Uses of Interface
org.forester.msa.Msa

Packages that use Msa

Package	Description
org.biojava.nbio.phylo
org.forester.archaeopteryx
org.forester.archaeopteryx.tools
org.forester.development
org.forester.evoinference.distance
org.forester.evoinference.tools
org.forester.io.parsers
org.forester.msa
org.forester.msa_compactor
org.forester.phylogeny

Uses of Msa in org.biojava.nbio.phylo

Methods in org.biojava.nbio.phylo that return Msa

Modifier and Type	Method	Description
static <C extends Sequence<D>,D extends Compound> Msa	ForesterWrapper.convert(MultipleSequenceAlignment<C,D> msa)	Convert a BioJava MultipleSequenceAlignment to a forester Msa.

Uses of Msa in org.forester.archaeopteryx

Methods in org.forester.archaeopteryx that return Msa

Modifier and Type	Method	Description
Msa	MainFrameApplication.getMsa()

Uses of Msa in org.forester.archaeopteryx.tools

Constructors in org.forester.archaeopteryx.tools with parameters of type Msa

Constructor	Description
PhylogeneticInferrer(Msa msa, PhylogeneticInferenceOptions options, MainFrameApplication mf)

Uses of Msa in org.forester.development

Constructors in org.forester.development with parameters of type Msa

Constructor	Description
MsaRenderer(Msa msa, int unit_size, javax.swing.JComponent parent)

Uses of Msa in org.forester.evoinference.distance

Methods in org.forester.evoinference.distance with parameters of type Msa

Modifier and Type	Method	Description
static BasicSymmetricalDistanceMatrix	PairwiseDistanceCalculator.calcFractionalDissimilarities(Msa msa)
static BasicSymmetricalDistanceMatrix	PairwiseDistanceCalculator.calcKimuraDistances(Msa msa)
static BasicSymmetricalDistanceMatrix	PairwiseDistanceCalculator.calcKimuraDistances(Msa msa, double value_for_too_large_distance_for_kimura_formula)
static BasicSymmetricalDistanceMatrix	PairwiseDistanceCalculator.calcPoissonDistances(Msa msa)

Uses of Msa in org.forester.evoinference.tools

Methods in org.forester.evoinference.tools that return Msa

Modifier and Type	Method	Description
static Msa[]	BootstrapResampler.resample(Msa msa, int n, long seed)

Methods in org.forester.evoinference.tools with parameters of type Msa

Modifier and Type	Method	Description
static Msa[]	BootstrapResampler.resample(Msa msa, int n, long seed)

Uses of Msa in org.forester.io.parsers

Methods in org.forester.io.parsers that return Msa

Modifier and Type	Method	Description
static Msa	GeneralMsaParser.parse(java.io.InputStream is)
static Msa	FastaParser.parseMsa(byte[] bytes)
static Msa	FastaParser.parseMsa(java.io.File f)
static Msa	FastaParser.parseMsa(java.io.InputStream is)
static Msa	FastaParser.parseMsa(java.lang.String s)

Uses of Msa in org.forester.msa

Classes in org.forester.msa that implement Msa

Modifier and Type	Class	Description
class	BasicMsa
class	DeleteableMsa
class	ResampleableMsa

Methods in org.forester.msa that return Msa

Modifier and Type	Method	Description
static Msa	BasicMsa.createInstance(java.util.List<MolecularSequence> seqs)
Msa	MsaMethods.deleteGapColumns(double max_allowed_gap_ratio, int min_allowed_length, Msa msa)
Msa	ClustalOmega.infer(java.io.File path_to_input_seqs, java.util.List<java.lang.String> opts)
Msa	ClustalOmega.infer(java.util.List<MolecularSequence> seqs, java.util.List<java.lang.String> opts)
Msa	Mafft.infer(java.io.File path_to_input_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.io.File path_to_input_seqs, java.util.List<java.lang.String> opts)
abstract Msa	MsaInferrer.infer(java.util.List<MolecularSequence> seqs, java.util.List<java.lang.String> opts)
static Msa	MsaMethods.removeSequence(Msa msa, java.lang.String to_remove_id)
static Msa	MsaMethods.removeSequences(Msa msa, java.util.List<java.lang.String> to_remove_ids)
static Msa	MsaMethods.removeSequencesByMinimalLength(Msa msa, int min_effective_length)
static Msa	MsaMethods.removeSequencesByRow(Msa msa, java.util.List<java.lang.Integer> to_remove_rows)

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

Modifier and Type	Method	Description
static DescriptiveStatistics	MsaMethods.calcBasicGapinessStatistics(Msa msa)
static double	MsaMethods.calcGapRatio(Msa msa)
static int	DeleteableMsa.calcGapSumPerColumn(Msa msa, int col)
static int	MsaMethods.calcGapSumPerColumn(Msa msa, int col)
static double	MsaMethods.calcNormalizedShannonsEntropy(int k, Msa msa)
static double	MsaMethods.calcNormalizedShannonsEntropy(int k, Msa msa, int col)
static int[]	MsaMethods.calcNumberOfGapsInMsa(Msa msa)
static DescriptiveStatistics	MsaMethods.calcNumberOfGapsStats(Msa msa)
static DescriptiveStatistics	MsaMethods.calculateEffectiveLengthStatistics(Msa msa)
static DescriptiveStatistics	MsaMethods.calculateIdentityRatio(int from, int to, Msa msa)
static double	MsaMethods.calculateIdentityRatio(Msa msa, int column)
static java.util.SortedMap<java.lang.Character,java.lang.Integer>	MsaMethods.calculateResidueDestributionPerColumn(Msa msa, int column)
static DeleteableMsa	DeleteableMsa.createInstance(Msa msa)
Msa	MsaMethods.deleteGapColumns(double max_allowed_gap_ratio, int min_allowed_length, Msa msa)
static Msa	MsaMethods.removeSequence(Msa msa, java.lang.String to_remove_id)
static Msa	MsaMethods.removeSequences(Msa msa, java.util.List<java.lang.String> to_remove_ids)
static Msa	MsaMethods.removeSequencesByMinimalLength(Msa msa, int min_effective_length)
static Msa	MsaMethods.removeSequencesByRow(Msa msa, java.util.List<java.lang.Integer> to_remove_rows)

Uses of Msa in org.forester.msa_compactor

Methods in org.forester.msa_compactor that return Msa

Modifier and Type	Method	Description
Msa	MsaCompactor.getMsa()

Constructors in org.forester.msa_compactor with parameters of type Msa

Constructor	Description
MsaProperties(Msa msa, java.lang.String removed_seq, boolean calculate_normalized_shannon_entropy)

Uses of Msa in org.forester.phylogeny

Methods in org.forester.phylogeny with parameters of type Msa

Modifier and Type	Method	Description
static void	PhylogenyMethods.addMolecularSeqsToTree(Phylogeny phy, Msa msa)