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java.lang.Object | +--pal.alignment.AbstractAlignment
abstract base class for any alignment data.
Field Summary | |
protected DataType |
dataType
data type |
protected double[] |
frequency
frequencies of the allowed states (scaled to sum to 1.0 and suitable for RateMatrix) |
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 |
Constructor Summary | |
AbstractAlignment()
|
Method Summary | |
java.lang.String |
getAlignedSequenceString(int seq)
Returns a string representing a single sequence (including gaps) from this alignment. |
abstract char |
getData(int seq,
int site)
sequence alignment at (sequence, site) |
DataType |
getDataType()
Returns the datatype of this alignment |
double[] |
getFrequency()
Returns frequency of character states. |
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 |
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. |
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 |
setFrequency(double[] f)
Sets frequency of character states. |
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 |
protected int numSeqs
protected int numSites
protected IdGroup idGroup
protected double[] frequency
protected DataType dataType
Constructor Detail |
public AbstractAlignment()
Method Detail |
public abstract char getData(int seq, int site)
getData
in interface Alignment
public boolean isGap(int seq, int site)
public void guessDataType()
public DataType getDataType()
getDataType
in interface Alignment
public void setDataType(DataType d)
setDataType
in interface Alignment
public java.lang.String toString()
toString
in class java.lang.Object
public void report(java.io.PrintWriter out)
Report
report
in interface Report
pal.misc.Report
out
- output streampublic int[][] getStates()
public final int getLength()
public final int getSequenceCount()
getSequenceCount
in interface Alignment
public final int getSiteCount()
getSiteCount
in interface Alignment
pal.alignment.Alignment
public java.lang.String getAlignedSequenceString(int seq)
getAlignedSequenceString
in interface Alignment
public Identifier getIdentifier(int i)
IdGroup
getIdentifier
in interface IdGroup
public void setIdentifier(int i, Identifier ident)
IdGroup
setIdentifier
in interface IdGroup
public int getIdCount()
IdGroup
getIdCount
in interface IdGroup
public int whichIdNumber(java.lang.String name)
IdGroup
whichIdNumber
in interface IdGroup
public double[] getFrequency()
Alignment
getFrequency
in interface Alignment
public void setFrequency(double[] f)
Alignment
setFrequency
in interface Alignment
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