static org.helm.notation2.parser.notation.HELM2Notation |
FastaFormat.convertIntoAnalogSequence(org.helm.notation2.parser.notation.HELM2Notation helm2Notation) |
method to convert all Peptides and RNAs into the natural analogue
sequence and generates HELM2Notation
|
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)
|
protected static org.helm.notation2.parser.notation.polymer.PolymerListElements |
FastaFormat.generateElementsOfPeptide(String sequence,
org.helm.notation2.parser.notation.polymer.HELMEntity entity) |
method to fill a peptide polymer with its elements (MonomerNotationUnits)
|
static String |
FastaFormat.generateFasta(org.helm.notation2.parser.notation.HELM2Notation helm2Notation2) |
method to generate for the whole HELM2Notation fasta-files, it contains
fasta for all rna and peptides
|
String |
WebService.generateFasta(String notation) |
method to generate FASTA-Formats for all rna and peptide sequences from
an HELM input
|
static String |
FastaFormat.generateFastaFromPeptidePolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) |
method to generate Fasta for peptide polymers
|
static String |
FastaFormat.generateFastaFromRNAPolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) |
method to generate Fasta for rna polymers
|
String |
WebService.generateHELMFromFastaNucleotide(String notation) |
method to generate HELM from a FASTA containing rna/dna sequences
|
String |
WebService.generateHELMFromFastaPeptide(String notation) |
method to generate HELM from a FASTA containing peptide sequence(s)
|
static org.helm.notation2.parser.notation.HELM2Notation |
FastaFormat.generatePeptidePolymersFromFASTAFormatHELM1(String fasta) |
method to read the information from a FastaFile-Format + generate peptide
polymers, be careful, it produces only polymers in the HELM1 standard, no
ambiguity
|
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.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 org.helm.notation2.parser.notation.HELM2Notation |
SequenceConverter.readPeptide(String notation) |
method to read a peptide sequence and generate a HELM2Notation object of
it
|
String |
WebService.readPeptide(String peptide) |
method to read a single peptide 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
|
String |
WebService.readRNA(String rna) |
method to read a single rna sequence and generates HELM
|