Uses of Interface
org.forester.sequence.MolecularSequence
Packages that use MolecularSequence
Package
Description
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Uses of MolecularSequence in org.forester.archaeopteryx
Methods in org.forester.archaeopteryx that return types with arguments of type MolecularSequence -
Uses of MolecularSequence in org.forester.archaeopteryx.tools
Constructor parameters in org.forester.archaeopteryx.tools with type arguments of type MolecularSequenceModifierConstructorDescriptionPhylogeneticInferrer
(List<MolecularSequence> seqs, PhylogeneticInferenceOptions options, MainFrameApplication mf) -
Uses of MolecularSequence in org.forester.io.parsers
Methods in org.forester.io.parsers that return types with arguments of type MolecularSequenceModifier and TypeMethodDescriptionstatic List
<MolecularSequence> static List
<MolecularSequence> FastaParser.parse
(InputStream is) -
Uses of MolecularSequence in org.forester.io.writers
Methods in org.forester.io.writers with parameters of type MolecularSequenceModifier and TypeMethodDescriptionstatic StringBuilder
SequenceWriter.toFasta
(MolecularSequence seq, int width) static void
SequenceWriter.toFasta
(MolecularSequence seq, Writer w, int width) Method parameters in org.forester.io.writers with type arguments of type MolecularSequenceModifier and TypeMethodDescriptionstatic void
SequenceWriter.writeSeqs
(List<MolecularSequence> seqs, File file, SequenceWriter.SEQ_FORMAT format, int width) static void
SequenceWriter.writeSeqs
(List<MolecularSequence> seqs, Writer writer, SequenceWriter.SEQ_FORMAT format, int width) -
Uses of MolecularSequence in org.forester.msa
Methods in org.forester.msa that return MolecularSequenceModifier and TypeMethodDescriptionfinal MolecularSequence
BasicMsa.getSequence
(int row) BasicMsa.getSequence
(String id) DeleteableMsa.getSequence
(int row) Msa.getSequence
(int row) Msa.getSequence
(String id) ResampleableMsa.getSequence
(int row) Methods in org.forester.msa that return types with arguments of type MolecularSequenceMethods in org.forester.msa with parameters of type MolecularSequenceModifier and TypeMethodDescriptionstatic final int
MsaMethods.calcNumberOfGaps
(MolecularSequence seq) Method parameters in org.forester.msa with type arguments of type MolecularSequenceModifier and TypeMethodDescriptionstatic Msa
BasicMsa.createInstance
(List<MolecularSequence> seqs) static final DeleteableMsa
DeleteableMsa.createInstance
(List<MolecularSequence> seqs) ClustalOmega.infer
(List<MolecularSequence> seqs, List<String> opts) Mafft.infer
(List<MolecularSequence> seqs, List<String> opts) abstract Msa
MsaInferrer.infer
(List<MolecularSequence> seqs, List<String> opts) -
Uses of MolecularSequence in org.forester.phylogeny.data
Constructors in org.forester.phylogeny.data with parameters of type MolecularSequence -
Uses of MolecularSequence in org.forester.sequence
Classes in org.forester.sequence that implement MolecularSequenceMethods in org.forester.sequence that return MolecularSequenceModifier and TypeMethodDescriptionstatic MolecularSequence
BasicSequence.copySequence
(MolecularSequence seq) static MolecularSequence
BasicSequence.createAaSequence
(String identifier, String mol_sequence) static MolecularSequence
BasicSequence.createDnaSequence
(String identifier, String mol_sequence) static MolecularSequence
BasicSequence.createRnaSequence
(String identifier, String mol_sequence) Methods in org.forester.sequence with parameters of type MolecularSequenceModifier and TypeMethodDescriptionstatic MolecularSequence
BasicSequence.copySequence
(MolecularSequence seq) -
Uses of MolecularSequence in org.forester.ws.seqdb
Methods in org.forester.ws.seqdb that return MolecularSequenceModifier and TypeMethodDescriptionEbiDbEntry.getMolecularSequence()
SequenceDatabaseEntry.getMolecularSequence()
UniProtEntry.getMolecularSequence()