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

Packages that use MonomerException 
Package Description
org.helm.notation2  
org.helm.notation2.tools  

  • Uses of MonomerException in org.helm.notation2

    Methods in org.helm.notation2 that throw MonomerException 
    Modifier and Type Method Description
    void MonomerStore.addMonomer​(Monomer monomer)
    Adds a monomer to the store
    void MonomerStore.addMonomer​(Monomer monomer, boolean dbChanged)
    Adds a monomer to the store and optionally sets the dbChanged flag
    void MonomerFactory.addNewMonomer​(Monomer monomer)
    To add new monomer into monomerCache
    void MonomerStore.addNewMonomer​(Monomer monomer)
    Adds a monomer to the store and makes it a temporary new monomer
    MonomerCache MonomerFactory.buildMonomerCacheFromXML​(String monomerDBXML)
    Build an MonomerCache object with monomerDBXML String
    static Attachment DeepCopy.copy​(Attachment attachment)  
    static Monomer DeepCopy.copy​(Monomer monomer)  
    Map<Monomer,​Monomer> MonomerFactory.getConflictedMonomerMap​(MonomerCache remoteMonomerCache)  
    void MonomerFactory.merge​(MonomerCache remoteMonomerCache)
    merge remote monomerCache with local monomerCache, will throw exception if conflicts found.
    void MonomerFactory.saveMonomerCache()
    save monomerCache to disk file
    void MonomerFactory.setMonomerCache​(MonomerCache remoteMonomerCache)
    replace local cache with remote one completely, may cause loss of data

  • Uses of MonomerException in org.helm.notation2.tools

    Methods in org.helm.notation2.tools that throw MonomerException 
    Modifier and Type Method Description
    static Nucleotide NucleotideParser.convertToNucleotide​(String id, boolean last)
    method to convert an string to an nucleotide
    static void MonomerParser.fillAttachmentInfo​(Attachment att)  
    static List<Monomer> Validation.getAllMonomers​(org.helm.notation2.parser.notation.polymer.MonomerNotation not, int position)
    method to get for one MonomerNotation all valid contained monomers
    static List<Monomer> Validation.getAllMonomersOnlyBase​(org.helm.notation2.parser.notation.polymer.MonomerNotation not)
    method to get for one MonomerNotation all valid contained monomers.
    static List<String> AminoAcidParser.getAminoAcidList​(String peptideSequence)
    This method converts peptide sequence into a List of amino acid
    static List<String> AminoAcidParser.getAminoAcidList​(String peptideSequence, String delimiter)
    This method converts peptide sequence into a List of amino acid with optional delimiter
    static List<Monomer> MethodsMonomerUtils.getListOfMonomer​(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations)
    method to get all monomers for all MonomerNotations
    static Monomer MethodsMonomerUtils.getMonomer​(String type, String id, String info)
    method to get the monomer from the database!
    static Monomer MonomerParser.getMonomer​(String monomerXMLString)  
    static Monomer MonomerParser.getMonomer​(org.jdom2.Element monomer)
    Convert monomer element to Monomer object
    static org.jdom2.Element MonomerParser.getMonomerElement​(Monomer monomer)
    This method converts Monomer to MONOMER XML element
    static List<Monomer> MonomerParser.getMonomerList​(String monomerXMLString)  
    static MonomerStore xHelmNotationParser.getMonomerStore​(org.jdom2.Element rootElement)
    Generates the monomer store from a given XHELM document
    static String xHelmNotationExporter.getXHELM​(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
    method to get xhelm for the helm notation, only if it was possible to convert the helm in the old format
    static String xHelmNotationExporter.getXHELM2​(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
    method to get xhelm for the helm2 notation with the new functionality
    static void ChangeObjects.replaceMonomer​(org.helm.notation2.parser.notation.HELM2Notation helm2notation, String polymerType, String existingMonomerID, String newMonomerID)
    method to replace the MonomerID with the new MonomerID for a given polymer type
    static boolean MonomerParser.validateAttachement​(Attachment attachment)
    This method validates Attachment by the following rules Attachment must have unique ID cap group SMILES must be valid cap group SMILES must contain one R group R group in SMILES must match R group label
    static void MonomerParser.validateAttachmentLabel​(String label)
    This method checks if attachment label is in the format of R#, where # is a number
    static boolean MonomerParser.validateMonomer​(Monomer monomer)
    This methods checks the validity of the monomer based on the following rules monomer cannot be null polymer type cannot be null and must be one of the defined polymer type monomer type cannot be null and must be one of the defined monomer type for a given polymer type Monomer ID cannot be null structure cannot be null for non-chemical type monomer structure SMILES must be valid attachment labels on monomer must be unique Attachment number on SMILES must match attachment List size Each attachment in attachment list must be valid (call validateAttachment()) Attachment labels on monomer must match atachment label on attachment list For non-chemical type monomers, modified monomer (ID length greater than 1) must have natural analog All monomers must have at least one attachment
    static void Validation.validateNotationObjects​(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
    method to check if the generated notation objects by the parser are correct the polymer ids have to be unique; all monomers have to be valid; all used polymer ids in the grouping section have to be there; all connections have to be valid
    void WebService.validateSyntaxHELM​(String helm)