Package pal.alignment
Interface Alignment
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
Fields Modifier and Type Field Description static char
GAP
character used to designate gapsstatic java.lang.String
GAP_TLA
A three letter acronym version of a gap.static java.lang.String
GAPS
Characters that might be used as gapsstatic char
UNKNOWN
character used to designate unknown charactersstatic java.lang.String
UNKNOWN_TLA
character used to designate unknown characters
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description 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 alignmentint
getSiteCount()
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Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Field Detail
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GAP
static final char GAP
character used to designate gaps- See Also:
- Constant Field Values
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UNKNOWN
static final char UNKNOWN
character used to designate unknown characters- See Also:
- Constant Field Values
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UNKNOWN_TLA
static final java.lang.String UNKNOWN_TLA
character used to designate unknown characters- See Also:
- Constant Field Values
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GAP_TLA
static final java.lang.String GAP_TLA
A three letter acronym version of a gap.- See Also:
- Constant Field Values
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GAPS
static final java.lang.String GAPS
Characters that might be used as gaps- See Also:
- Constant Field Values
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Method Detail
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getData
char getData(int seq, int site)
sequence alignment at (sequence, site)
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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
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getDataType
DataType getDataType()
Return DataType of this alignment.
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getAlignedSequenceString
java.lang.String getAlignedSequenceString(int sequence)
Returns string representation of single sequence in alignment with gap characters included.
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