A B C D E F G I K L M N P Q R S T U V W

A

addChild(KDTreeNode) - Method in class SIGRS.KDTreeNode

addElement(byte, byte[]) - Static method in class SIGRS.Methods

Adds an element to the end of an array

addElement(byte[], byte[][]) - Static method in class SIGRS.Methods

Adds an element to the end of an array

addElement(double[], double[][]) - Static method in class SIGRS.Methods

Adds an element to the end of an array

addElement(int, int[]) - Static method in class SIGRS.Methods

Adds an element to the end of an array

addElement(File, File[]) - Static method in class SIGRS.Methods

Adds an element to the end of an array

addElement(Object, Object[]) - Static method in class SIGRS.Methods

Adds an element to the end of an array

addElement(String, String[]) - Static method in class SIGRS.Methods

Adds an element to the end of an array

append(byte[], byte[]) - Static method in class SIGRS.Methods

Appends an array to the end of another array

append(int, int, byte[], byte[]) - Static method in class SIGRS.Methods

append(char[], char[]) - Static method in class SIGRS.Methods

Appends an array to the end of another array

append(int, int, char[], char[]) - Static method in class SIGRS.Methods

append(double[], double[]) - Static method in class SIGRS.Methods

Appends an array to the end of another array

append(double[][], double[][]) - Static method in class SIGRS.Methods

Appends an array to the end of another array

append(File, File) - Static method in class SIGRS.Methods

Appends the contents of one file to the other

append(int[], int[]) - Static method in class SIGRS.Methods

Appends an array to the end of another array

append(String[], String[]) - Static method in class SIGRS.Methods

Appends an array to the end of another array

append(String[][], String[][]) - Static method in class SIGRS.Methods

Appends an array to the end of another array

B

buildTree(int[], int, KDTreeNode) - Method in class SIGRS.KDTreeNode

buildTree(int[], int, KDTreeStructure) - Method in class SIGRS.KDTreeStructure

C

calculateBackgroundFrequencies(byte[][], LogWriter) - Method in class SIGRS.SIGRSScoreObject

calculateFrequencies(File) - Static method in class SIGRS.SIGRSScoreObject

Calculates a set of frequencies from a set of input sequences

calculateFrequencies(byte[][]) - Static method in class SIGRS.SIGRSScoreObject

calculateFrequencies(int[][], int[][][]) - Static method in class SIGRS.SIGRSScoreObject

calculateScores(byte[][], byte[][], LogWriter) - Method in class SIGRS.SIGRSScoreObject

Calculates the frequencies, scores and associated parameters for the M0 and M1 model

calculateScores(File, File, LogWriter) - Method in class SIGRS.SIGRSScoreObject

calculateScores(LogWriter) - Method in class SIGRS.SIGRSScoreObject

calculateScores(double[][], double[][]) - Static method in class SIGRS.SIGRSScoreObject

Calculates score matrix based on target and background frequencies according to s = C*log(tg/bg) and rounded to the closest integer Equivalent to calling calculateScores(background,target,10.,2.)

calculateScores(double[][], double[][], double, double) - Static method in class SIGRS.SIGRSScoreObject

Calculates score matrix based on target and background frequencies according to s = C*log(tg/bg) and rounded to the closest integer

calculateTargetFrequencies(byte[][], LogWriter) - Method in class SIGRS.SIGRSScoreObject

checkError() - Method in class SIGRS.LogWriter

close() - Method in class SIGRS.LogWriter

concatenateFile(File, File) - Static method in class SIGRS.Methods

countDiNucleotides(byte[]) - Static method in class SIGRS.Methods

Counts the number of each dinucleotide in a sequence Only A,C,G and T is counted.

countDiNucleotides(File) - Static method in class SIGRS.Methods

Counts the number of each dinucleotide in a sequence Only A,C,G and T is counted.

countMonoNucleotides(byte[]) - Static method in class SIGRS.Methods

Counts the number of each nucleotide in a sequence Only A,C,G and T is counted.

countMonoNucleotides(File) - Static method in class SIGRS.Methods

Counts the number of each nucleotide in a sequence Only A,C,G and T is counted.

cutoff(double, int, double, double) - Static method in class SIGRS.KAStatistics

Determines the bit score cutoff at significance level alpha.

D

decode(byte[]) - Static method in class SIGRS.Methods

E

encode(String) - Static method in class SIGRS.Methods

Encodes a nucleotide sequence into bytes where 1=A, 2=C, 3=G, 4=T, 5=X (Masked), any other nucleotide is encoded as 0=N

entropy(double[][], double[][], double) - Static method in class SIGRS.KAStatistics

Calculates the entropy of a scoring matrix

estimateK(double[][], double[][], double, double) - Static method in class SIGRS.KAStatistics

Estimates the parameter K for the independant nucleotides case For details, see page 8 in BLAST scoring parameters

expect(double, double, double, double) - Static method in class SIGRS.KAStatistics

Calculates the expect value of a score according to Karlin & Altschul (1993) p.5875 [y=K*N*exp(-lambda*x)]

expect(double[][], double[][]) - Static method in class SIGRS.KDStatistics

Calculates the expected score based on a score matrix and the associated probabilities

F

findCCRs(int) - Method in class SIGRS.SIGRSScanForCCR

Scores an input sequence and identifies contrasting composition regions (CCRs)

findNode(int, Vector) - Method in class SIGRS.KDTreeNode

flush() - Method in class SIGRS.LogWriter

G

gcd(double, double) - Static method in class SIGRS.KAStatistics

Finds the greatest common divisor of two numbers using the Euclidian algorithm

getBackgroundFrequencies() - Method in class SIGRS.SIGRSScoreObject

Returns the value of backgroundFrequencies.

getChildren() - Method in class SIGRS.KDTreeNode

getColumn(int, double[][]) - Static method in class SIGRS.Methods

Returns the desired column from a matrix array

getColumn(int, String[][]) - Static method in class SIGRS.Methods

Returns the desired column from a matrix array

getFileContents(File) - Static method in class SIGRS.Methods

Reads the entire content of a file into a string

getH0() - Method in class SIGRS.SIGRSScoreObject

Returns the value of H0.

getH1() - Method in class SIGRS.SIGRSScoreObject

Returns the value of H1.

getK0() - Method in class SIGRS.SIGRSScoreObject

Returns the value of K0.

getK1() - Method in class SIGRS.SIGRSScoreObject

Returns the value of K1.

getL0() - Method in class SIGRS.SIGRSScoreObject

Returns the value of L0.

getL1() - Method in class SIGRS.SIGRSScoreObject

Returns the value of L1.

getLabel() - Method in class SIGRS.KDTreeNode

getM0ScoreMatrix() - Method in class SIGRS.SIGRSScoreObject

Returns the value of M0ScoreMatrix.

getM1ScoreMatrix() - Method in class SIGRS.SIGRSScoreObject

Returns the value of M1ScoreMatrix.

getModel() - Method in class SIGRS.SIGRSScanForCCR

getN() - Method in class SIGRS.SIGRSScanForCCR

getParent() - Method in class SIGRS.LogWriter

getPath(int, int) - Method in class SIGRS.KDTreeNode

getPath(int, int, int) - Method in class SIGRS.KDTreeStructure

getRoot() - Method in class SIGRS.KDTreeStructure

getScoreObject(File, File, boolean) - Static method in class SIGRS.SIGRSMain

Creates a SIGRSScoreObject that calculates the scores and parameters from the given backgound and target sequence files

getScoreObject(File, LogWriter) - Static method in class SIGRS.SIGRSScoreObject

getSeqId() - Method in class SIGRS.SIGRSScanForCCR

getSeqLength() - Method in class SIGRS.SIGRSScanForCCR

getTargetFrequencies() - Method in class SIGRS.SIGRSScoreObject

Returns the value of targetFrequencies.

I

indexOf(int, int[]) - Static method in class SIGRS.Methods

Finds the index of an element within an array

indexOf(String, String[]) - Static method in class SIGRS.Methods

Finds the index of an element within an array

K

K(double, double[], double[][], double[][]) - Static method in class SIGRS.KDStatistics

Estimates the parameter K for a score matrix assuming Markov-dependant letters.

KAStatistics - Class in SIGRS

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process.

KAStatistics() - Constructor for class SIGRS.KAStatistics

KDStatistics - Class in SIGRS

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process.

KDStatistics() - Constructor for class SIGRS.KDStatistics

KDTreeNode - Class in SIGRS

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process.

KDTreeNode(int, Matrix) - Constructor for class SIGRS.KDTreeNode

KDTreeStructure - Class in SIGRS

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process.

KDTreeStructure() - Constructor for class SIGRS.KDTreeStructure

L

lambda(double[][], double[][]) - Static method in class SIGRS.KAStatistics

Estimates lambda by an iterative Newton-Rhapson until convergence Terminates execution if convergence is not reached within 10000 iterations

logN(double, double) - Static method in class SIGRS.Methods

Calculates the logarithm in an arbitrary base

LogWriter - Class in SIGRS

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process.

LogWriter() - Constructor for class SIGRS.LogWriter

LogWriter(String) - Constructor for class SIGRS.LogWriter

LogWriter(File) - Constructor for class SIGRS.LogWriter

LogWriter(File, boolean) - Constructor for class SIGRS.LogWriter

LogWriter(String, boolean) - Constructor for class SIGRS.LogWriter

LogWriter(OutputStream) - Constructor for class SIGRS.LogWriter

LogWriter(OutputStream, boolean) - Constructor for class SIGRS.LogWriter

LogWriter(Writer) - Constructor for class SIGRS.LogWriter

LogWriter(Writer, boolean) - Constructor for class SIGRS.LogWriter

M

main(String[]) - Static method in class SIGRS.SIGRSMain

Main method.

max(double[]) - Static method in class SIGRS.Methods

Finds the greatest element in the input array

max(double[][]) - Static method in class SIGRS.Methods

Finds the greatest element in the input array

Methods - Class in SIGRS

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process.

Methods() - Constructor for class SIGRS.Methods

min(double[]) - Static method in class SIGRS.Methods

Finds the minimum element in the input array

min(double[][]) - Static method in class SIGRS.Methods

Finds the minimum element in the input array

N

newDoubleArray(int, double) - Static method in class SIGRS.Methods

Creates a new array of specified length and with all elements set to a specified value

newLine() - Method in class SIGRS.LogWriter

nucleotideCharCode - Static variable in class SIGRS.Methods

nucleotideCode - Static variable in class SIGRS.Methods

P

pad(String, int) - Static method in class SIGRS.Methods

Pads a string with whitespaces to a specified length.

parseBigFasta(File) - Static method in class SIGRS.Methods

parseFasta(File) - Static method in class SIGRS.Methods

Parses a file in FASTA format and returns an array with the identifiers and sequences.

print(boolean) - Method in class SIGRS.LogWriter

print(char) - Method in class SIGRS.LogWriter

print(char[]) - Method in class SIGRS.LogWriter

print(double) - Method in class SIGRS.LogWriter

print(float) - Method in class SIGRS.LogWriter

print(int) - Method in class SIGRS.LogWriter

print(long) - Method in class SIGRS.LogWriter

print(Object) - Method in class SIGRS.LogWriter

print(String) - Method in class SIGRS.LogWriter

println() - Method in class SIGRS.LogWriter

println(boolean) - Method in class SIGRS.LogWriter

println(char) - Method in class SIGRS.LogWriter

println(char[]) - Method in class SIGRS.LogWriter

println(double) - Method in class SIGRS.LogWriter

println(float) - Method in class SIGRS.LogWriter

println(int) - Method in class SIGRS.LogWriter

println(long) - Method in class SIGRS.LogWriter

println(Object) - Method in class SIGRS.LogWriter

println(String) - Method in class SIGRS.LogWriter

Q

quickSort(int[]) - Static method in class SIGRS.Methods

Sorts an array in ascending order

R

removeElementAt(int, byte[][]) - Static method in class SIGRS.Methods

Removes an element from an array and shifts the remaining elements to the left

reset(Vector) - Method in class SIGRS.KDTreeNode

reset(Vector) - Method in class SIGRS.KDTreeStructure

reshape(double[][], double[][]) - Static method in class SIGRS.KAStatistics

Returns a matrix spanning the scores in s where the first column of each row is a score and the second column is the total probability of observing that score

reverse(int[]) - Static method in class SIGRS.Methods

Reverse the order of the elements in an array

reverseComplement(byte[]) - Static method in class SIGRS.Methods

Gets the reverse complement of a byte encoded sequence

reverseComplement(File, File) - Static method in class SIGRS.Methods

reverseComplement(char) - Static method in class SIGRS.Methods

S

scanForCCRs(File[], int, SIGRSScoreObject, double, int, boolean, String, LogWriter, LogWriter) - Static method in class SIGRS.SIGRSMain

Scans the input files in both directions for contrasting composition regions (CCRs)

setAlpha(double) - Method in class SIGRS.SIGRSScanForCCR

setBackgroundFrequencies(double[][][]) - Method in class SIGRS.SIGRSScoreObject

Sets the value of backgroundFrequencies.

setChildren(Object[]) - Method in class SIGRS.KDTreeNode

setColumn(double[][], int, double[]) - Static method in class SIGRS.Methods

Set a column of a matrix

setExpect(double) - Method in class SIGRS.SIGRSScanForCCR

setH0(double) - Method in class SIGRS.SIGRSScoreObject

Sets the value of H0.

setH1(double) - Method in class SIGRS.SIGRSScoreObject

Sets the value of H1.

setInFile(File[]) - Method in class SIGRS.SIGRSScanForCCR

setK0(double) - Method in class SIGRS.SIGRSScoreObject

Sets the value of K0.

setK1(double) - Method in class SIGRS.SIGRSScoreObject

Sets the value of K1.

setL0(double) - Method in class SIGRS.SIGRSScoreObject

Sets the value of L0.

setL1(double) - Method in class SIGRS.SIGRSScoreObject

Sets the value of L1.

setM0ScoreMatrix(double[][]) - Method in class SIGRS.SIGRSScoreObject

Sets the value of M0ScoreMatrix.

setM1ScoreMatrix(double[][]) - Method in class SIGRS.SIGRSScoreObject

Sets the value of M1ScoreMatrix.

setModel(int) - Method in class SIGRS.SIGRSScanForCCR

setN(int) - Method in class SIGRS.SIGRSScanForCCR

setRoot(KDTreeNode) - Method in class SIGRS.KDTreeStructure

setTargetFrequencies(double[][][]) - Method in class SIGRS.SIGRSScoreObject

Sets the value of targetFrequencies.

setValue(Matrix) - Method in class SIGRS.KDTreeNode

SIGRS - package SIGRS

SIGRSMain - Class in SIGRS

This is the main class for the SIGRS routines.

SIGRSMain() - Constructor for class SIGRS.SIGRSMain

SIGRSScanForCCR - Class in SIGRS

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process.

SIGRSScanForCCR(SIGRSScoreObject) - Constructor for class SIGRS.SIGRSScanForCCR

SIGRSScoreObject - Class in SIGRS

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process.

SIGRSScoreObject() - Constructor for class SIGRS.SIGRSScoreObject

skipIdLine(char[], int, int) - Static method in class SIGRS.Methods

skipLineBreak(char[], int, int) - Static method in class SIGRS.Methods

subarray(int, int, char[]) - Static method in class SIGRS.Methods

Extracts a subsegment of an array

subarray(int, int, double[]) - Static method in class SIGRS.Methods

Extracts a subsegment of an array

subarray(int, int, double[][]) - Static method in class SIGRS.Methods

Extracts a subsegment of an array

subarray(int, int[]) - Static method in class SIGRS.Methods

Extracts the last subsegment of an array

subarray(int, int, int[]) - Static method in class SIGRS.Methods

Extracts a subsegment of an array

subarray(int, String[][]) - Static method in class SIGRS.Methods

Extracts a subsegment of an array

subarray(int, int, String[][]) - Static method in class SIGRS.Methods

sum(double[]) - Static method in class SIGRS.Methods

Sums the element in an array

sum(int[]) - Static method in class SIGRS.Methods

Sums the element in an array

T

theta(double[][], double[][]) - Static method in class SIGRS.KDStatistics

Estimateds the parameter theta* of Step 1 on p. 137 of Karlin & Dembo (1992) Includes a simple routine for numerical approximation.

toString() - Method in class SIGRS.SIGRSScoreObject

Returns a string with the contents of the score object

U

updateTree(int[], Matrix[], int) - Method in class SIGRS.KDTreeNode

updateTree(int[], Matrix[]) - Method in class SIGRS.KDTreeStructure

V

vectorAdd(double[], double) - Static method in class SIGRS.Methods

Adds a scalar to an array

vectorAdd(int[], int[]) - Static method in class SIGRS.Methods

Adds to arrays together

vectorAdd(int[][], int[][]) - Static method in class SIGRS.Methods

Adds to arrays together

vectorDivide(double[], double) - Static method in class SIGRS.Methods

Divides an array by a scalar

vectorDivide(double[][], double) - Static method in class SIGRS.Methods

Divides an array by a scalar

vectorInnerProduct(double[], double[]) - Static method in class SIGRS.Methods

Calculates the inner product of two vectors

vectorMultiply(double[], double) - Static method in class SIGRS.Methods

Multiplies an array by a scalar

vectorMultiply(double[], double[]) - Static method in class SIGRS.Methods

Multiplies the values of two arrays

vectorMultiply(double[][], double) - Static method in class SIGRS.Methods

Multiplies a matrix by a scalar

vectorMultiply(int[], int) - Static method in class SIGRS.Methods

Multiplies an array by a scalar

W

write(char[]) - Method in class SIGRS.LogWriter

write(char[], int, int) - Method in class SIGRS.LogWriter

write(int) - Method in class SIGRS.LogWriter

write(String) - Method in class SIGRS.LogWriter

write(String, int, int) - Method in class SIGRS.LogWriter

writeGFFAnnotationOfCCRs(double[][], String[], int, String, LogWriter) - Static method in class SIGRS.SIGRSMain

Writes the contrasting composition regions (CCRs) to output in GFF format.

A B C D E F G I K L M N P Q R S T U V W