Package pal.alignment
Interface Alignment
- All Superinterfaces:
IdGroup
,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
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
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final char
character used to designate gapsstatic final String
A three letter acronym version of a gap.static final String
Characters that might be used as gapsstatic final char
character used to designate unknown charactersstatic final String
character used to designate unknown characters -
Method Summary
Modifier and TypeMethodDescriptiongetAlignedSequenceString
(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)Return DataType of this alignment.int
Return number of sequences in this alignmentint
Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Field Details
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GAP
static final char GAPcharacter used to designate gaps- See Also:
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UNKNOWN
static final char UNKNOWNcharacter used to designate unknown characters- See Also:
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UNKNOWN_TLA
character used to designate unknown characters- See Also:
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GAP_TLA
A three letter acronym version of a gap.- See Also:
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GAPS
Characters that might be used as gaps- See Also:
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Method Details
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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
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getSequenceCount
int getSequenceCount()Return number of sequences in this alignment -
getDataType
DataType getDataType()Return DataType of this alignment. -
getAlignedSequenceString
Returns string representation of single sequence in alignment with gap characters included.
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