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

Packages that use FastaFormatException

Package	Description
org.helm.notation2.tools

Uses of FastaFormatException in org.helm.notation2.tools

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

Modifier and Type	Method and Description
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) 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
String	WebService.readPeptide(String peptide) method to read a single peptide sequence and generates HELM
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.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