/*
* SimpleSiteList.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.*;
import dr.evolution.util.Taxon;
import dr.evolution.util.TaxonList;
import java.util.List;
import java.util.Iterator;
/**
* Stores a set of site patterns. This is setup by loading site patterns using the
* addPattern method. It is assumed they are added in order.
*
* @author Andrew Rambaut
* @author Alexei Drummond
*
* @version $Id: SimpleSiteList.java,v 1.1 2005/06/23 13:53:41 rambaut Exp $
*/
public class SimpleSiteList implements SiteList {
private final TaxonList taxonList;
private final DataType dataType;
private int siteCount = 0;
private int[][] sitePatterns = new int[0][];
public SimpleSiteList(DataType dataType) {
this.taxonList = null;
this.dataType = dataType;
}
public SimpleSiteList(DataType dataType, TaxonList taxonList) {
this.taxonList = taxonList;
this.dataType = dataType;
}
public int addPattern(int[] pattern) {
int capacity = sitePatterns.length;
if (siteCount >= capacity) {
capacity += 10000;
int[][] newSitePatterns = new int[capacity][];
for (int i = 0; i < siteCount; i++) {
newSitePatterns[i] = sitePatterns[i];
}
sitePatterns = newSitePatterns;
}
sitePatterns[siteCount] = pattern;
siteCount++;
return siteCount - 1;
}
// **************************************************************
// SiteList IMPLEMENTATION
// **************************************************************
/**
* @return number of sites
*/
public int getSiteCount() {
return siteCount;
}
/**
* Gets the pattern of site as an array of state numbers (one per sequence)
* @return the site pattern at siteIndex
*/
public int[] getSitePattern(int siteIndex) {
return sitePatterns[siteIndex];
}
/**
* Gets the pattern index at a particular site
* @return the patternIndex
*/
public int getPatternIndex(int siteIndex) {
return siteIndex;
}
/**
* @return the sequence state at (taxon, site)
*/
public int getState(int taxonIndex, int siteIndex) {
return getSitePattern(siteIndex)[taxonIndex];
}
// **************************************************************
// PatternList IMPLEMENTATION
// **************************************************************
/**
* @return number of patterns
*/
public int getPatternCount() {
return getSiteCount();
}
/**
* @return number of states for this siteList
*/
public int getStateCount() {
return dataType.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() {
return getTaxonCount();
}
/**
* Gets the pattern as an array of state numbers (one per sequence)
* @return the pattern at patternIndex
*/
public int[] getPattern(int patternIndex) {
return getSitePattern(patternIndex);
}
/**
* @return state at (taxonIndex, patternIndex)
*/
public int getPatternState(int taxonIndex, int patternIndex) {
return getSitePattern(patternIndex)[taxonIndex];
}
/**
* Gets the weight of a site pattern
*/
public double getPatternWeight(int patternIndex) {
return 1.0;
}
/**
* @return the array of pattern weights
*/
public double[] getPatternWeights() {
double[] weights = new double[getSiteCount()];
for (int i = 0; i < getSiteCount(); i++) {
weights[i] = 1.0;
}
return weights;
}
/**
* @return the DataType of this siteList
*/
public DataType getDataType() {
return dataType;
}
/**
* @return the frequency of each state
*/
public double[] getStateFrequencies() {
return Utils.empiricalStateFrequencies(this);
}
@Override
public boolean areUnique() {
return false;
}
// **************************************************************
// TaxonList IMPLEMENTATION
// **************************************************************
/**
* @return a count of the number of taxa in the list.
*/
public int getTaxonCount() {
if (taxonList == null) throw new RuntimeException("SimpleSiteList has no taxonList");
return taxonList.getTaxonCount();
}
/**
* @return the ith taxon.
*/
public Taxon getTaxon(int taxonIndex) {
if (taxonList == null) throw new RuntimeException("SimpleSiteList has no taxonList");
return taxonList.getTaxon(taxonIndex);
}
/**
* @return the ID of the ith taxon.
*/
public String getTaxonId(int taxonIndex) {
if (taxonList == null) throw new RuntimeException("SimpleSiteList has no taxonList");
return taxonList.getTaxonId(taxonIndex);
}
/**
* returns the index of the taxon with the given id.
*/
public int getTaxonIndex(String id) {
if (taxonList == null) throw new RuntimeException("SimpleSiteList has no taxonList");
return taxonList.getTaxonIndex(id);
}
/**
* returns the index of the given taxon.
*/
public int getTaxonIndex(Taxon taxon) {
if (taxonList == null) throw new RuntimeException("SimpleSiteList has no taxonList");
return taxonList.getTaxonIndex(taxon);
}
public List<Taxon> asList() {
if (taxonList == null) throw new RuntimeException("SimpleSiteList has no taxonList");
return taxonList.asList();
}
public Iterator<Taxon> iterator() {
if (taxonList == null) throw new RuntimeException("SimpleSiteList has no taxonList");
return taxonList.iterator();
}
/**
* @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 (taxonList == null) throw new RuntimeException("SimpleSiteList has no taxonList");
return taxonList.getTaxonAttribute(taxonIndex, name);
}
// **************************************************************
// 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;
}
}