org.forester.msa

Class DeleteableMsa

java.lang.Object

org.forester.msa.BasicMsa

org.forester.msa.DeleteableMsa

All Implemented Interfaces:

Msa

public final class DeleteableMsa
extends BasicMsa

Nested Class Summary

Nested classes/interfaces inherited from interface org.forester.msa.Msa

Msa.MSA_FORMAT

Method Summary

Modifier and Type	Method and Description
double[]	calcGappiness()
static int	calcGapSumPerColumn(Msa msa, int col)
static DeleteableMsa	createInstance(List<MolecularSequence> seqs)
static DeleteableMsa	createInstance(Msa msa)
void	deleteGapColumns(double max_allowed_gap_ratio)
void	deleteGapOnlyColumns()
MolecularSequence	deleteRow(String id, boolean return_removed_seq)
short	determineMaxIdLength()
String	getIdentifier(int row)
int	getLength()
int	getNumberOfSequences()
char	getResidueAt(int row, int col)
MolecularSequence	getSequence(int row)
boolean	isAllGap(int col)
void	setIdentifier(int row, String id)
void	setResidueAt(int row, int col, char residue)

Methods inherited from class org.forester.msa.BasicMsa

asSequenceList, getColumnAt, getSequence, getSequenceAsString, getType, isGapAt, toString, write

Methods inherited from class java.lang.Object

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

Method Detail

calcGappiness

public final double[] calcGappiness()

calcGapSumPerColumn

public static int calcGapSumPerColumn(Msa msa,
                                      int col)

determineMaxIdLength

public short determineMaxIdLength()

deleteGapColumns

public final void deleteGapColumns(double max_allowed_gap_ratio)

deleteGapOnlyColumns

public final void deleteGapOnlyColumns()

deleteRow

public final MolecularSequence deleteRow(String id,
                                         boolean return_removed_seq)

getIdentifier

public final String getIdentifier(int row)

Specified by:

getIdentifier in interface Msa

Overrides:

getIdentifier in class BasicMsa

getLength

public final int getLength()

Specified by:

getLength in interface Msa

Overrides:

getLength in class BasicMsa

getNumberOfSequences

public final int getNumberOfSequences()

Specified by:

getNumberOfSequences in interface Msa

Overrides:

getNumberOfSequences in class BasicMsa

getResidueAt

public final char getResidueAt(int row,
                               int col)

Specified by:

getResidueAt in interface Msa

Overrides:

getResidueAt in class BasicMsa

getSequence

public MolecularSequence getSequence(int row)

Specified by:

getSequence in interface Msa

Overrides:

getSequence in class BasicMsa

isAllGap

public final boolean isAllGap(int col)

setIdentifier

public final void setIdentifier(int row,
                                String id)

Specified by:

setIdentifier in interface Msa

Overrides:

setIdentifier in class BasicMsa

setResidueAt

public final void setResidueAt(int row,
                               int col,
                               char residue)

Specified by:

setResidueAt in interface Msa

Overrides:

setResidueAt in class BasicMsa

createInstance

public static final DeleteableMsa createInstance(List<MolecularSequence> seqs)

createInstance

public static final DeleteableMsa createInstance(Msa msa)