|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectutil.classificationFeatures.implementations.test.NearestEqualClassificationFeature
public class NearestEqualClassificationFeature
Field Summary | |
---|---|
static int |
POSSIBLE_SOLUTIONS
|
Fields inherited from interface util.classificationFeatures.ClassificationFeature |
---|
ERROR_STRING |
Constructor Summary | |
---|---|
NearestEqualClassificationFeature()
|
Method Summary | |
---|---|
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 |
getDownstream_range()
|
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 |
int |
getUpstream_range()
|
ClassificationFeature |
make_copy()
Makes a copy of this particular classificationfeature. |
boolean |
makesMatch(java.lang.String base,
java.lang.String match)
|
boolean |
needCompositionalTypes()
Asks whether the computer needs to precompute compositional types. |
java.lang.String |
rotateString(java.lang.String s)
|
void |
setDownstream_range(int downstream_range)
|
void |
setLength(int length)
|
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 |
void |
setUpstream_range(int upstream_range)
|
java.lang.String |
toInverseString(java.lang.String s)
|
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 |
---|
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
---|
public static final int POSSIBLE_SOLUTIONS
Constructor Detail |
---|
public NearestEqualClassificationFeature()
Method Detail |
---|
public boolean needCompositionalTypes()
needCompositionalTypes
in interface ClassificationFeature
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 boolean makesMatch(java.lang.String base, java.lang.String match)
public java.lang.String toInverseString(java.lang.String s)
public java.lang.String rotateString(java.lang.String s)
public Conversion getConversion()
getConversion
in interface ClassificationFeature
public java.lang.String toStringUnderscore()
toStringUnderscore
in interface ClassificationFeature
public java.lang.String toString()
toString
in interface ClassificationFeature
toString
in class java.lang.Object
public java.lang.String toNoRangeString()
toNoRangeString
in interface ClassificationFeature
public AttributeDescription getLocationDescription(int loc)
getLocationDescription
in interface ClassificationFeature
loc
- The location
public int getNumberOfAttributes()
getNumberOfAttributes
in interface ClassificationFeature
public void setParameters(java.lang.String[] args) throws IncorrectClassificationFeatureException
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 ClassificationFeatureDrawing getClassificationFeatureDrawing()
getClassificationFeatureDrawing
in interface ClassificationFeature
public int[] getUpDownRanges()
getUpDownRanges
in interface ClassificationFeature
public void setUpDownRanges(int up, int down)
setUpDownRanges
in interface ClassificationFeature
up
- The new upstream rangedown
- The new downstream rangepublic int getLength()
getLength
in interface ClassificationFeature
public int getDownstream_range()
public void setDownstream_range(int downstream_range)
public int getUpstream_range()
public void setUpstream_range(int upstream_range)
public void setLength(int length)
public ClassificationFeature make_copy()
make_copy
in interface ClassificationFeature
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |