without path to monomer categorization resource.
- getWebserviceMonomersFullURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns URL and Path to monomer resource combined.
- getWebserviceMonomersPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns path to monomer resource.
- getWebserviceMonomersPutFullURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns URL and Path to monomer PUT resource combined.
- getWebserviceMonomersURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns URL without path to monomer resource.
- getWebserviceNucleotidesFullURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns URL and Path to nucleotide resource combined.
- getWebserviceNucleotidesPath() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns path to nucleotide resource.
- getWebserviceNucleotidesPutFullURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns URL and Path to nucleotide PUT resource combined.
- getWebserviceNucleotidesURL() - Method in class org.helm.notation2.wsadapter.MonomerStoreConfiguration
-
Returns URL without path to nucleotide resource.
- getXHELM(HELM2Notation) - Static method in class org.helm.notation2.tools.xHelmNotationExporter
-
method to get xhelm for the helm notation, only if it was possible to
convert the helm in the old format
- getXHELM2(HELM2Notation) - Static method in class org.helm.notation2.tools.xHelmNotationExporter
-
method to get xhelm for the helm2 notation with the new functionality
- GroupingNotationException - Exception in org.helm.notation2.exception
-
GroupingNotationException
- GroupingNotationException(String) - Constructor for exception org.helm.notation2.exception.GroupingNotationException
-