public final class MsaMethods
extends java.lang.Object
Modifier and Type | Method and Description |
---|---|
static DescriptiveStatistics |
calcBasicGapinessStatistics(Msa msa) |
static int |
calcGapSumPerColumn(Msa msa,
int col) |
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() |
java.util.ArrayList<java.lang.String> |
getIgnoredSequenceIds() |
Msa |
removeGapColumns(double max_allowed_gap_ratio,
int min_allowed_length,
Msa msa) |
public java.util.ArrayList<java.lang.String> getIgnoredSequenceIds()
public static MsaMethods createInstance()
public java.lang.Object clone()
clone
in class java.lang.Object
public static int calcGapSumPerColumn(Msa msa, int col)
public Msa removeGapColumns(double max_allowed_gap_ratio, int min_allowed_length, Msa msa)
public static double calculateIdentityRatio(Msa msa, int column)
public static java.util.SortedMap<java.lang.Character,java.lang.Integer> calculateResidueDestributionPerColumn(Msa msa, int column)
public static DescriptiveStatistics calcBasicGapinessStatistics(Msa msa)