Hi,
I want to put a two-headed markov model in a SimpleModelInState.
But when I attempt to call DPFactory.DEFAULT.createDP, I get a
NullPointerException from inside the org.biojava.bio.dp.FlatModel
constructor.
I get the same problem from the biojava-1.30-jdk13.jar,
biojava-1.30-jdk14.jar, and biojava-1.3.1.jar distributions.
Also, I turned up a similar thread in Dec. 2002 biojava-l archive
entitled "SimpleModelInState Problem?". Matthew Pocock responded to the
query saying he was about to work on the issue, but there is no
followup.
My questions: Is this a real bug? If so, should I expect this API
(ModelInState for two-headed models) to be supported in the near future,
or should I simply build a flat model?
The stack trace, possible problem biojava code, and snippets of my test
code are below.
Thanks very much for any help.
Doug
Here is the stack trace:
------------------------
Exception in thread "main" java.lang.NullPointerException
at org.biojava.bio.dp.FlatModel.<init>(FlatModel.java:251)
at org.biojava.bio.dp.DP.flatView(DP.java:168)
at
org.biojava.bio.dp.DPFactory$DefaultFactory.createDP(DPFactory.java:52)
at ltr.ModelInStateExample.main(ModelInStateExample.java:124)
rethrown as org.biojava.utils.NestedError: Can't align.
at ltr.ModelInStateExample.main(ModelInStateExample.java:133)
The NPE seems to be coming from the following FlatModel code:
-------------------------------------------------------------
//
// FIXME -- [SOMEONE (ed.)] broked this...
//
TranslatedDistribution dist = null;
// TranslatedDistribution dist TranslatedDistribution.getDistribution(
// delegate.transitionsFrom(s),
// sModel.getWeights(sOrig)
// );
SimpleReversibleTranslationTable table =
(SimpleReversibleTranslationTable) dist.getTable();
Here is the model creation code:
--------------------------------
...
FiniteAlphabet singleAlphabet = DNATools.getDNA();
FiniteAlphabet doubleAlphabet =
( FiniteAlphabet ) AlphabetManager.getCrossProductAlphabet(
Collections.nCopies( 2, singleAlphabet ) );
State matchState = new SimpleEmissionState(
"match",
Annotation.EMPTY_ANNOTATION,
new int[] { 1, 1 },
new UniformDistribution( doubleAlphabet )
);
State insertState = new SimpleEmissionState(
"insert",
Annotation.EMPTY_ANNOTATION,
new int[] { 0, 1 },
new PairDistribution(
new GapDistribution( singleAlphabet ),
new UniformDistribution( singleAlphabet )
) );
State deleteState = new SimpleEmissionState(
"delete",
Annotation.EMPTY_ANNOTATION,
new int[] { 1, 0 },
new PairDistribution(
new UniformDistribution( singleAlphabet ),
new GapDistribution( singleAlphabet )
) );
SimpleMarkovModel innerModel =
new SimpleMarkovModel( 2, doubleAlphabet, "inner");
innerModel.addState( matchState );
innerModel.addState( insertState );
innerModel.addState( deleteState );
innerModel.createTransition( innerModel.magicalState(), matchState );
innerModel.createTransition( matchState, insertState );
innerModel.createTransition( matchState, deleteState );
innerModel.createTransition( matchState, matchState );
innerModel.createTransition( matchState, innerModel.magicalState() );
innerModel.createTransition( insertState, matchState );
innerModel.createTransition( insertState, insertState );
innerModel.createTransition( deleteState, matchState );
innerModel.createTransition( deleteState, deleteState );
double d = 0.1;
double e = 0.1;
double t = 0.1;
innerModel.getWeights( innerModel.magicalState() )
.setWeight( matchState, 1.0 );
Distribution fromMatch = innerModel.getWeights( matchState );
fromMatch.setWeight( insertState, d );
fromMatch.setWeight( deleteState, d );
fromMatch.setWeight( matchState, 1-2*d-t );
fromMatch.setWeight( innerModel.magicalState(), t );
Distribution fromInsert = innerModel.getWeights( insertState );
fromInsert.setWeight( matchState, 1-e );
fromInsert.setWeight( insertState, e );
Distribution fromDelete = innerModel.getWeights( deleteState );
fromDelete.setWeight( matchState, 1-e );
fromDelete.setWeight( deleteState, e );
State innerModelInState =
new SimpleModelInState( innerModel, "modelInState" );
SimpleMarkovModel outerModel =
new SimpleMarkovModel( 2, doubleAlphabet, "outer" );
outerModel.addState( innerModelInState );
outerModel.createTransition(
outerModel.magicalState(), innerModelInState );
outerModel.createTransition(
innerModelInState, outerModel.magicalState() );
outerModel.getWeights( outerModel.magicalState() )
.setWeight( innerModelInState, 1.0 );
outerModel.getWeights( innerModelInState )
.setWeight( outerModel.magicalState(), 1.0 );
...
DPFactory.DEFAULT.createDP( outerModel ); <==================== NPE
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