org.forester.msa

Class MsaMethods

java.lang.Object

org.forester.msa.MsaMethods

public final class MsaMethods
extends Object

Method Summary

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 SortedMap<Character,Integer>	calculateResidueDestributionPerColumn(Msa msa, int column)
Object	clone()
static MsaMethods	createInstance()
Msa	deleteGapColumns(double max_allowed_gap_ratio, int min_allowed_length, Msa msa)
ArrayList<String>	getIgnoredSequenceIds()
static Msa	removeSequence(Msa msa, String to_remove_id)
static Msa	removeSequences(Msa msa, List<String> to_remove_ids)
static Msa	removeSequencesByMinimalLength(Msa msa, int min_effective_length)
static Msa	removeSequencesByRow(Msa msa, List<Integer> to_remove_rows)

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

clone

public Object clone()

Overrides:

clone in class Object

deleteGapColumns

public final Msa deleteGapColumns(double max_allowed_gap_ratio,
                                  int min_allowed_length,
                                  Msa msa)

getIgnoredSequenceIds

public ArrayList<String> getIgnoredSequenceIds()

calcNumberOfGapsStats

public static final DescriptiveStatistics calcNumberOfGapsStats(Msa msa)

calcNumberOfGapsInMsa

public static final int[] calcNumberOfGapsInMsa(Msa msa)

calcNumberOfGaps

public static final int calcNumberOfGaps(MolecularSequence seq)

calcBasicGapinessStatistics

public static DescriptiveStatistics calcBasicGapinessStatistics(Msa msa)

calcGapRatio

public static double calcGapRatio(Msa msa)

calcGapSumPerColumn

public static int calcGapSumPerColumn(Msa msa,
                                      int col)

calcNormalizedShannonsEntropy

public static final double calcNormalizedShannonsEntropy(int k,
                                                         Msa msa)

calcNormalizedShannonsEntropy

public static final double calcNormalizedShannonsEntropy(int k,
                                                         Msa msa,
                                                         int col)

calculateEffectiveLengthStatistics

public static final DescriptiveStatistics calculateEffectiveLengthStatistics(Msa msa)

calculateIdentityRatio

public static final DescriptiveStatistics calculateIdentityRatio(int from,
                                                                 int to,
                                                                 Msa msa)

calculateIdentityRatio

public static final double calculateIdentityRatio(Msa msa,
                                                  int column)

calculateResidueDestributionPerColumn

public static SortedMap<Character,Integer> calculateResidueDestributionPerColumn(Msa msa,
                                                                                 int column)

createInstance

public static MsaMethods createInstance()

removeSequence

public static final Msa removeSequence(Msa msa,
                                       String to_remove_id)

removeSequences

public static final Msa removeSequences(Msa msa,
                                        List<String> to_remove_ids)

removeSequencesByMinimalLength

public static Msa removeSequencesByMinimalLength(Msa msa,
                                                 int min_effective_length)

removeSequencesByRow

public static final Msa removeSequencesByRow(Msa msa,
                                             List<Integer> to_remove_rows)