pal.alignment
Interface Alignment

All Superinterfaces:

IdGroup, java.io.Serializable

All Known Subinterfaces:

AnnotationAlignment

All Known Implementing Classes:

AbstractAlignment, AlignmentReaders.PhylipClustalAlignment, AlignmentReaders.UnalignedAlignment, BootstrappedAlignment, ConcatenatedAlignment, ConcatenatedAnnotatedAlignment, GapBalancedAlignment, IndelAlignment, IndelAnnotatedAlignment, JumbledAlignment, MultiLocusAnnotatedAlignment, ReadAlignment, ReadAlignmentOld, SimpleAlignment, SimpleAnnotatedAlignment, SimulatedAlignment, SitePattern, StrippedAlignment, StrippedAnnotatedAlignment

public interface Alignment
extends java.io.Serializable, IdGroup

interface for any alignment data.

Version:

$Id: Alignment.java,v 1.15 2003/03/23 00:12:57 matt Exp $

Author:

Alexei Drummond, Korbinian Strimmer

Nested Class Summary

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

IdGroup.Utils

Field Summary

static char	GAP character used to designate gaps
static java.lang.String	GAP_TLA A three letter acronym version of a gap.
static java.lang.String	GAPS Characters that might be used as gaps
static char	UNKNOWN character used to designate unknown characters
static java.lang.String	UNKNOWN_TLA character used to designate unknown characters

Method Summary

java.lang.String	getAlignedSequenceString(int sequence) Returns string representation of single sequence in alignment with gap characters included.
char	getData(int seq, int site) sequence alignment at (sequence, site)
DataType	getDataType() Return DataType of this alignment.
int	getSequenceCount() Return number of sequences in this alignment
int	getSiteCount()

Methods inherited from interface pal.misc.IdGroup

getIdCount, getIdentifier, setIdentifier, whichIdNumber

Field Detail

GAP

static final char GAP

character used to designate gaps

See Also:

Constant Field Values

UNKNOWN

static final char UNKNOWN

character used to designate unknown characters

See Also:

Constant Field Values

UNKNOWN_TLA

static final java.lang.String UNKNOWN_TLA

character used to designate unknown characters

See Also:

Constant Field Values

GAP_TLA

static final java.lang.String GAP_TLA

A three letter acronym version of a gap.

See Also:

Constant Field Values

GAPS

static final java.lang.String GAPS

Characters that might be used as gaps

See Also:

Constant Field Values

Method Detail

getData

char getData(int seq,
             int site)

sequence alignment at (sequence, site)

getSiteCount

int getSiteCount()

Returns:

number of sites for each sequence in this alignment

getSequenceCount

int getSequenceCount()

Return number of sequences in this alignment

getDataType

DataType getDataType()

Return DataType of this alignment.

getAlignedSequenceString

java.lang.String getAlignedSequenceString(int sequence)

Returns string representation of single sequence in alignment with gap characters included.