Uses of Interface
org.forester.msa.Msa
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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>
MsaForesterWrapper. convert(MultipleSequenceAlignment<C,D> msa)
Convert a BioJavaMultipleSequenceAlignment
to a foresterMsa
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Uses of Msa in org.forester.archaeopteryx
Methods in org.forester.archaeopteryx that return Msa Modifier and Type Method Description Msa
MainFrameApplication. getMsa()
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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