Uses of Interface
org.forester.sequence.MolecularSequence

Packages that use MolecularSequence

Package	Description
org.forester.archaeopteryx
org.forester.archaeopteryx.tools
org.forester.io.parsers
org.forester.io.writers
org.forester.msa
org.forester.phylogeny.data
org.forester.sequence
org.forester.ws.seqdb

Uses of MolecularSequence in org.forester.archaeopteryx

Methods in org.forester.archaeopteryx that return types with arguments of type MolecularSequence

Modifier and Type	Method and Description
List<MolecularSequence>	MainFrameApplication.getSeqs()

Uses of MolecularSequence in org.forester.archaeopteryx.tools

Constructor parameters in org.forester.archaeopteryx.tools with type arguments of type MolecularSequence

Constructor and Description
PhylogeneticInferrer(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 MolecularSequence

Modifier and Type	Method and Description
static List<MolecularSequence>	FastaParser.parse(File f)
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 MolecularSequence

Modifier and Type	Method and Description
static 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 MolecularSequence

Modifier and Type	Method and Description
static 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 MolecularSequence

Modifier and Type	Method and Description
MolecularSequence	DeleteableMsa.deleteRow(String id, boolean return_removed_seq)
MolecularSequence	BasicMsa.getSequence(int row)
MolecularSequence	ResampleableMsa.getSequence(int row)
MolecularSequence	Msa.getSequence(int row)
MolecularSequence	DeleteableMsa.getSequence(int row)
MolecularSequence	BasicMsa.getSequence(String id)
MolecularSequence	Msa.getSequence(String id)

Methods in org.forester.msa that return types with arguments of type MolecularSequence

Modifier and Type	Method and Description
List<MolecularSequence>	BasicMsa.asSequenceList()
List<MolecularSequence>	Msa.asSequenceList()

Methods in org.forester.msa with parameters of type MolecularSequence

Modifier and Type	Method and Description
static int	MsaMethods.calcNumberOfGaps(MolecularSequence seq)

Method parameters in org.forester.msa with type arguments of type MolecularSequence

Modifier and Type	Method and Description
static Msa	BasicMsa.createInstance(List<MolecularSequence> seqs)
static DeleteableMsa	DeleteableMsa.createInstance(List<MolecularSequence> seqs)
abstract Msa	MsaInferrer.infer(List<MolecularSequence> seqs, List<String> opts)
Msa	Mafft.infer(List<MolecularSequence> seqs, List<String> opts)
Msa	ClustalOmega.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

Constructor and Description
Sequence(MolecularSequence mol_seq)

Uses of MolecularSequence in org.forester.sequence

Classes in org.forester.sequence that implement MolecularSequence

Modifier and Type	Class and Description
class	BasicSequence

Methods in org.forester.sequence that return MolecularSequence

Modifier and Type	Method and Description
static 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 MolecularSequence

Modifier and Type	Method and Description
static MolecularSequence	BasicSequence.copySequence(MolecularSequence seq)

Uses of MolecularSequence in org.forester.ws.seqdb

Methods in org.forester.ws.seqdb that return MolecularSequence

Modifier and Type	Method and Description
MolecularSequence	SequenceDatabaseEntry.getMolecularSequence()
MolecularSequence	EbiDbEntry.getMolecularSequence()
MolecularSequence	UniProtEntry.getMolecularSequence()