org.biojava.bio.program.hmmer
Class HmmerProfileHMM

java.lang.Object
  extended byorg.biojava.utils.AbstractChangeable
      extended byorg.biojava.bio.dp.SimpleMarkovModel
          extended byorg.biojava.bio.dp.ProfileHMM
              extended byorg.biojava.bio.program.hmmer.HmmerProfileHMM
All Implemented Interfaces:
Changeable, MarkovModel, java.io.Serializable

public class HmmerProfileHMM
extends ProfileHMM

This is a class for representing HMMER generated Profile HMM. It differs from the normal ProfileHMM only in the states which are connected: - there are no insert <-> delete transitions allowed - there is no iO initial insert state (between begin and initial match states) - there is not iN final insert state (between final match state and end state)

Author:
Lachlan Coin
See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.dp.MarkovModel
MarkovModel.DistributionForwarder
 
Field Summary
 
Fields inherited from class org.biojava.bio.dp.SimpleMarkovModel
serialVersionUID
 
Fields inherited from interface org.biojava.bio.dp.MarkovModel
ARCHITECTURE, PARAMETER
 
Constructor Summary
protected HmmerProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, java.lang.String name)
           
 
Method Summary
protected  void connectModel()
          This is called by constructor in setting up the allowed transitions in the model
protected static double log2(double x)
           
protected  EmissionState makeNewInsertState(java.lang.String str, Annotation ann, int[] adv, Distribution dis)
           
protected  EmissionState makeNewMatchState(java.lang.String str, Annotation ann, int[] adv, Distribution dis)
           
 double transScore(State from, State to, Symbol symFrom, Symbol symTo)
           
 
Methods inherited from class org.biojava.bio.dp.ProfileHMM
columns, getDelete, getInsert, getMatch
 
Methods inherited from class org.biojava.bio.dp.SimpleMarkovModel
addState, containsTransition, createTransition, destroyTransition, emissionAlphabet, getChangeSupport, getWeights, heads, magicalState, removeState, setWeights, stateAlphabet, transitionsFrom, transitionsTo
 
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

Constructor Detail

HmmerProfileHMM

protected HmmerProfileHMM(Alphabet alpha,
                          int columns,
                          DistributionFactory matchFactory,
                          DistributionFactory insertFactory,
                          java.lang.String name)
                   throws IllegalSymbolException,
                          IllegalTransitionException,
                          IllegalAlphabetException
Method Detail

connectModel

protected void connectModel()
                     throws ChangeVetoException,
                            IllegalSymbolException,
                            IllegalTransitionException,
                            IllegalAlphabetException
This is called by constructor in setting up the allowed transitions in the model

Overrides:
connectModel in class ProfileHMM
Throws:
ChangeVetoException
IllegalSymbolException
IllegalTransitionException
IllegalAlphabetException

transScore

public double transScore(State from,
                         State to,
                         Symbol symFrom,
                         Symbol symTo)
                  throws IllegalSymbolException
Throws:
IllegalSymbolException

log2

protected static double log2(double x)

makeNewInsertState

protected EmissionState makeNewInsertState(java.lang.String str,
                                           Annotation ann,
                                           int[] adv,
                                           Distribution dis)

makeNewMatchState

protected EmissionState makeNewMatchState(java.lang.String str,
                                          Annotation ann,
                                          int[] adv,
                                          Distribution dis)