pal.alignment

Class AbstractAlignment

java.lang.Object

pal.alignment.AbstractAlignment

All Implemented Interfaces:

java.io.Serializable, Alignment, IdGroup, Report

Direct Known Subclasses:

BootstrappedAlignment, ConcatenatedAlignment, ConcatenatedAnnotatedAlignment, GapBalancedAlignment, IndelAlignment, JumbledAlignment, ReadAlignment, ReadAlignmentOld, SimpleAlignment, SimulatedAlignment, SitePattern, StrippedAlignment

public abstract class AbstractAlignment
extends java.lang.Object
implements Alignment, java.io.Serializable, IdGroup, Report

abstract base class for any alignment data.

Version:

$Id: AbstractAlignment.java,v 1.7 2003/03/23 00:12:57 matt Exp $

Author:

Alexei Drummond, Korbinian Strimmer

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Field Summary

Fields

Modifier and Type	Field and Description
protected IdGroup	idGroup sequence identifiers
protected int	numSeqs number of sequences
protected int	numSites length of each sequence

Fields inherited from interface pal.alignment.Alignment

GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA

Constructor Summary

Constructors

Constructor and Description
AbstractAlignment()

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getAlignedSequenceString(int seq) Returns a string representing a single sequence (including gaps) from this alignment.
protected char	getChar(int state) Same as getDataType().getChar(state)
abstract char	getData(int seq, int site) sequence alignment at (sequence, site)
DataType	getDataType() Returns the datatype of this alignment
int	getIdCount() Returns the number of identifiers in this group
Identifier	getIdentifier(int i) Returns the ith identifier.
int	getLength() Return number of sites in this alignment
int	getSequenceCount() Return number of sequences in this alignment
int	getSiteCount() Return number of sites for each sequence in this alignment
protected int	getState(char c) Same as getDataType().getState(char)
int[][]	getStates() Fills a [numsequences][length] matrix with indices.
void	guessDataType() Guess data type
boolean	isGap(int seq, int site) returns true if there is a gap in the give position.
protected boolean	isUnknownState(int state) Same as getDataType().isUnknownState(state)
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)
void	setDataType(DataType d) Sets the datatype of this alignment
void	setIdentifier(int i, Identifier ident) Sets the ith identifier.
java.lang.String	toString() returns representation of this alignment as a string
int	whichIdNumber(java.lang.String name) returns the index of the identifier with the given name.

Methods inherited from class java.lang.Object

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

Field Detail

numSeqs

protected int numSeqs

number of sequences

numSites

protected int numSites

length of each sequence

idGroup

protected IdGroup idGroup

sequence identifiers

Constructor Detail

AbstractAlignment

public AbstractAlignment()

Method Detail

getData

public abstract char getData(int seq,
           int site)

sequence alignment at (sequence, site)

Specified by:

getData in interface Alignment

isGap

public boolean isGap(int seq,
            int site)

returns true if there is a gap in the give position.

guessDataType

public void guessDataType()

Guess data type

getChar

protected final char getChar(int state)

Same as getDataType().getChar(state)

getState

protected final int getState(char c)

Same as getDataType().getState(char)

isUnknownState

protected final boolean isUnknownState(int state)

Same as getDataType().isUnknownState(state)

getDataType

public final DataType getDataType()

Returns the datatype of this alignment

Specified by:

getDataType in interface Alignment

setDataType

public final void setDataType(DataType d)

Sets the datatype of this alignment

toString

public java.lang.String toString()

returns representation of this alignment as a string

Overrides:

toString in class java.lang.Object

report

public void report(java.io.PrintWriter out)

Description copied from interface: Report

print human readable report (e.g., on parameters and associated model)

Specified by:

report in interface Report

Parameters:

out - output stream

getStates

public int[][] getStates()

Fills a [numsequences][length] matrix with indices. Each index represents the sequence state, -1 means a gap.

getLength

public final int getLength()

Return number of sites in this alignment

getSequenceCount

public final int getSequenceCount()

Return number of sequences in this alignment

Specified by:

getSequenceCount in interface Alignment

getSiteCount

public final int getSiteCount()

Return number of sites for each sequence in this alignment

Specified by:

getSiteCount in interface Alignment

Returns:

number of sites for each sequence in this alignment

getAlignedSequenceString

public java.lang.String getAlignedSequenceString(int seq)

Returns a string representing a single sequence (including gaps) from this alignment.

Specified by:

getAlignedSequenceString in interface Alignment

getIdentifier

public Identifier getIdentifier(int i)

Description copied from interface: IdGroup

Returns the ith identifier.

Specified by:

getIdentifier in interface IdGroup

setIdentifier

public void setIdentifier(int i,
                 Identifier ident)

Description copied from interface: IdGroup

Sets the ith identifier.

Specified by:

setIdentifier in interface IdGroup

getIdCount

public int getIdCount()

Description copied from interface: IdGroup

Returns the number of identifiers in this group

Specified by:

getIdCount in interface IdGroup

whichIdNumber

public int whichIdNumber(java.lang.String name)

Description copied from interface: IdGroup

returns the index of the identifier with the given name.

Specified by:

whichIdNumber in interface IdGroup