B C D E F G H I L M N O P R S T U

B

basePairs - Variable in class taskspaces.rna.DatabaseEntry

Holds the valid base pairs.

BM - class taskspaces.rna.BM.

BM() - Constructor for class taskspaces.rna.BM

Boyer-Moore text search

C

characters(char[], int, int) - Method in class taskspaces.rna.MotifsParser

Catches data from element.

compile(String) - Method in class taskspaces.rna.BM

Compiles the text pattern for searching.

composition - Variable in class taskspaces.rna.DatabaseEntry

Holds the current percentage composition of bases.

constraint - Variable in class taskspaces.rna.MotifsParser

Holds entry constraint values.

constraints - Variable in class taskspaces.rna.DatabaseEntry

Holds integer arrays representing pairing rules for this entry.

constraints - Variable in class taskspaces.rna.MotifsParser

Holds entry constraint arrays.

D

d - Variable in class taskspaces.rna.BM

Internal BM table.

DatabaseEntry - class taskspaces.rna.DatabaseEntry.

DatabaseEntry represents a lab-isolated set of motifs, structures and constraints.

DatabaseEntry(String, String[], String[], ArrayList) - Constructor for class taskspaces.rna.DatabaseEntry

E

elementName - Variable in class taskspaces.rna.MotifsParser

Holds name of the current element.

embed(String[], String) - Static method in class taskspaces.rna.SequenceGenerator

Embeds modules into a background sequence at specified points.

embedCompositionModules(String[], int) - Static method in class taskspaces.rna.SequenceGenerator

Generates a random sequence with embedded modules, based on the composition of the modules.

embedModules(String[], int) - Static method in class taskspaces.rna.SequenceGenerator

Generates a random sequence with embedded modules in random but ascending positions.

embedModules(String[], int, float[]) - Static method in class taskspaces.rna.SequenceGenerator

Generates a sequence with the base composition of the passed composition percentage values and with embedded database modules in random but ascending positions.

embedModules(String[], int, String) - Static method in class taskspaces.rna.SequenceGenerator

Generates a sequence with the base composition of the passed base sequence with embedded database modules in random but ascending positions.

endElement(String, String, String) - Method in class taskspaces.rna.MotifsParser

Catches end element event.

entries - Static variable in class taskspaces.rna.MotifsParser

Holds the parsed entries.

F

fill(int, int) - Method in class taskspaces.rna.Partition

Sets the partition array to the correct values.

G

generateModules() - Method in class taskspaces.rna.DatabaseEntry

Modifies modules to match the entry's set of pairing constraints.

getCompositionBase(float[]) - Static method in class taskspaces.rna.SequenceGenerator

Returns a base with the given composition.

getCompositionPair(String) - Static method in class taskspaces.rna.SequenceGenerator

Returns a base pair using the composition of the passed sequence.

getCompositionSequence(String, int) - Static method in class taskspaces.rna.SequenceGenerator

Returns a random piece of the input String or a lengthened randomized String of the input length.

getConstraints() - Method in class taskspaces.rna.DatabaseEntry

Returns this entry's constraints.

getEntries() - Static method in class taskspaces.rna.MotifsParser

Returns the parsed entries.

getInsertionPoints(int, int) - Static method in class taskspaces.rna.SequenceGenerator

Generates an integer array of sorted points for inserting modules into sequences.

getModuleNumber() - Method in class taskspaces.rna.Partition

Returns the current number of modules.

getModules() - Method in class taskspaces.rna.DatabaseEntry

Returns this entry's sequence modules.

getName() - Method in class taskspaces.rna.DatabaseEntry

Returns this entry's name.

getObjectNumber() - Method in class taskspaces.rna.Partition

Returns the current number of objects.

getPair() - Method in class taskspaces.rna.DatabaseEntry

Returns a pair of bases using the probabilities in the pairProbs array set by the initializeArrays method.

getPairingBase(char) - Static method in class taskspaces.rna.SequenceGenerator

Returns the pair of the passed base.

getPairMap(String) - Static method in class taskspaces.rna.PairList

Constructs a pair list map indicating what indices are paired in a given dot-bracket notation structure.

getPartitions() - Method in class taskspaces.rna.Partition

Returns the partition array.

getPartitionSequence(int[]) - Static method in class taskspaces.rna.SequenceGenerator

Returns a randomized sequence with the given base composition.

getPercentages(float) - Method in class taskspaces.rna.Partition

Returns the partition percentages when passed a percentage.

getRandomBase(long) - Static method in class taskspaces.rna.SequenceGenerator

Returns a random base.

getRandomizedSequences(String, int) - Static method in class taskspaces.rna.SequenceGenerator

Generates the input number of random sequences using the input String.

getRandomPair(boolean) - Static method in class taskspaces.rna.SequenceGenerator

Returns a random base pair.

getRandomSequence(int, long) - Static method in class taskspaces.rna.SequenceGenerator

Generates a random sequence using the MersenneTwisterFast class.

getRandomSequences(int, int, long) - Static method in class taskspaces.rna.SequenceGenerator

Generates an input number of random sequences using the MersenneTwisterFast class.

getStructures() - Method in class taskspaces.rna.DatabaseEntry

Returns this entry's sequence structures.

GOOD_SEED - Static variable in class taskspaces.rna.MersenneTwisterFast

gu - Variable in class taskspaces.rna.DatabaseEntry

Indicates whether to allow GU or UG pairs.

H

haveNextNextGaussian - Variable in class taskspaces.rna.MersenneTwisterFast

I

initializeArrays() - Method in class taskspaces.rna.DatabaseEntry

Initializes the pairProbs probabilities array with the probabilities of each base pair being selected based on the percentages in the composition array.

L

LOWER_MASK - Static variable in class taskspaces.rna.MersenneTwisterFast

M

M - Static variable in class taskspaces.rna.MersenneTwisterFast

mag01 - Variable in class taskspaces.rna.MersenneTwisterFast

main(String[]) - Static method in class taskspaces.rna.MersenneTwisterFast

Tests the code.

match(String[], String, int[]) - Static method in class taskspaces.rna.Matcher

Finds a given set of patterns in a given text at specified indices.

match(String[], String, int[], List) - Static method in class taskspaces.rna.Matcher

Finds a given set of patterns in a given text at specified indices meeting specified constraints.

match(String, String, int) - Static method in class taskspaces.rna.Matcher

Finds a patterns in a text at a specified index.

matchBM(String[], String) - Static method in class taskspaces.rna.Matcher

Finds a given set of patterns in a given text using a Boyer-Moore search.

matchBM(String[], String, int[]) - Static method in class taskspaces.rna.Matcher

Finds a given set of patterns in a given text at specific indices using a Boyer-Moore search.

matchBM(String, String) - Static method in class taskspaces.rna.Matcher

Finds a given pattern in a given text using a Boyer-Moore search.

matchBM(String, String, int) - Static method in class taskspaces.rna.Matcher

Finds a given pattern in a given text at a given index using a Boyer-Moore search.

Matcher - class taskspaces.rna.Matcher.

Class Matcher contains methods to match Strings using the BM (Boyer-Moore) class and Java methods.

Matcher() - Constructor for class taskspaces.rna.Matcher

MATRIX_A - Static variable in class taskspaces.rna.MersenneTwisterFast

MAXCHAR - Static variable in class taskspaces.rna.BM

Maximum chars in character set.

MersenneTwisterFast - class taskspaces.rna.MersenneTwisterFast.

Mersenne Twister and MersenneTwisterFast:

MersenneTwisterFast() - Constructor for class taskspaces.rna.MersenneTwisterFast

Constructor using the default seed.

MersenneTwisterFast(long) - Constructor for class taskspaces.rna.MersenneTwisterFast

Constructor using a given seed.

modules - Variable in class taskspaces.rna.DatabaseEntry

Holds the entry sequence modules.

modules - Variable in class taskspaces.rna.MotifsParser

Holds entry sequence modules.

modules - Variable in class taskspaces.rna.Partition

Holds number of modules.

motifName - Variable in class taskspaces.rna.MotifsParser

Holds name of the motif.

MotifsParser - class taskspaces.rna.MotifsParser.

Parses XML (using Apache Xerces SAX parser) documents conforming to Motifs.dtd definition and creates java.util.ArrayList of DatabaseEntry objects.

MotifsParser(String) - Constructor for class taskspaces.rna.MotifsParser

Parses Entry XML file.

mt - Variable in class taskspaces.rna.MersenneTwisterFast

mti - Variable in class taskspaces.rna.MersenneTwisterFast

N

N - Static variable in class taskspaces.rna.MersenneTwisterFast

name - Variable in class taskspaces.rna.DatabaseEntry

Holds the name of the entry.

next() - Method in class taskspaces.rna.Partition

Returns the next permutation of the partition array.

nextBoolean() - Method in class taskspaces.rna.MersenneTwisterFast

nextByte() - Method in class taskspaces.rna.MersenneTwisterFast

nextBytes(byte[]) - Method in class taskspaces.rna.MersenneTwisterFast

nextChar() - Method in class taskspaces.rna.MersenneTwisterFast

nextDouble() - Method in class taskspaces.rna.MersenneTwisterFast

nextFloat() - Method in class taskspaces.rna.MersenneTwisterFast

nextGaussian() - Method in class taskspaces.rna.MersenneTwisterFast

nextInt() - Method in class taskspaces.rna.MersenneTwisterFast

nextInt(int) - Method in class taskspaces.rna.MersenneTwisterFast

Returns an integer drawn uniformly from 0 to n-1.

nextLong() - Method in class taskspaces.rna.MersenneTwisterFast

nextNextGaussian - Variable in class taskspaces.rna.MersenneTwisterFast

nextShort() - Method in class taskspaces.rna.MersenneTwisterFast

O

objects - Variable in class taskspaces.rna.Partition

Holds number of objects.

P

PairList - class taskspaces.rna.PairList.

Encapsulates a methods to create a map of paired indices given a dot-bracket notation structure.

PairList() - Constructor for class taskspaces.rna.PairList

pairProbs - Variable in class taskspaces.rna.DatabaseEntry

Holds the probabilities for each base pair being selected based on the current composition.

partial - Variable in class taskspaces.rna.BM

Bytes of a partial match found at the end of a text buffer.

partialMatch() - Method in class taskspaces.rna.BM

Returns the position at the end of the text buffer where a partial match was found.

Partition - class taskspaces.rna.Partition.

Contains methods to generate random RNA sequence Strings from a sequence over a set space of partitions given a number of objects and modules.

Partition() - Constructor for class taskspaces.rna.Partition

partitions - Variable in class taskspaces.rna.Partition

Holds partition values.

pat - Variable in class taskspaces.rna.BM

Byte representation of pattern.

patLen - Variable in class taskspaces.rna.BM

Length of pattern.

R

reset() - Static method in class taskspaces.rna.MotifsParser

Resets the entries ArrayList.

reset() - Method in class taskspaces.rna.Partition

Resets the partitions.

S

search(byte[], int, int) - Method in class taskspaces.rna.BM

Search for the compiled pattern in the given text.

SequenceGenerator - class taskspaces.rna.SequenceGenerator.

Contains methods to generate random RNA sequence Strings from a sequence, generate structures from sequences, generate a given number of random RNA sequences of a given length, and create random base pairs.

SequenceGenerator() - Constructor for class taskspaces.rna.SequenceGenerator

setComposition(float[], boolean) - Method in class taskspaces.rna.DatabaseEntry

Sets the composition for this entry.

setModuleNumber(int) - Method in class taskspaces.rna.Partition

Sets the current number of modules.

setObjectNumber(int) - Method in class taskspaces.rna.Partition

Sets the current number of objects.

setPartitions(int[]) - Method in class taskspaces.rna.Partition

Sets the partition array to the given array.

setSeed(long) - Method in class taskspaces.rna.MersenneTwisterFast

Initalize the pseudo random number generator.

shuffleInts(int[]) - Static method in class taskspaces.rna.Shuffler

Randomly shuffles an integer array.

Shuffler - class taskspaces.rna.Shuffler.

Encapsulates a method to shuffle a string using the Yates-Fischer method and a method to randomize an array of integers.

Shuffler() - Constructor for class taskspaces.rna.Shuffler

shuffleString(String, int, int) - Static method in class taskspaces.rna.Shuffler

Randomly shuffles a String using the Yates-Fischer method.

skip - Variable in class taskspaces.rna.BM

Internal BM table.

startElement(String, String, String, Attributes) - Method in class taskspaces.rna.MotifsParser

Catches a start element event.

structures - Variable in class taskspaces.rna.DatabaseEntry

Holds the entry sequence structures.

structures - Variable in class taskspaces.rna.MotifsParser

Holds entry structures.

sum(int[]) - Method in class taskspaces.rna.Partition

Sums the elements of a given int[].

T

TEMPERING_MASK_B - Static variable in class taskspaces.rna.MersenneTwisterFast

TEMPERING_MASK_C - Static variable in class taskspaces.rna.MersenneTwisterFast

U

UPPER_MASK - Static variable in class taskspaces.rna.MersenneTwisterFast

B C D E F G H I L M N O P R S T U