contextFold.features
Class FeatureManager
java.lang.Object
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
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 |
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
FeatureManager
public FeatureManager(StructureRecognizer sr)
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()