pal.alignment
Class AbstractAlignment

java.lang.Object
  extended by pal.alignment.AbstractAlignment
All Implemented Interfaces:
java.io.Serializable, Alignment, IdGroup, Report
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

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
 
Field Summary
protected  IdGroup idGroup
          sequence identifiers
protected  int numSeqs
          number of sequences
protected  int numSites
          length of each sequence
 
Fields inherited from interface pal.alignment.Alignment
GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA
 
Constructor Summary
AbstractAlignment()
           
 
Method Summary
 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 alignment
 int getIdCount()
          Returns the number of identifiers in this group
 Identifier getIdentifier(int i)
          Returns the ith identifier.
 int getLength()
          Return number of sites in this alignment
 int getSequenceCount()
          Return number of sequences in this alignment
 int getSiteCount()
          Return number of sites for each sequence in this alignment
protected  int getState(char c)
          Same as getDataType().getState(char)
 int[][] getStates()
          Fills a [numsequences][length] matrix with indices.
 void guessDataType()
          Guess data type
 boolean 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 alignment
 void setIdentifier(int i, Identifier ident)
          Sets the ith identifier.
 java.lang.String toString()
          returns representation of this alignment as a string
 int whichIdNumber(java.lang.String name)
          returns the index of the identifier with the given name.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

numSeqs

protected int numSeqs
number of sequences


numSites

protected int numSites
length of each sequence


idGroup

protected IdGroup idGroup
sequence identifiers

Constructor Detail

AbstractAlignment

public AbstractAlignment()
Method Detail

getData

public abstract char getData(int seq,
                             int site)
sequence alignment at (sequence, site)

Specified by:
getData in interface Alignment

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

public final DataType getDataType()
Returns the datatype of this alignment

Specified by:
getDataType in interface Alignment

setDataType

public final void setDataType(DataType d)
Sets the datatype of this alignment


toString

public java.lang.String toString()
returns representation of this alignment as a string

Overrides:
toString in class java.lang.Object

report

public void report(java.io.PrintWriter out)
Description copied from interface: Report
print human readable report (e.g., on parameters and associated model)

Specified by:
report in interface Report
Parameters:
out - output stream

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 interface Alignment

getSiteCount

public final int getSiteCount()
Return number of sites for each sequence in this alignment

Specified by:
getSiteCount in interface Alignment
Returns:
number of sites for each sequence in this alignment

getAlignedSequenceString

public java.lang.String getAlignedSequenceString(int seq)
Returns a string representing a single sequence (including gaps) from this alignment.

Specified by:
getAlignedSequenceString in interface Alignment

getIdentifier

public Identifier getIdentifier(int i)
Description copied from interface: IdGroup
Returns the ith identifier.

Specified by:
getIdentifier in interface IdGroup

setIdentifier

public void setIdentifier(int i,
                          Identifier ident)
Description copied from interface: IdGroup
Sets the ith identifier.

Specified by:
setIdentifier in interface IdGroup

getIdCount

public int getIdCount()
Description copied from interface: IdGroup
Returns the number of identifiers in this group

Specified by:
getIdCount in interface IdGroup

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 interface IdGroup