org.forester.msa
Class MsaMethods

java.lang.Object
  org.forester.msa.MsaMethods

public final class MsaMethods
extends java.lang.Object

Method Summary

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)

Methods inherited from class java.lang.Object

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

Method Detail

getIgnoredSequenceIds

public java.util.ArrayList<java.lang.String> getIgnoredSequenceIds()

createInstance

public static MsaMethods createInstance()

clone

public java.lang.Object clone()

Overrides:

clone in class java.lang.Object

calcGapSumPerColumn

public static int calcGapSumPerColumn(Msa msa,
                                      int col)

removeGapColumns

public Msa removeGapColumns(double max_allowed_gap_ratio,
                            int min_allowed_length,
                            Msa msa)

calculateIdentityRatio

public static double calculateIdentityRatio(Msa msa,
                                            int column)

calculateResidueDestributionPerColumn

public static java.util.SortedMap<java.lang.Character,java.lang.Integer> calculateResidueDestributionPerColumn(Msa msa,
                                                                                                               int column)

calcBasicGapinessStatistics

public static DescriptiveStatistics calcBasicGapinessStatistics(Msa msa)