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.