Package org.forester.msa
Class MsaMethods
- java.lang.Object
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- org.forester.msa.MsaMethods
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public final class MsaMethods extends java.lang.Object
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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)
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Method Detail
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clone
public java.lang.Object clone()
- Overrides:
clone
in classjava.lang.Object
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deleteGapColumns
public final Msa deleteGapColumns(double max_allowed_gap_ratio, int min_allowed_length, Msa msa)
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getIgnoredSequenceIds
public java.util.ArrayList<java.lang.String> getIgnoredSequenceIds()
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calcNumberOfGapsStats
public static final DescriptiveStatistics calcNumberOfGapsStats(Msa msa)
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calcNumberOfGapsInMsa
public static final int[] calcNumberOfGapsInMsa(Msa msa)
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calcNumberOfGaps
public static final int calcNumberOfGaps(MolecularSequence seq)
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calcBasicGapinessStatistics
public static DescriptiveStatistics calcBasicGapinessStatistics(Msa msa)
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calcGapRatio
public static double calcGapRatio(Msa msa)
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calcGapSumPerColumn
public static int calcGapSumPerColumn(Msa msa, int col)
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calcNormalizedShannonsEntropy
public static final double calcNormalizedShannonsEntropy(int k, Msa msa)
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calcNormalizedShannonsEntropy
public static final double calcNormalizedShannonsEntropy(int k, Msa msa, int col)
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calculateEffectiveLengthStatistics
public static final DescriptiveStatistics calculateEffectiveLengthStatistics(Msa msa)
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calculateIdentityRatio
public static final DescriptiveStatistics calculateIdentityRatio(int from, int to, Msa msa)
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calculateIdentityRatio
public static final double calculateIdentityRatio(Msa msa, int column)
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calculateResidueDestributionPerColumn
public static java.util.SortedMap<java.lang.Character,java.lang.Integer> calculateResidueDestributionPerColumn(Msa msa, int column)
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createInstance
public static MsaMethods createInstance()
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removeSequences
public static final Msa removeSequences(Msa msa, java.util.List<java.lang.String> to_remove_ids)
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removeSequencesByMinimalLength
public static Msa removeSequencesByMinimalLength(Msa msa, int min_effective_length)
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