/*
* ResamplePatterns.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evolution.alignment;
import dr.evolution.datatype.AminoAcids;
import dr.evolution.datatype.Codons;
import dr.evolution.datatype.DataType;
import dr.evolution.datatype.Nucleotides;
import dr.evolution.util.Taxon;
import java.util.*;
/**
* Provides an abstract base class for resampling patterns (i.e. bootstrap and jackknife).
*
* @version $Id: ResamplePatterns.java,v 1.12 2005/05/24 20:25:55 rambaut Exp $
*
* @author Andrew Rambaut
*/
public abstract class ResamplePatterns implements PatternList, dr.util.XHTMLable
{
/** the source patterns */
protected SiteList patterns = null;
/** number of site patterns */
protected int patternCount = 0;
/** weights of each site pattern */
protected double[] weights;
/** bootstrapped pattern -> source pattern */
protected int[] patternIndices;
/**
* Sets the source of patterns
*/
public void setPatterns(SiteList patterns) {
this.patterns = patterns;
}
/**
* Perform a resampling of the patterns
*/
public abstract void resamplePatterns();
// **************************************************************
// PatternList IMPLEMENTATION
// **************************************************************
/**
* @return number of patterns
*/
public int getPatternCount() {
return patternCount;
}
/**
* @return number of states for this siteList
*/
public int getStateCount() {
if (patterns == null) throw new RuntimeException("ResamplePatterns has no source patterns");
return patterns.getStateCount();
}
/**
* Gets the length of the pattern strings which will usually be the
* same as the number of taxa
* @return the length of patterns
*/
public int getPatternLength() {
if (patterns == null) throw new RuntimeException("ResamplePatterns has no source patterns");
return patterns.getPatternLength();
}
/**
* Gets the pattern as an array of state numbers (one per sequence)
* @return the pattern at patternIndex
*/
public int[] getPattern(int patternIndex) {
if (patterns == null) throw new RuntimeException("ResamplePatterns has no source patterns");
return patterns.getPattern(patternIndices[patternIndex]);
}
/**
* @return state at (taxonIndex, patternIndex)
*/
public int getPatternState(int taxonIndex, int patternIndex) {
return getPattern(patternIndex)[taxonIndex];
}
/**
* Gets the weight of a site pattern
*/
public double getPatternWeight(int patternIndex) {
return weights[patternIndex];
}
/**
* @return the array of pattern weights
*/
public double[] getPatternWeights() {
return weights;
}
/**
* @return the DataType of this siteList
*/
public DataType getDataType() {
if (patterns == null) throw new RuntimeException("ResamplePatterns has no source patterns");
return patterns.getDataType();
}
/**
* @return the frequency of each state
*/
public double[] getStateFrequencies() {
return PatternList.Utils.empiricalStateFrequencies(this);
}
@Override
public boolean areUnique() {
return patterns.areUnique();
}
// **************************************************************
// TaxonList IMPLEMENTATION
// **************************************************************
/**
* @return a count of the number of taxa in the list.
*/
public int getTaxonCount() {
if (patterns == null) throw new RuntimeException("ResamplePatterns has no source patterns");
return patterns.getTaxonCount();
}
/**
* @return the ith taxon.
*/
public Taxon getTaxon(int taxonIndex) {
if (patterns == null) throw new RuntimeException("ResamplePatterns has no source patterns");
return patterns.getTaxon(taxonIndex);
}
/**
* @return the ID of the ith taxon.
*/
public String getTaxonId(int taxonIndex) {
if (patterns == null) throw new RuntimeException("ResamplePatterns has no source patterns");
return patterns.getTaxonId(taxonIndex);
}
/**
* returns the index of the taxon with the given id.
*/
public int getTaxonIndex(String id) {
if (patterns == null) throw new RuntimeException("ResamplePatterns has no source patterns");
return patterns.getTaxonIndex(id);
}
/**
* returns the index of the given taxon.
*/
public int getTaxonIndex(Taxon taxon) {
if (patterns == null) throw new RuntimeException("SitePatterns has no alignment");
return patterns.getTaxonIndex(taxon);
}
/**
* @return an object representing the named attributed for the given taxon.
* @param taxonIndex the index of the taxon whose attribute is being fetched.
* @param name the name of the attribute of interest.
*/
public Object getTaxonAttribute(int taxonIndex, String name) {
if (patterns == null) throw new RuntimeException("ResamplePatterns has no source patterns");
return patterns.getTaxonAttribute(taxonIndex, name);
}
public List<Taxon> asList() {
List<Taxon> taxa = new ArrayList<Taxon>();
for (int i = 0, n = getTaxonCount(); i < n; i++) {
taxa.add(getTaxon(i));
}
return taxa;
}
public Iterator<Taxon> iterator() {
return new Iterator<Taxon>() {
private int index = -1;
public boolean hasNext() {
return index < getTaxonCount() - 1;
}
public Taxon next() {
index ++;
return getTaxon(index);
}
public void remove() { /* do nothing */ }
};
}
// **************************************************************
// Identifiable IMPLEMENTATION
// **************************************************************
protected String id = null;
/**
* @return the id.
*/
public String getId() {
return id;
}
/**
* Sets the id.
*/
public void setId(String id) {
this.id = id;
}
// **************************************************************
// XHTMLable IMPLEMENTATION
// **************************************************************
public String toXHTML() {
String xhtml = "<p><em>Jackknife Pattern List</em> pattern count = ";
xhtml += getPatternCount();
xhtml += "</p>";
xhtml += "<pre>";
int count, state;
int type = getDataType().getType();
count = getPatternCount();
int length, maxLength = 0;
for (int i = 0; i < count; i++) {
length = Integer.toString((int)getPatternWeight(i)).length();
if (length > maxLength)
maxLength = length;
}
for (int i = 0; i < count; i++) {
length = Integer.toString(i+1).length();
for (int j = length; j < maxLength; j++)
xhtml += " ";
xhtml += Integer.toString(i+1) + ": ";
length = Integer.toString((int)getPatternWeight(i)).length();
xhtml += Integer.toString((int)getPatternWeight(i));
for (int j = length; j <= maxLength; j++)
xhtml += " ";
for (int j = 0; j < getTaxonCount(); j++) {
state = getPatternState(j, i);
if (type == DataType.NUCLEOTIDES) {
xhtml += Nucleotides.INSTANCE.getChar(state) + " ";
} else if (type == DataType.CODONS) {
xhtml += Codons.UNIVERSAL.getTriplet(state) + " ";
} else {
xhtml += AminoAcids.INSTANCE.getChar(state) + " ";
}
}
xhtml += "\n";
}
xhtml += "</pre>";
return xhtml;
}
}