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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

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