contextFold.features
Class FeatureManager

java.lang.Object
  extended by contextFold.features.FeatureManager
All Implemented Interfaces:
java.io.Serializable

public class FeatureManager
extends java.lang.Object
implements java.io.Serializable

A parameterization object.

See Also:
Serialized Form

Nested Class Summary
static class FeatureManager.Feature
           
 
Field Summary
static java.util.Comparator<FeatureManager.Feature> absWeightComparator
           
static java.util.Comparator<FeatureManager.Feature> nullComparator
           
 StructureRecognizer sr
           
static java.util.Comparator<FeatureManager.Feature> weightComparator
           
 
Constructor Summary
FeatureManager(StructureRecognizer sr)
           
 
Method Summary
 void addAllBasepairContextUpToLength(int length)
           
 void addBaseContext(ContextFeatureExtractor context, java.lang.Boolean isReversed)
          Context adding
 void addBaseContexts(SinglePosContext[] contexts)
           
 void addBasepairContext(ContextFeatureExtractor context, java.lang.Boolean isReversed)
           
 void addBasepairContext(FeatureExtractor firstPosContext, FeatureExtractor secondPosContext)
           
 java.util.Collection<FeatureTemplate> addBasepairTemplates(java.lang.String namePrefix)
           
 java.util.Collection<FeatureTemplate> addBaseTemplates(java.lang.String namePrefix)
           
 FeatureTemplate addTemplate(java.lang.String name, FeatureExtractor featureExtractor)
           
 FeatureTemplate addTemplate(java.lang.String name, ValueCalculator valueCalculator)
           
 java.util.Collection<FeatureTemplate> addTemplates(java.lang.String name, FeatureExtractor... featureExtractors)
           
 java.lang.String allFeatureValues(java.util.Comparator<FeatureManager.Feature> featureComparator, boolean fiterZeros)
           
 void bindElementTypeToFeatureTemplate(int elementType, java.lang.Boolean isReversed, java.util.Collection<FeatureTemplate> templates)
           
 void bindElementTypeToFeatureTemplates(int elementType, java.lang.Boolean isReversed, java.util.Collection<FeatureTemplate>... templatesCollections)
           
 void bindElementTypeToFeatureTemplates(int elementType, java.util.Collection<FeatureTemplate>... templatesCollections)
          Feature-templates binding
 void bindFeatureTemplateToElementTypes(java.util.Collection<FeatureTemplate> templates, java.lang.Boolean isReversed, int... elementTypes)
           
 void bindFeatureTemplateToElementTypes(java.util.Collection<FeatureTemplate> templates, int... elementTypes)
           
 void compress()
           
 int effectiveFeatureCount()
           
 float filterWeights(float propOfMaxWeight)
           
 void finalize()
           
 AbstractFeatureVector getElementFeaturs(RNA rna, int elementType, int val1)
           
 float getElementScore(RNA rna, int elementType, int val)
           
 StructreElementsScorer getElementScorer(RNA rna)
           
 AbstractFeatureVector getElementWeightedFeaturs(RNA rna, int elementType, int val1)
           
 DenseFeatureVector getFeatureWeights()
           
 void initWeight(java.util.Collection<FeatureTemplate> basepairTemplates, FeatureExtractor firstPosContext, FeatureExtractor secondPosContext, float initialWeight, java.lang.String... contextFeatures)
           
 void loadWeights(java.lang.String initialWeightsFile)
           
 void loadWeights(java.lang.String initialWeightsFile, float propOfMaxWeight)
           
static FeatureManager make(java.lang.String model)
           
 void makeRepresentativeContexts(int maxSuperContextCardinality)
           
 int numOfFeatures()
           
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

sr

public StructureRecognizer sr

nullComparator

public static java.util.Comparator<FeatureManager.Feature> nullComparator

weightComparator

public static java.util.Comparator<FeatureManager.Feature> weightComparator

absWeightComparator

public static java.util.Comparator<FeatureManager.Feature> absWeightComparator
Constructor Detail

FeatureManager

public FeatureManager(StructureRecognizer sr)
Method Detail

addBaseContext

public void addBaseContext(ContextFeatureExtractor context,
                           java.lang.Boolean isReversed)
Context adding

Parameters:
isReversed -

addBasepairContext

public void addBasepairContext(ContextFeatureExtractor context,
                               java.lang.Boolean isReversed)

addAllBasepairContextUpToLength

public void addAllBasepairContextUpToLength(int length)

addTemplate

public FeatureTemplate addTemplate(java.lang.String name,
                                   FeatureExtractor featureExtractor)

addTemplate

public FeatureTemplate addTemplate(java.lang.String name,
                                   ValueCalculator valueCalculator)

addTemplates

public java.util.Collection<FeatureTemplate> addTemplates(java.lang.String name,
                                                          FeatureExtractor... featureExtractors)

addBaseTemplates

public java.util.Collection<FeatureTemplate> addBaseTemplates(java.lang.String namePrefix)

addBasepairTemplates

public java.util.Collection<FeatureTemplate> addBasepairTemplates(java.lang.String namePrefix)

bindElementTypeToFeatureTemplates

public void bindElementTypeToFeatureTemplates(int elementType,
                                              java.util.Collection<FeatureTemplate>... templatesCollections)
Feature-templates binding


bindElementTypeToFeatureTemplates

public void bindElementTypeToFeatureTemplates(int elementType,
                                              java.lang.Boolean isReversed,
                                              java.util.Collection<FeatureTemplate>... templatesCollections)

bindFeatureTemplateToElementTypes

public void bindFeatureTemplateToElementTypes(java.util.Collection<FeatureTemplate> templates,
                                              int... elementTypes)

bindFeatureTemplateToElementTypes

public void bindFeatureTemplateToElementTypes(java.util.Collection<FeatureTemplate> templates,
                                              java.lang.Boolean isReversed,
                                              int... elementTypes)

bindElementTypeToFeatureTemplate

public void bindElementTypeToFeatureTemplate(int elementType,
                                             java.lang.Boolean isReversed,
                                             java.util.Collection<FeatureTemplate> templates)

numOfFeatures

public int numOfFeatures()

finalize

public void finalize()
Overrides:
finalize in class java.lang.Object

makeRepresentativeContexts

public void makeRepresentativeContexts(int maxSuperContextCardinality)

getElementScorer

public StructreElementsScorer getElementScorer(RNA rna)

getFeatureWeights

public DenseFeatureVector getFeatureWeights()

loadWeights

public void loadWeights(java.lang.String initialWeightsFile)
                 throws java.io.IOException
Throws:
java.io.IOException

loadWeights

public void loadWeights(java.lang.String initialWeightsFile,
                        float propOfMaxWeight)
                 throws java.io.IOException
Throws:
java.io.IOException

getElementWeightedFeaturs

public AbstractFeatureVector getElementWeightedFeaturs(RNA rna,
                                                       int elementType,
                                                       int val1)

getElementFeaturs

public AbstractFeatureVector getElementFeaturs(RNA rna,
                                               int elementType,
                                               int val1)

initWeight

public void initWeight(java.util.Collection<FeatureTemplate> basepairTemplates,
                       FeatureExtractor firstPosContext,
                       FeatureExtractor secondPosContext,
                       float initialWeight,
                       java.lang.String... contextFeatures)

addBasepairContext

public void addBasepairContext(FeatureExtractor firstPosContext,
                               FeatureExtractor secondPosContext)

addBaseContexts

public void addBaseContexts(SinglePosContext[] contexts)

make

public static FeatureManager make(java.lang.String model)

getElementScore

public float getElementScore(RNA rna,
                             int elementType,
                             int val)

effectiveFeatureCount

public int effectiveFeatureCount()

allFeatureValues

public java.lang.String allFeatureValues(java.util.Comparator<FeatureManager.Feature> featureComparator,
                                         boolean fiterZeros)

filterWeights

public float filterWeights(float propOfMaxWeight)
Parameters:
propOfMaxWeight - a fraction s.t. weights whose absolute values are below this faction with respect to the absolute maximum weight, are set to 0.
Returns:
the proportion of filtered weights with respect to all non-zero weights.

compress

public void compress()