taskspaces.rna
Class SequenceGenerator

java.lang.Object
  |
  +--taskspaces.rna.SequenceGenerator

All Implemented Interfaces:

java.io.Serializable

public class SequenceGenerator

extends java.lang.Object

implements java.io.Serializable

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.

Version:

1.00

Author:

Rob Markel

See Also:

Serialized Form

Constructor Summary

SequenceGenerator()

Method Summary

private static java.util.List	embed(java.lang.String[] modules, java.lang.String spacer) Embeds modules into a background sequence at specified points.
static java.util.List	embedCompositionModules(java.lang.String[] modules, int sequenceLength) Generates a random sequence with embedded modules, based on the composition of the modules.
static java.util.List	embedModules(java.lang.String[] modules, int sequenceLength) Generates a random sequence with embedded modules in random but ascending positions.
static java.util.List	embedModules(java.lang.String[] modules, int sequenceLength, float[] composition) Generates a sequence with the base composition of the passed composition percentage values and with embedded database modules in random but ascending positions.
static java.util.List	embedModules(java.lang.String[] modules, int sequenceLength, java.lang.String baseSequence) Generates a sequence with the base composition of the passed base sequence with embedded database modules in random but ascending positions.
static char	getCompositionBase(float[] f) Returns a base with the given composition.
static char[]	getCompositionPair(java.lang.String baseSequence) Returns a base pair using the composition of the passed sequence.
static java.lang.String	getCompositionSequence(java.lang.String baseSequence, int length) Returns a random piece of the input String or a lengthened randomized String of the input length.
private static int[]	getInsertionPoints(int moduleNum, int spacerLength) Generates an integer array of sorted points for inserting modules into sequences.
static char	getPairingBase(char c) Returns the pair of the passed base.
static java.lang.String	getPartitionSequence(int[] composition) Returns a randomized sequence with the given base composition.
static char	getRandomBase(long seed) Returns a random base.
static java.lang.String[]	getRandomizedSequences(java.lang.String seq, int num) Generates the input number of random sequences using the input String.
static char[]	getRandomPair(boolean b) Returns a random base pair.
static java.lang.String	getRandomSequence(int sequenceLength, long seed) Generates a random sequence using the MersenneTwisterFast class.
static java.lang.String[]	getRandomSequences(int num, int sequenceLength, long seed) Generates an input number of random sequences using the MersenneTwisterFast class.

Methods inherited from class java.lang.Object

, clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, toString, wait, wait, wait

Constructor Detail

SequenceGenerator

public SequenceGenerator()

Method Detail

getRandomizedSequences

public static java.lang.String[] getRandomizedSequences(java.lang.String seq,
                                                        int num)
                                                 throws java.lang.Exception

Generates the input number of random sequences using the input String. It is randomized using the shuffleString() method of the Shuffle class.

Parameters:

sequence - the sequence to randomize.

num - number of sequences to return.

Returns:

the randomized sequences.

getCompositionSequence

public static java.lang.String getCompositionSequence(java.lang.String baseSequence,
                                                      int length)
                                               throws java.lang.Exception

Returns a random piece of the input String or a lengthened randomized String of the input length. The character composition is maintained.

Parameters:

input - sequence for input.

Returns:

the shuffled sequence, either a piece or shuffled concatenation of the input sequence up to the given length.

getCompositionPair

public static char[] getCompositionPair(java.lang.String baseSequence)

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

Parameters:

baseSequence - a sequence.

Returns:

randomly selected base pair from the passed sequence.

getPairingBase

public static char getPairingBase(char c)

Returns the pair of the passed base.

Parameters:

c - an RNA base.

Returns:

the pairing RNA base.

getRandomSequences

public static java.lang.String[] getRandomSequences(int num,
                                                    int sequenceLength,
                                                    long seed)

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

Parameters:

num - number of sequences to generate.

sequenceLength - desired length of generated sequences.

seed - a random seed.

Returns:

the generated random sequences.

getRandomSequence

public static java.lang.String getRandomSequence(int sequenceLength,
                                                 long seed)

Generates a random sequence using the MersenneTwisterFast class.

Parameters:

sequenceLength - desired length of generated sequence.

seed - a random seed.

Returns:

the generated random sequences.

getRandomBase

public static char getRandomBase(long seed)

Returns a random base.

Parameters:

seed - a random seed.

Returns:

the random base.

getCompositionBase

public static char getCompositionBase(float[] f)

Returns a base with the given composition.

Parameters:

composition - base composition percentages.

Returns:

the selected base.

getRandomPair

public static char[] getRandomPair(boolean b)

Returns a random base pair.

Parameters:

b - if true include GU and UG as valid pairs.

Returns:

a base pair.

getPartitionSequence

public static java.lang.String getPartitionSequence(int[] composition)

Returns a randomized sequence with the given base composition.

Parameters:

composition - base composition percentage values.

Returns:

the randomized sequence String.

embedModules

public static java.util.List embedModules(java.lang.String[] modules,
                                          int sequenceLength,
                                          float[] composition)
                                   throws java.lang.Exception

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

Parameters:

modules - sequence modules.

sequenceLength - the desired sequence length.

composition - the desired base composition of the spacer.

Returns:

the generated String.

embedModules

public static java.util.List embedModules(java.lang.String[] modules,
                                          int sequenceLength,
                                          java.lang.String baseSequence)
                                   throws java.lang.Exception

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

Parameters:

modules - sequence modules.

sequenceLength - the desired sequence length.

Returns:

the generated String.

embedModules

public static java.util.List embedModules(java.lang.String[] modules,
                                          int sequenceLength)
                                   throws java.lang.Exception

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

Parameters:

modules - module sequences.

sequenceLength - the desired sequence length.

Returns:

the generated String.

embedCompositionModules

public static java.util.List embedCompositionModules(java.lang.String[] modules,
                                                     int sequenceLength)
                                              throws java.lang.Exception

Generates a random sequence with embedded modules, based on the composition of the modules. NOTE: This method only works with sequence lengths which are multiples of 20.

Parameters:

modules - sequence modules.

Returns:

the generated String.

getInsertionPoints

private static int[] getInsertionPoints(int moduleNum,
                                        int spacerLength)

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

Parameters:

moduleNum - the number of modules.

Returns:

the random but ascending values.

embed

private static java.util.List embed(java.lang.String[] modules,
                                    java.lang.String spacer)

Embeds modules into a background sequence at specified points.

Parameters:

modules - the sequence modules.

sequence - the background sequence.

Returns:

List containing generated sequence and insertion points.