/* * 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.dp; import org.biojava.bio.Annotation; import org.biojava.bio.BioError; import org.biojava.bio.dist.DistributionFactory; import org.biojava.bio.symbol.Alphabet; import org.biojava.bio.symbol.IllegalAlphabetException; import org.biojava.bio.symbol.IllegalSymbolException; import org.biojava.utils.ChangeVetoException; /** * @author Matthew Pocock * @author Lachlan Coin */ public class ProfileHMM extends SimpleMarkovModel { /** * The advance array. */ private final static int [] advance = { 1 }; /** * The number of columns in this model. */ private final int columns; /** * Match states array. *
* matchStates[0] == matchStates[columns+1] == magicalState(). */ private final EmissionState [] matchStates; /** * Insert states array. *
* From 0 .. columns(). */ private final EmissionState [] insertStates; /** * Delete states array. *
* From 0 .. columns()-1 corresponding to indexes 1..columns(). */ private final DotState [] deleteStates; /** * Retrieve the number of columns in the model. * * @return the number of columns */ public int columns() { return columns; } /** * Retrieve the match state at column indx. *
* The first match state is at index 1, and the last match state is at * column columns(). The states at index 0 and columns()+1 are both the * magical state. This is so that the whole model backbone can be addressed * without writing lots of special-case code. * * @param indx the index of the column to retrieve the match state for * @return the match state for column indx * @throws IndexOutOfBoundsException if indx is negative or above columns()+1 */ public EmissionState getMatch(int indx) throws IndexOutOfBoundsException { if(indx < 0 || indx > (columns+1) ) { throw new IndexOutOfBoundsException( "Match-state index must be within (0.." + (columns + 1) + "), not " + indx ); } return matchStates[indx]; } /** * Retrieves the insert state at column indx. *
* Insert_0 is the insert that is accessible directly from the magical state. * Insert_1..columns() are 'above' each propper match state. There is no * insert state above the magical state at the end of the model, as insert_columns * already models trailing inserts. * * @param indx the index of the column to retrieve the insert state for * @return the insert state for column indx * @throws IndexOutOfBoundsException if indx is negative or above columns() */ public EmissionState getInsert(int indx) throws IndexOutOfBoundsException { if(indx < 0 || indx > columns ) { throw new IndexOutOfBoundsException( "Insert-state index must be within (0.." + columns + "), not " + indx ); } return insertStates[indx]; } /** * Retrieves the delete state for column indx. *
* Delete states are 'above' the match state that they delete. There is no * delete state for the magical state at either the beginning or end of the * model, so the delete state indx can range within (1..columns()). * * @param indx the index of the column to retrieve the insert state for * @return the insert state for column indx * @throws IndexOutOfBoundsException if indx is negative or above columns() */ public DotState getDelete(int indx) throws IndexOutOfBoundsException { if(indx < 1 || indx > columns ) { throw new IndexOutOfBoundsException( "delete-state index must be within (1.." + columns + "), not " + indx ); } return deleteStates[indx-1]; } /** * @deprecated */ public ProfileHMM( Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory) throws IllegalSymbolException, IllegalTransitionException, IllegalAlphabetException { this(alpha, columns, matchFactory, insertFactory,""); } /** * Create a new ProfileHMM. *
* The profile will be over the Alphabet alpha. It will have 'columns' match states, * 'columns' delete states and 'columns'+1 insert states. The match states will be * created by matchFactory, and the insert states will be created by * insertFactory. This gives you great freedom for changing how the states are * implemented. For example, insertFactory may always return views onto a single * underlying probability distribution in which case all insert states will * emit the same type of stuff - or it may create an individual state for * each insert state, in which case each insert can be a different type of thing. * You could make the insert state a view onto your null model, or onto a * protein-specific distribution. * * @param alpha the Alphabet that the profile hmm will emit * @param columns the number of match states * @param matchFactory the StateFactory to use for creating the match states * @param insertFactory the stateFactory to use for creating the insert states */ public ProfileHMM( Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name) throws IllegalSymbolException, IllegalTransitionException, IllegalAlphabetException { super(1, alpha,name); try { this.columns = columns; this.matchStates = new EmissionState[columns+2]; this.insertStates = new EmissionState[columns+1]; this.deleteStates = new DotState[columns]; EmissionState mO = magicalState(); EmissionState iO = new SimpleEmissionState( "i-0", Annotation.EMPTY_ANNOTATION, advance, insertFactory.createDistribution(alpha) ); matchStates[0] = mO; insertStates[0] = iO; // first column - a leading insert & the magical state addState(iO); // 'body' columns for(int i = 1; i <= columns; i++) { EmissionState mN = new SimpleEmissionState( "m-" + i, Annotation.EMPTY_ANNOTATION, advance, matchFactory.createDistribution(alpha) ); EmissionState iN = new SimpleEmissionState( "i-" + i, Annotation.EMPTY_ANNOTATION, advance, insertFactory.createDistribution(alpha) ); DotState dN = new SimpleDotState("d-" + i); addState(mN); addState(iN); addState(dN); matchStates[i] = mN; insertStates[i] = iN; deleteStates[i-1] = dN; mO = mN; iO = iN; } matchStates[columns+1] = magicalState(); connectModel(); } catch (ChangeVetoException cve) { throw new BioError( "Unable to construct profile HMM", cve ); } } /** This is called by constructor in setting up the allowed transitions in the model */ protected void connectModel() throws ChangeVetoException, IllegalSymbolException, IllegalTransitionException,IllegalAlphabetException{ EmissionState mO = getMatch(0); EmissionState iO = getInsert(0); DotState dO = null; createTransition(mO,iO); createTransition(iO,iO); for(int i = 1; i <= columns(); i++){ EmissionState mN = getMatch(i); EmissionState iN = getInsert(i); DotState dN = getDelete(i); // from a model state createTransition(mO, mN); createTransition(mN, iN); createTransition(mO, dN); // from an insert state createTransition(iN, iN); createTransition(iO, mN); createTransition(iO, dN); // from a delete state if(i > 1) { createTransition(dO, dN); createTransition(dO, mN); } createTransition(dN,iN); mO = mN; iO = iN; dO = dN; } // for the transitions to end createTransition(mO, magicalState()); createTransition(iO, magicalState()); createTransition(dO, magicalState()); } }