public final class MsaMethods
extends java.lang.Object
Modifier and Type | Method and Description |
---|---|
static DescriptiveStatistics |
calcBasicGapinessStatistics(Msa msa) |
static double |
calcGapRatio(Msa msa) |
static int |
calcGapSumPerColumn(Msa msa,
int col) |
static double |
calcNormalizedShannonsEntropy(int k,
Msa msa) |
static double |
calcNormalizedShannonsEntropy(int k,
Msa msa,
int col) |
static int |
calcNumberOfGaps(MolecularSequence seq) |
static int[] |
calcNumberOfGapsInMsa(Msa msa) |
static DescriptiveStatistics |
calcNumberOfGapsStats(Msa msa) |
static DescriptiveStatistics |
calculateEffectiveLengthStatistics(Msa msa) |
static DescriptiveStatistics |
calculateIdentityRatio(int from,
int to,
Msa msa) |
static double |
calculateIdentityRatio(Msa msa,
int column) |
static java.util.SortedMap<java.lang.Character,java.lang.Integer> |
calculateResidueDestributionPerColumn(Msa msa,
int column) |
java.lang.Object |
clone() |
static MsaMethods |
createInstance() |
Msa |
deleteGapColumns(double max_allowed_gap_ratio,
int min_allowed_length,
Msa msa) |
java.util.ArrayList<java.lang.String> |
getIgnoredSequenceIds() |
static Msa |
removeSequence(Msa msa,
java.lang.String to_remove_id) |
static Msa |
removeSequences(Msa msa,
java.util.List<java.lang.String> to_remove_ids) |
static Msa |
removeSequencesByMinimalLength(Msa msa,
int min_effective_length) |
static Msa |
removeSequencesByRow(Msa msa,
java.util.List<java.lang.Integer> to_remove_rows) |
public java.lang.Object clone()
clone
in class java.lang.Object
public final Msa deleteGapColumns(double max_allowed_gap_ratio, int min_allowed_length, Msa msa)
public java.util.ArrayList<java.lang.String> getIgnoredSequenceIds()
public static final DescriptiveStatistics calcNumberOfGapsStats(Msa msa)
public static final int[] calcNumberOfGapsInMsa(Msa msa)
public static final int calcNumberOfGaps(MolecularSequence seq)
public static DescriptiveStatistics calcBasicGapinessStatistics(Msa msa)
public static double calcGapRatio(Msa msa)
public static int calcGapSumPerColumn(Msa msa, int col)
public static final double calcNormalizedShannonsEntropy(int k, Msa msa)
public static final double calcNormalizedShannonsEntropy(int k, Msa msa, int col)
public static final DescriptiveStatistics calculateEffectiveLengthStatistics(Msa msa)
public static final DescriptiveStatistics calculateIdentityRatio(int from, int to, Msa msa)
public static final double calculateIdentityRatio(Msa msa, int column)
public static java.util.SortedMap<java.lang.Character,java.lang.Integer> calculateResidueDestributionPerColumn(Msa msa, int column)
public static MsaMethods createInstance()
public static final Msa removeSequences(Msa msa, java.util.List<java.lang.String> to_remove_ids)
public static Msa removeSequencesByMinimalLength(Msa msa, int min_effective_length)