/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojava.bio.dist; import java.util.Iterator; import org.biojava.bio.BioError; import org.biojava.bio.symbol.Alphabet; import org.biojava.bio.symbol.AtomicSymbol; import org.biojava.bio.symbol.FiniteAlphabet; import org.biojava.bio.symbol.IllegalAlphabetException; import org.biojava.bio.symbol.IllegalSymbolException; import org.biojava.bio.symbol.Symbol; import org.biojava.utils.AbstractChangeable; import org.biojava.utils.ChangeEvent; import org.biojava.utils.ChangeForwarder; import org.biojava.utils.ChangeSupport; import org.biojava.utils.ChangeType; import org.biojava.utils.ChangeVetoException; /** * An abstract implementation of Distribution. *
* You will need to override getWeight()
for a simple
* implementation. You may also wish to override the other methods if the
* default implementation is not suitable.
*
* The registerWithTrainer
method registers
* an IgnoreCountsTrainer
. To make an AbstractDistribution
* subclass trainable, this method must be overridden.
*
* Do not inform any listeners. This has already been done for you. Just * update state. *
* * @param sym the AtomicSymbol to update for * @param weight the new weight for that symbol * @throws IllegalSymbolException if the symbol is not known * @throws ChangeVetoException if the change is to be prevented */ abstract protected void setWeightImpl(AtomicSymbol sym, double weight) throws IllegalSymbolException, ChangeVetoException; /** * Set the weight of a given symbol in this distribution. ** This implementation informs all listeners of the change, and then calls * setWeightImpl to make the actual change. Sub-classes should over-ride * setWeightImpl to implement the actual storage of the weights. * * @param sym the Symbol to set the weight for * @param weight it's new weight * @throws IllegalSymbolException if sym is not known * @throws ChangeVetoException if the update was prevented */ final public void setWeight(Symbol sym, double weight) throws IllegalSymbolException, ChangeVetoException { if(!hasListeners()) { doSetWeight(sym, weight); } else { ChangeEvent ce = new ChangeEvent( this, Distribution.WEIGHTS, new Object[] {sym, new Double(weight)}, new Object[] {sym, new Double(getWeight(sym))} ); ChangeSupport changeSupport = super.getChangeSupport(Distribution.WEIGHTS); synchronized(changeSupport) { changeSupport.firePreChangeEvent(ce); doSetWeight(sym, weight); changeSupport.firePostChangeEvent(ce); } } } private void doSetWeight(Symbol sym, double weight) throws IllegalSymbolException, ChangeVetoException { if(sym instanceof AtomicSymbol) { setWeightImpl((AtomicSymbol) sym, weight); } else { //need to divide the weight up amongst the atomic symbols according //to the null model FiniteAlphabet fa = (FiniteAlphabet) sym.getMatches(); double totalNullWeight = this.getNullModel().getWeight(sym); for(Iterator si = fa.iterator(); si.hasNext(); ) { AtomicSymbol as = (AtomicSymbol) si.next(); double symNullWeight = this.getNullModel().getWeight(as); setWeightImpl(as, weight * symNullWeight / totalNullWeight); } } } /** * Implement this to set the null model. * *
* You should not inform any change listeners in this method. All of that * work has been done for you. *
* * @param nullModel the new null model Distribution * @throws IllegalAlphabetException if the null model is for the wrong alphabet * @throws ChangeVetoException if your implementation wishes to block this * opperation */ abstract protected void setNullModelImpl(Distribution nullModel) throws IllegalAlphabetException, ChangeVetoException; final public void setNullModel(Distribution nullModel) throws IllegalAlphabetException, ChangeVetoException { if(nullModel.getAlphabet() != getAlphabet()) { throw new IllegalAlphabetException( "Could not use distribution " + nullModel + " as its alphabet is " + nullModel.getAlphabet().getName() + " and this distribution's alphabet is " + getAlphabet().getName() ); } Distribution oldModel = getNullModel(); if(nullModelForwarder != null) { if(oldModel != null) { oldModel.removeChangeListener(nullModelForwarder); } nullModel.addChangeListener(nullModelForwarder); } if(!hasListeners()) { // if there are no listeners yet, don't go through the overhead of // synchronized regions or of trying to inform them. setNullModelImpl(nullModel); } else { // OK - so somebody is intereted in me. Do it properly this time. ChangeEvent ce = new ChangeEvent( this, Distribution.NULL_MODEL, nullModel, oldModel ); ChangeSupport changeSupport = super.getChangeSupport(Distribution.NULL_MODEL); synchronized(changeSupport) { changeSupport.firePreChangeEvent(ce); setNullModelImpl(nullModel); changeSupport.firePostChangeEvent(ce); } } } /** * Retrieve the weight for this distribution. ** Performs the standard munge to handle ambiguity symbols. The actual weights * for each atomic symbol should be calculated by the getWeightImpl * functions. * * @param sym the Symbol to find the probability of * @return the probability that one of the symbols matching amb was emitted * @throws IllegalSymbolException if for any reason the symbols within amb * are not recognized by this state */ public final double getWeight(Symbol sym) throws IllegalSymbolException { if(sym instanceof AtomicSymbol) { return getWeightImpl((AtomicSymbol) sym); } else { Alphabet ambA = sym.getMatches(); if(((FiniteAlphabet) ambA).size() == 0) { // a gap getAlphabet().validate(sym); double totalWeight = 0.0; for (Iterator i = ((FiniteAlphabet)getAlphabet()).iterator(); i.hasNext(); ) { Symbol s = (Symbol)i.next(); totalWeight += getWeight(s); } return 1.0 - totalWeight; } if(ambA instanceof FiniteAlphabet) { FiniteAlphabet fa = (FiniteAlphabet) ambA; double sum = 0.0; for(Iterator i = fa.iterator(); i.hasNext(); ) { Object obj = i.next(); if(!(obj instanceof AtomicSymbol)) { throw new BioError( "Assertion Failure: Not an instance of AtomicSymbol: " + obj ); } AtomicSymbol as = (AtomicSymbol) obj; sum += getWeightImpl(as); } return sum; } else { throw new IllegalSymbolException( "Can't find weight for infinite set of symbols matched by " + sym.getName() ); } } } /** * Override this method to implement getting the weight for an atomic * symbol. You should just do what is necessary to fetch state. All the work * with exceptions and listeners will have been handled for you. * * @param sym the AtomicSymbol to get the weight for * @return the weight * @throws IllegalSymbolException if sym is not known */ protected abstract double getWeightImpl(AtomicSymbol sym) throws IllegalSymbolException; public Symbol sampleSymbol() { double p = Math.random(); try { for(Iterator i = ((FiniteAlphabet) getAlphabet()).iterator(); i.hasNext(); ) { AtomicSymbol s = (AtomicSymbol) i.next(); p -= getWeight(s); if( p <= 0) { return s; } } return getAlphabet().getGapSymbol(); // StringBuffer sb = new StringBuffer(); // for(Iterator i = ((FiniteAlphabet) this.getAlphabet()).iterator(); i.hasNext(); ) { // AtomicSymbol s = (AtomicSymbol) i.next(); // double w = getWeight(s); // sb.append("\t" + s.getName() + " -> " + w + "\n"); // } // throw new BioError( // "Could not find a symbol to emit from alphabet " + getAlphabet() + // ". Do the probabilities sum to 1?" + "\np=" + p + "\n" + sb.substring(0) // ); } catch (IllegalSymbolException ire) { throw new BioError( "Unable to iterate over all symbols in alphabet - " + "things changed beneath me!", ire ); } } /** * Register an IgnoreCountsTrainer instance as the trainer for this * distribution. Override this if you wish to implement a trainable * distribution. * * @param dtc the context to register with */ public void registerWithTrainer(DistributionTrainerContext dtc) { dtc.registerTrainer(this, IgnoreCountsTrainer.getInstance()); } public int hashCode() { int hc = 0; try { for (Iterator i = ((FiniteAlphabet) getAlphabet()).iterator(); i.hasNext(); ) { Symbol s = (Symbol) i.next(); hc = hc ^ (int) (getWeight(s) * (1 << 30)); } } catch (IllegalSymbolException ex) { throw new BioError("Assertion failed", ex); } return hc; } public boolean equals(Object o) { if (o instanceof Distribution) { Distribution d = (Distribution) o; if (d.getAlphabet() != this.getAlphabet()) { return false; } try { for (Iterator i = ((FiniteAlphabet) getAlphabet()).iterator(); i.hasNext(); ) { Symbol s = (Symbol) i.next(); if (this.getWeight(s) != d.getWeight(s)) { return false; } } return true; } catch (IllegalSymbolException ex) { throw new BioError(ex); } } return false; } }