This code is my fault, and I haven't looked at the nested model support in a couple of years. Hopefully we will get time to look at it over the weekend.
Matthew
ps I'm writing a CpG finder using the lib today, so at least I have the right javadocs open.
Russell Smithies wrote:
I'm trying to create a reasonably complex markov model so have split it into bits to make it a little easier to handle.
I'm then trying to re-assemble the bits into another model by creating SimpleModelInState's from the sub-models.
The problem is that I keep getting errors and not sure why.
heres some code I did as a test, the top portion creates a sub-model (which compiles correctly) but when I try to add them to create the DP for, I get null pointer errors and was getting errors about null back pointers?
heres some testy code :
(sorry if HotMail munges it) :-)
import java.util.*;
import org.biojava.bio.*;
import org.biojava.bio.dist.*;
import org.biojava.bio.dp.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
public class modelInStateTest {
public static void main(String[] args) throws Exception {
// sequence to test
SymbolList sl = DNATools.createDNA("actgatcgactgtacgatgagatgcgactga"+
"tcgactgactgctgcgtatcgatcgatcgatgactgacg");
int[] advance = { 1 };
//create order n alphabet
Alphabet orderNAlpha = AlphabetManager.getCrossProductAlphabet(
Collections.nCopies(3, DNATools.getDNA()));
//create uniform distribution for emission states
Distribution uni_dist = new UniformDistribution(DNATools.getDNA());
// create simple markov model
SimpleMarkovModel mm = new SimpleMarkovModel(1, DNATools.getDNA(), "mm");
//create emission states
EmissionState es1 = new SimpleEmissionState("1_es", Annotation.EMPTY_ANNOTATION, advance, uni_dist);
EmissionState es2 = new SimpleEmissionState("2_es", Annotation.EMPTY_ANNOTATION, advance, uni_dist);
// add states to model
mm.addState(es1);
mm.addState(es2);
// create transitions between all states
mm.createTransition(mm.magicalState(), es1);
mm.createTransition(mm.magicalState(), es2);
mm.createTransition(es1, es1);
mm.createTransition(es1, es2);
mm.createTransition(es2, es2);
mm.createTransition(es2, es1);
mm.createTransition(es2, mm.magicalState());
mm.createTransition(es1, mm.magicalState());
//set weights on transitions
mm.setWeights(mm.magicalState(), new UniformDistribution(mm.transitionsFrom(mm.magicalState())));
mm.setWeights(es1, new UniformDistribution(mm.transitionsFrom(es1)));
mm.setWeights(es2, new UniformDistribution(mm.transitionsFrom(es2)));
sl = SymbolListViews.orderNSymbolList(sl, 3);
SymbolList[] sla = { sl };
// create the dynamic programming object
DP dp = DPFactory.DEFAULT.createDP(mm);
//create statepath
StatePath sp = dp.viterbi(sla, ScoreType.PROBABILITY);
///////// TRY TO CREATE SUB MODELS AND INTEGRATE THEM ///////////////////////////
SimpleMarkovModel mm2 = new SimpleMarkovModel(1, DNATools.getDNA(), "2_mm");
//create states
SimpleModelInState smis1 = new SimpleModelInState(mm, "1_smis");
SimpleModelInState smis2 = new SimpleModelInState(mm, "2_smis");
mm2.addState(smis1);
mm2.addState(smis2);
// create transitions between all states
mm2.createTransition(mm2.magicalState(), smis1);
mm2.createTransition(mm2.magicalState(), smis2);
mm2.createTransition(smis1, smis1);
mm2.createTransition(smis1, smis2);
mm2.createTransition(smis2, smis2);
mm2.createTransition(smis2, smis1);
mm2.createTransition(smis2, mm2.magicalState());
mm2.createTransition(smis1, mm2.magicalState());
//set weights on transitions
mm2.setWeights(mm2.magicalState(), new UniformDistribution(mm2.transitionsFrom(mm2.magicalState())));
mm2.setWeights(smis1, new UniformDistribution(mm2.transitionsFrom(smis1)));
mm2.setWeights(smis2, new UniformDistribution(mm2.transitionsFrom(smis2)));
// create the dynamic programming object
DP dp2 = DPFactory.DEFAULT.createDP(mm2); //<<<<-----------------
//create statepath
StatePath sp2 = dp2.viterbi(sla, ScoreType.PROBABILITY);
/*
java.lang.NullPointerException
at org.biojava.bio.dp.FlatModel.<init>(FlatModel.java:229)
at org.biojava.bio.dp.DP.flatView(DP.java:96)
at org.biojava.bio.dp.DPFactory$DefaultFactory.createDP(DPFactory.java:51)
at markov.modelInStateTest.main(modelInStateTest.java:89)
Exception in thread "main"
*/
}
}
_________________________________________________________________
The new MSN 8: advanced junk mail protection and 2 months FREE* http://join.msn.com/?page=features/junkmail
_______________________________________________
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
-- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk
__________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
