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 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 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, String rnaDesignType)
    this method converts nucleotide sequences into HELM notation based on design pattern
    static org.helm.notation2.parser.notation.HELM2Notation SiRNANotation.getSiRNANotation​(String senseSeq, String antiSenseSeq)
    this method converts nucleotide sequences into HELM2Notation
    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
    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
    String WebService.readRNA​(String rna)
    method to read a single rna sequence and generates HELM