Uses of Interface
org.forester.sequence.MolecularSequence
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Uses of MolecularSequence in org.forester.archaeopteryx
Methods in org.forester.archaeopteryx that return types with arguments of type MolecularSequence Modifier and Type Method Description java.util.List<MolecularSequence>
MainFrameApplication. getSeqs()
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Uses of MolecularSequence in org.forester.archaeopteryx.tools
Constructor parameters in org.forester.archaeopteryx.tools with type arguments of type MolecularSequence Constructor Description PhylogeneticInferrer(java.util.List<MolecularSequence> seqs, PhylogeneticInferenceOptions options, MainFrameApplication mf)
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Uses of MolecularSequence in org.forester.io.parsers
Methods in org.forester.io.parsers that return types with arguments of type MolecularSequence Modifier and Type Method Description static java.util.List<MolecularSequence>
FastaParser. parse(java.io.File f)
static java.util.List<MolecularSequence>
FastaParser. parse(java.io.InputStream is)
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Uses of MolecularSequence in org.forester.io.writers
Methods in org.forester.io.writers with parameters of type MolecularSequence Modifier and Type Method Description static java.lang.StringBuilder
SequenceWriter. toFasta(MolecularSequence seq, int width)
static void
SequenceWriter. toFasta(MolecularSequence seq, java.io.Writer w, int width)
Method parameters in org.forester.io.writers with type arguments of type MolecularSequence Modifier and Type Method Description static void
SequenceWriter. writeSeqs(java.util.List<MolecularSequence> seqs, java.io.File file, SequenceWriter.SEQ_FORMAT format, int width)
static void
SequenceWriter. writeSeqs(java.util.List<MolecularSequence> seqs, java.io.Writer writer, SequenceWriter.SEQ_FORMAT format, int width)
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Uses of MolecularSequence in org.forester.msa
Methods in org.forester.msa that return MolecularSequence Modifier and Type Method Description MolecularSequence
DeleteableMsa. deleteRow(java.lang.String id, boolean return_removed_seq)
MolecularSequence
BasicMsa. getSequence(int row)
MolecularSequence
BasicMsa. getSequence(java.lang.String id)
MolecularSequence
DeleteableMsa. getSequence(int row)
MolecularSequence
Msa. getSequence(int row)
MolecularSequence
Msa. getSequence(java.lang.String id)
MolecularSequence
ResampleableMsa. getSequence(int row)
Methods in org.forester.msa that return types with arguments of type MolecularSequence Modifier and Type Method Description java.util.List<MolecularSequence>
BasicMsa. asSequenceList()
java.util.List<MolecularSequence>
Msa. asSequenceList()
Methods in org.forester.msa with parameters of type MolecularSequence Modifier and Type Method Description static int
MsaMethods. calcNumberOfGaps(MolecularSequence seq)
Method parameters in org.forester.msa with type arguments of type MolecularSequence Modifier and Type Method Description static Msa
BasicMsa. createInstance(java.util.List<MolecularSequence> seqs)
static DeleteableMsa
DeleteableMsa. createInstance(java.util.List<MolecularSequence> seqs)
Msa
ClustalOmega. infer(java.util.List<MolecularSequence> seqs, java.util.List<java.lang.String> opts)
Msa
Mafft. infer(java.util.List<MolecularSequence> seqs, java.util.List<java.lang.String> opts)
abstract Msa
MsaInferrer. infer(java.util.List<MolecularSequence> seqs, java.util.List<java.lang.String> opts)
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Uses of MolecularSequence in org.forester.phylogeny.data
Constructors in org.forester.phylogeny.data with parameters of type MolecularSequence Constructor Description Sequence(MolecularSequence mol_seq)
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Uses of MolecularSequence in org.forester.sequence
Classes in org.forester.sequence that implement MolecularSequence Modifier and Type Class Description class
BasicSequence
Methods in org.forester.sequence that return MolecularSequence Modifier and Type Method Description static MolecularSequence
BasicSequence. copySequence(MolecularSequence seq)
static MolecularSequence
BasicSequence. createAaSequence(java.lang.String identifier, java.lang.String mol_sequence)
static MolecularSequence
BasicSequence. createDnaSequence(java.lang.String identifier, java.lang.String mol_sequence)
static MolecularSequence
BasicSequence. createRnaSequence(java.lang.String identifier, java.lang.String mol_sequence)
Methods in org.forester.sequence with parameters of type MolecularSequence Modifier and Type Method Description static MolecularSequence
BasicSequence. copySequence(MolecularSequence seq)
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Uses of MolecularSequence in org.forester.ws.seqdb
Methods in org.forester.ws.seqdb that return MolecularSequence Modifier and Type Method Description MolecularSequence
EbiDbEntry. getMolecularSequence()
MolecularSequence
SequenceDatabaseEntry. getMolecularSequence()
MolecularSequence
UniProtEntry. getMolecularSequence()
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