Package pal.alignment
Class AbstractAlignment
java.lang.Object
pal.alignment.AbstractAlignment
- All Implemented Interfaces:
Serializable
,Alignment
,IdGroup
,Report
- Direct Known Subclasses:
BootstrappedAlignment
,ConcatenatedAlignment
,ConcatenatedAnnotatedAlignment
,GapBalancedAlignment
,IndelAlignment
,JumbledAlignment
,ReadAlignment
,ReadAlignmentOld
,SimpleAlignment
,SimulatedAlignment
,SitePattern
,StrippedAlignment
public abstract class AbstractAlignment
extends Object
implements Alignment, 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:
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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 TypeFieldDescriptionprotected IdGroup
sequence identifiersprotected int
number of sequencesprotected int
length of each sequence -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetAlignedSequenceString
(int seq) Returns a string representing a single sequence (including gaps) from this alignment.protected final char
getChar
(int state) Same as getDataType().getChar(state)abstract char
getData
(int seq, int site) sequence alignment at (sequence, site)final DataType
Returns the datatype of this alignmentint
Returns the number of identifiers in this groupgetIdentifier
(int i) Returns the ith identifier.final int
Return number of sites in this alignmentfinal int
Return number of sequences in this alignmentfinal int
Return number of sites for each sequence in this alignmentprotected final int
getState
(char c) Same as getDataType().getState(char)int[][]
Fills a [numsequences][length] matrix with indices.void
Guess data typeboolean
isGap
(int seq, int site) returns true if there is a gap in the give position.protected final boolean
isUnknownState
(int state) Same as getDataType().isUnknownState(state)void
report
(PrintWriter out) print human readable report (e.g., on parameters and associated model)final void
Sets the datatype of this alignmentvoid
setIdentifier
(int i, Identifier ident) Sets the ith identifier.toString()
returns representation of this alignment as a stringint
whichIdNumber
(String name) returns the index of the identifier with the given name.
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Field Details
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numSeqs
protected int numSeqsnumber of sequences -
numSites
protected int numSiteslength of each sequence -
idGroup
sequence identifiers
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Constructor Details
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AbstractAlignment
public AbstractAlignment()
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Method Details
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getData
public abstract char getData(int seq, int site) sequence alignment at (sequence, site) -
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
Returns the datatype of this alignment- Specified by:
getDataType
in interfaceAlignment
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setDataType
Sets the datatype of this alignment -
toString
returns representation of this alignment as a string -
report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model) -
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 interfaceAlignment
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getSiteCount
public final int getSiteCount()Return number of sites for each sequence in this alignment- Specified by:
getSiteCount
in interfaceAlignment
- Returns:
- number of sites for each sequence in this alignment
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getAlignedSequenceString
Returns a string representing a single sequence (including gaps) from this alignment.- Specified by:
getAlignedSequenceString
in interfaceAlignment
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getIdentifier
Description copied from interface:IdGroup
Returns the ith identifier.- Specified by:
getIdentifier
in interfaceIdGroup
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setIdentifier
Description copied from interface:IdGroup
Sets the ith identifier.- Specified by:
setIdentifier
in interfaceIdGroup
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getIdCount
public int getIdCount()Description copied from interface:IdGroup
Returns the number of identifiers in this group- Specified by:
getIdCount
in interfaceIdGroup
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whichIdNumber
Description copied from interface:IdGroup
returns the index of the identifier with the given name.- Specified by:
whichIdNumber
in interfaceIdGroup
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