Package pal.alignment
Class AbstractAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- Direct Known Subclasses:
BootstrappedAlignment
,ConcatenatedAlignment
,ConcatenatedAnnotatedAlignment
,GapBalancedAlignment
,IndelAlignment
,JumbledAlignment
,ReadAlignment
,ReadAlignmentOld
,SimpleAlignment
,SimulatedAlignment
,SitePattern
,StrippedAlignment
public abstract class AbstractAlignment extends java.lang.Object implements Alignment, java.io.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:
- Serialized Form
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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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Constructor Summary
Constructors Constructor Description AbstractAlignment()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description java.lang.String
getAlignedSequenceString(int seq)
Returns a string representing a single sequence (including gaps) from this alignment.protected char
getChar(int state)
Same as getDataType().getChar(state)abstract char
getData(int seq, int site)
sequence alignment at (sequence, site)DataType
getDataType()
Returns the datatype of this alignmentint
getIdCount()
Returns the number of identifiers in this groupIdentifier
getIdentifier(int i)
Returns the ith identifier.int
getLength()
Return number of sites in this alignmentint
getSequenceCount()
Return number of sequences in this alignmentint
getSiteCount()
Return number of sites for each sequence in this alignmentprotected int
getState(char c)
Same as getDataType().getState(char)int[][]
getStates()
Fills a [numsequences][length] matrix with indices.void
guessDataType()
Guess data typeboolean
isGap(int seq, int site)
returns true if there is a gap in the give position.protected boolean
isUnknownState(int state)
Same as getDataType().isUnknownState(state)void
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model)void
setDataType(DataType d)
Sets the datatype of this alignmentvoid
setIdentifier(int i, Identifier ident)
Sets the ith identifier.java.lang.String
toString()
returns representation of this alignment as a stringint
whichIdNumber(java.lang.String name)
returns the index of the identifier with the given name.
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Field Detail
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numSeqs
protected int numSeqs
number of sequences
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numSites
protected int numSites
length of each sequence
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idGroup
protected IdGroup idGroup
sequence identifiers
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Method Detail
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getData
public abstract char getData(int seq, int site)
sequence alignment at (sequence, site)
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isGap
public boolean isGap(int seq, int site)
returns true if there is a gap in the give position.
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guessDataType
public void guessDataType()
Guess data type
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getChar
protected final char getChar(int state)
Same as getDataType().getChar(state)
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getState
protected final int getState(char c)
Same as getDataType().getState(char)
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isUnknownState
protected final boolean isUnknownState(int state)
Same as getDataType().isUnknownState(state)
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getDataType
public final DataType getDataType()
Returns the datatype of this alignment- Specified by:
getDataType
in interfaceAlignment
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setDataType
public final void setDataType(DataType d)
Sets the datatype of this alignment
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toString
public java.lang.String toString()
returns representation of this alignment as a string- Overrides:
toString
in classjava.lang.Object
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report
public void report(java.io.PrintWriter out)
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)
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getStates
public int[][] getStates()
Fills a [numsequences][length] matrix with indices. Each index represents the sequence state, -1 means a gap.
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getLength
public final int getLength()
Return number of sites in this alignment
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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
public java.lang.String getAlignedSequenceString(int seq)
Returns a string representing a single sequence (including gaps) from this alignment.- Specified by:
getAlignedSequenceString
in interfaceAlignment
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getIdentifier
public Identifier getIdentifier(int i)
Description copied from interface:IdGroup
Returns the ith identifier.- Specified by:
getIdentifier
in interfaceIdGroup
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setIdentifier
public void setIdentifier(int i, Identifier ident)
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
public int whichIdNumber(java.lang.String name)
Description copied from interface:IdGroup
returns the index of the identifier with the given name.- Specified by:
whichIdNumber
in interfaceIdGroup
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