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java.lang.Objectutil.classificationFeatures.ClassificationFeatureUtils
public class ClassificationFeatureUtils
This class contains some different utility methods for feature extraction.
Nested Class Summary | |
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static class |
ClassificationFeatureUtils.CLASSIFICATIONFEATURE_TYPES
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Method Summary | |
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static java.lang.String |
convertFullSecToReducedSec(java.lang.String t)
Replace all ( and ) by | in the secondary structure string |
static java.util.List<java.util.List<ValPosCombination>> |
divide(java.util.List<ClassificationFeature> cfList,
java.util.List<ValPosCombination> vpcList)
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static java.lang.String[] |
generateCompositionalTypes(int length)
Recursively computes all possible n-nucleotides (with n being the length) |
static java.lang.String[] |
generateFullSecStructCompositionalTypes(int length)
Recursively computes all possible combinations of stems and loops of length n 3 possible characters : ( ) . |
static java.lang.String[] |
generateGeneralCompositionalTypes(int length,
char[] alphabet)
Generates all possible combinations, according to the provided alphabet and the required length of the combinations. |
static java.lang.String[] |
generateGeneralCompositionalTypes(int length,
java.lang.String[] alphabet)
Generates all possible combinations, according to the provided alphabet and the required length of the combinations. |
static java.lang.String[] |
generateReducedCompositionalTypes(int length)
Recusrively computes all possible n-nucleotides that are reduced to the set of purines and pyrimidines. |
static java.lang.String[] |
generateReducedSecStructCompositionalTypes(int length)
Recursively computes all possible combinations of stems and loops of length n 2 possible characters : | . |
static int |
getMaximum(java.util.List<java.lang.Integer> list)
Selects and returns te maximum value of integers in a list. |
static void |
main(java.lang.String[] args)
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static boolean |
mergeListFeatureVector(java.util.List<java.lang.Integer> list,
int[] featureVec)
Adds all items from the featurevector (represented by an array) to the list with items. |
static ClassificationFeature |
parseFeatureFromString(java.lang.String s)
This method creates a ClassificationFeature from a string, by using the java-reflection to locate the correct ClassificationFeature implementation. |
static ClassificationFeature |
parseFeatureFromString(java.lang.String[] split)
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static ClassificationFeature |
parseFeatureFromStringJar(java.lang.String[] split)
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static ClassificationFeature |
parseFeatureFromStringNonJar(java.lang.String[] split)
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Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static ClassificationFeature parseFeatureFromString(java.lang.String[] split)
public static ClassificationFeature parseFeatureFromStringJar(java.lang.String[] split)
public static ClassificationFeature parseFeatureFromStringNonJar(java.lang.String[] split)
public static ClassificationFeature parseFeatureFromString(java.lang.String s)
s
- The String representation of the ClassificationFeature, as defined in a configuration file
public static java.util.List<java.util.List<ValPosCombination>> divide(java.util.List<ClassificationFeature> cfList, java.util.List<ValPosCombination> vpcList)
public static int getMaximum(java.util.List<java.lang.Integer> list)
list
- The list with integer data
public static java.lang.String[] generateCompositionalTypes(int length)
length
- The length of the nucleotides
public static java.lang.String[] generateGeneralCompositionalTypes(int length, char[] alphabet)
length
- The length of the combinationsalphabet
- The alphabet used to produce the combinations
public static java.lang.String[] generateGeneralCompositionalTypes(int length, java.lang.String[] alphabet)
length
- The length of the combinationsalphabet
- The alphabet used to produce the combinations
public static java.lang.String[] generateReducedCompositionalTypes(int length)
length
- The length of the combinations
public static java.lang.String[] generateFullSecStructCompositionalTypes(int length)
length
- The length of the combinations
public static java.lang.String[] generateReducedSecStructCompositionalTypes(int length)
length
- The length of the combinations
public static java.lang.String convertFullSecToReducedSec(java.lang.String t)
t
- original string
public static boolean mergeListFeatureVector(java.util.List<java.lang.Integer> list, int[] featureVec)
list
- The existing listfeatureVec
- The featurevector
public static void main(java.lang.String[] args)
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