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public interface ClassificationFeature
This interface contains all methods that a classification feature should implement to be fully functional. While it is possible that some of these methods do not explicitly need to be implemented (as they are not currently used within the project), it is advised to follow the standard procedure of implementing all the methods.
Field Summary | |
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static java.lang.String |
ERROR_STRING
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Method Summary | |
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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. |
Field Detail |
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static final java.lang.String ERROR_STRING
Method Detail |
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boolean needCompositionalTypes()
Conversion getConversion()
ClassificationFeature make_copy()
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
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.java.lang.String toStringUnderscore()
java.lang.String toString()
toString
in class java.lang.Object
java.lang.String toNoRangeString()
int getNumberOfAttributes()
void setParameters(java.lang.String[] args) throws IncorrectClassificationFeatureException
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.ClassificationFeatureDrawing getClassificationFeatureDrawing()
int[] getUpDownRanges()
void setUpDownRanges(int up, int down)
up
- The new upstream rangedown
- The new downstream rangeint getLength()
AttributeDescription getLocationDescription(int loc)
loc
- The location
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