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java.lang.Objectutil.classificationFeatures.implementations.BranchpointClassificationFeature
public class BranchpointClassificationFeature
Field Summary | |
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static double[][] |
BASEPAIRMATRIX
A basepairmatrix, which describes the binding force between different nucleotides. |
Fields inherited from interface util.classificationFeatures.ClassificationFeature |
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ERROR_STRING |
Constructor Summary | |
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BranchpointClassificationFeature()
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Method Summary | |
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int |
countInterAg(java.lang.String sequence,
int start,
int stop)
Finds the number of other possible acceptorsites ("AG") between two locations (mostly used between a branchpoint and an acceptorsite) |
int |
countPyrimidines(java.lang.String sequence,
int start,
int stop)
Counts the number of pyrimidines between the possible splicesite and the possible acceptorsite |
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). |
double[] |
getBasePairScore(java.lang.String sequence,
int location,
char[] u2RNA,
int loc_dash)
Computes basepairscores for possible branchpoints |
int |
getBPVal(char c)
Returns the place wihtin the basepairbinding matrix for a nucleotide |
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 |
getMaximum_upstream()
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int |
getMinimum_upstream()
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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. |
java.lang.String |
reverseString(java.lang.String string)
reverses the U2RNA string |
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 |
Field Detail |
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public static final double[][] BASEPAIRMATRIX
Constructor Detail |
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public BranchpointClassificationFeature()
Method Detail |
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public int[] getUpDownRanges()
getUpDownRanges
in interface ClassificationFeature
public Conversion getConversion()
getConversion
in interface ClassificationFeature
public void setUpDownRanges(int up, int down)
setUpDownRanges
in interface ClassificationFeature
up
- The new upstream rangedown
- The new downstream rangepublic 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 int countInterAg(java.lang.String sequence, int start, int stop)
sequence
- The sequence in which the number of AG's should be countedstart
- The starting point in the sequencestop
- The stop point in the sequence
public int countPyrimidines(java.lang.String sequence, int start, int stop)
sequence
- The sequence in which the pyrimidines should be countedstart
- startlocation from which to start countingstop
- Stoplocation from which to stop counting
public int getBPVal(char c)
c
- The nucleotide
public double[] getBasePairScore(java.lang.String sequence, int location, char[] u2RNA, int loc_dash)
sequence
- The sequencelocation
- Location of the possible branchpointu2RNA
- The U2RNA sequenceloc_dash
- The location of the binding-nucleotide within the u2RNA sequence
public java.lang.String reverseString(java.lang.String string)
string
- Original U2RNA sequence
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 int getNumberOfAttributes()
getNumberOfAttributes
in interface ClassificationFeature
public AttributeDescription getLocationDescription(int loc)
getLocationDescription
in interface ClassificationFeature
loc
- The location
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 getMaximum_upstream()
public int getMinimum_upstream()
public int getLength()
ClassificationFeature
getLength
in interface ClassificationFeature
public ClassificationFeature make_copy()
make_copy
in interface ClassificationFeature
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