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java.lang.Objectutil.classificationFeatures.implementations.test.VarianceClassificationFeature
public class VarianceClassificationFeature
Field Summary |
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Fields inherited from interface util.classificationFeatures.ClassificationFeature |
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ERROR_STRING |
Constructor Summary | |
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VarianceClassificationFeature()
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Method Summary | |
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int |
countOccurences(java.lang.String motif,
java.lang.String sequence)
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java.util.List<java.lang.Double> |
extractFeatures(java.lang.String[] sequences,
int splicesite,
java.lang.String[] types,
java.util.List<Conversion> conversions,
java.lang.String[] conversion_sequences)
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature). |
ClassificationFeatureDrawing |
getClassificationFeatureDrawing()
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures. |
Conversion |
getConversion()
This method asks the classificationfeature for its conversion-type. |
int |
getLength()
This method returns the length of the feature. |
AttributeDescription |
getLocationDescription(int loc)
Returns a standardized description of the location that is indicated. |
int |
getNumberOfAttributes()
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges). |
int[] |
getUpDownRanges()
This method asks for the up- and downstreamranges of the feature |
ClassificationFeature |
make_copy()
Makes a copy of this particular classificationfeature. |
boolean |
needCompositionalTypes()
Asks whether the computer needs to precompute compositional types. |
void |
setParameters(java.lang.String[] args)
This method sets the necessary parameters for the classificationfeature. |
void |
setUpDownRanges(int up,
int down)
This method sets the new upstream and downstream ranges |
java.lang.String |
toNoRangeString()
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements. |
java.lang.String |
toString()
String representation of the classificationFeature |
java.lang.String |
toStringUnderscore()
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public VarianceClassificationFeature()
Method Detail |
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public java.util.List<java.lang.Double> extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences) throws FeatureExtractionException
extractFeatures
in interface ClassificationFeature
sequences
- The sequence from which the features should be extracted.splicesite
- The location of the splicesite (pseudo or real)types
- The compositional types (if requested, otherwise null).conversions
- A list with all the conversion typesconversion_sequences
- An array with all the converted sequences.
FeatureExtractionException
- Thrown when something goes wrong when extracting the features.public int countOccurences(java.lang.String motif, java.lang.String sequence)
public ClassificationFeatureDrawing getClassificationFeatureDrawing()
ClassificationFeature
getClassificationFeatureDrawing
in interface ClassificationFeature
public Conversion getConversion()
ClassificationFeature
getConversion
in interface ClassificationFeature
public int getLength()
ClassificationFeature
getLength
in interface ClassificationFeature
public AttributeDescription getLocationDescription(int loc)
ClassificationFeature
getLocationDescription
in interface ClassificationFeature
loc
- The location
public int getNumberOfAttributes()
ClassificationFeature
getNumberOfAttributes
in interface ClassificationFeature
public int[] getUpDownRanges()
ClassificationFeature
getUpDownRanges
in interface ClassificationFeature
public ClassificationFeature make_copy()
ClassificationFeature
make_copy
in interface ClassificationFeature
public boolean needCompositionalTypes()
ClassificationFeature
needCompositionalTypes
in interface ClassificationFeature
public void setParameters(java.lang.String[] args) throws IncorrectClassificationFeatureException
ClassificationFeature
setParameters
in interface ClassificationFeature
args
- The array with the parameters in string format
IncorrectClassificationFeatureException
- Can be thrown when the parameters
are incorrect (outside possible ranges) and/or the parameters could not be parsed.public void setUpDownRanges(int up, int down)
ClassificationFeature
setUpDownRanges
in interface ClassificationFeature
up
- The new upstream rangedown
- The new downstream rangepublic java.lang.String toNoRangeString()
ClassificationFeature
toNoRangeString
in interface ClassificationFeature
public java.lang.String toStringUnderscore()
ClassificationFeature
toStringUnderscore
in interface ClassificationFeature
public java.lang.String toString()
ClassificationFeature
toString
in interface ClassificationFeature
toString
in class java.lang.Object
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