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

A

ANY_STRAND - Static variable in class org.gersteinlab.act.data.Interval

The official symbol to indicate that the strand is not important.

attributes - Variable in class org.gersteinlab.act.data.Interval

Additional attributes of the interval.

B

backwardCompareTo(Interval) - Method in class org.gersteinlab.act.data.Interval

Compare this interval with an input interval based on backward ordering.

BedFilesReader - Class in org.gersteinlab.act.io

This class defines a reader of data files in BED format.

BedFilesReader(Reader) - Constructor for class org.gersteinlab.act.io.BedFilesReader

Create a new reader with source data from an input reader.

BIN_BINARY - Static variable in class org.gersteinlab.act.BinFileCreator

Use the presence of signal as the summary statistic of a bin.

BIN_BINARY_ID - Static variable in class org.gersteinlab.act.BinFileCreator

Use the presence of signal as the summary statistic of a bin.

BIN_MAX - Static variable in class org.gersteinlab.act.BinFileCreator

Use the maximum signal as the summary statistic of a bin.

BIN_MAX_ID - Static variable in class org.gersteinlab.act.BinFileCreator

Use the maximum signal as the summary statistic of a bin.

BIN_MEAN - Static variable in class org.gersteinlab.act.BinFileCreator

Use the mean signal as the summary statistic of a bin.

BIN_MEAN_ID - Static variable in class org.gersteinlab.act.BinFileCreator

Use the mean signal as the summary statistic of a bin.

BinFileCreator - Class in org.gersteinlab.act

This class converts an input signal file into a bin file with a specified bin size.

BinFileCreator() - Constructor for class org.gersteinlab.act.BinFileCreator

br - Variable in class org.gersteinlab.act.io.DataFilesReader

The input reader.

buffer - Variable in class org.gersteinlab.act.util.StringTokenizer2

Data buffer

C

choose(int, int) - Static method in class org.gersteinlab.act.SaturationPlotsCreator

Get the number of ways to choose r balls from n balls.

close() - Method in class org.gersteinlab.act.io.DataFilesReader

Close the reader.

compareTo(Interval) - Method in class org.gersteinlab.act.data.Interval

Compare this interval with an input interval based on natural ordering.

Config - Class in org.gersteinlab.act.util

This class defines a set of configurations.

Config(File) - Constructor for class org.gersteinlab.act.util.Config

Create a new configuration set by reading from a configuration file.

CorrelationsCalculator - Class in org.gersteinlab.act

This class computes the correlations between different datasets.

CorrelationsCalculator() - Constructor for class org.gersteinlab.act.CorrelationsCalculator

countIntervals() - Method in class org.gersteinlab.act.io.DataFilesReader

Get the total number of intervals.

countTokens() - Method in class org.gersteinlab.act.util.StringTokenizer2

D

DataFilesReader - Class in org.gersteinlab.act.io

This class defines a reader of data files.

DataFilesReader(Reader) - Constructor for class org.gersteinlab.act.io.DataFilesReader

Create a new reader with source data from an input reader.

DEF_MAX_COM - Static variable in class org.gersteinlab.act.SaturationPlotsCreator

Default maximum number of combinations.

delim - Variable in class org.gersteinlab.act.util.StringTokenizer2

The delimiters

doubleValue - Variable in class org.gersteinlab.act.data.Interval

The double value of the interval.

doubleValue - Variable in class org.gersteinlab.act.io.WigFilesReader

Double value of the last interval

E

end - Variable in class org.gersteinlab.act.data.Interval

The ending position of the interval, 0-based, not included.

equals(Object) - Method in class org.gersteinlab.act.data.Interval

Check if this interval is semantically equivalent to an input object.

F

forwardCompareTo(Interval) - Method in class org.gersteinlab.act.data.Interval

Compare this interval with an input interval based on forward ordering.

G

getAttribute(String) - Method in class org.gersteinlab.act.data.Interval

Get the value of an attribute.

getChr() - Method in class org.gersteinlab.act.data.Interval

Get the chromosome of the interval.

getConfig(String) - Method in class org.gersteinlab.act.util.Config

Get the value a certain configuration.

getConfigNames() - Method in class org.gersteinlab.act.util.Config

Get the names of the configurations.

getConfigs(String) - Method in class org.gersteinlab.act.util.Config

Get the values of a certain configuration.

getDoubleValue() - Method in class org.gersteinlab.act.data.Interval

Get the double value of the interval.

getEnd() - Method in class org.gersteinlab.act.data.Interval

Get the ending position of the interval.

getLength() - Method in class org.gersteinlab.act.data.Interval

Get the length of the interval.

getMaxOutlier(int, int) - Method in class org.gersteinlab.act.SaturationPlotsCreator.DefaultBoxAndWhiskerCategoryDatasetWithNoFarOuts

getMaxOutlier(Comparable, Comparable) - Method in class org.gersteinlab.act.SaturationPlotsCreator.DefaultBoxAndWhiskerCategoryDatasetWithNoFarOuts

getMinOutlier(int, int) - Method in class org.gersteinlab.act.SaturationPlotsCreator.DefaultBoxAndWhiskerCategoryDatasetWithNoFarOuts

getMinOutlier(Comparable, Comparable) - Method in class org.gersteinlab.act.SaturationPlotsCreator.DefaultBoxAndWhiskerCategoryDatasetWithNoFarOuts

getNormalScoreCorrelation(double[], double[]) - Static method in class org.gersteinlab.act.CorrelationsCalculator

Compute the normal score correlation between two vectors.

getNormalScores(double[]) - Static method in class org.gersteinlab.act.CorrelationsCalculator

Get the normal scores of a set of ranks.

getPearsonCorrelation(double[], double[]) - Static method in class org.gersteinlab.act.CorrelationsCalculator

Compute the Pearson correlation between two vectors.

getRanks(double[]) - Static method in class org.gersteinlab.act.CorrelationsCalculator

Get the ranks [0..length-1] of the values in a vector.

getReader(Config, File) - Static method in class org.gersteinlab.act.io.DataFilesReader

Get a data file reader for a data file.

getSpearmanCorrelation(double[], double[]) - Static method in class org.gersteinlab.act.CorrelationsCalculator

Compute the Spearman correlation between two vectors.

getStart() - Method in class org.gersteinlab.act.data.Interval

Get the starting position of the interval.

getStrand() - Method in class org.gersteinlab.act.data.Interval

Get the strand of the interval.

getUniqueValues(double[]) - Static method in class org.gersteinlab.act.CorrelationsCalculator

Get the unique values and their ranks [0..length-1] in a vector.

GtfFilesReader - Class in org.gersteinlab.act.io

This class defines a reader of data files in GTF format.

GtfFilesReader(Reader) - Constructor for class org.gersteinlab.act.io.GtfFilesReader

Create a new reader with source data from an input reader.

H

hashCode() - Method in class org.gersteinlab.act.data.Interval

Get the hash code of this interval.

hasMoreElements() - Method in class org.gersteinlab.act.util.StringTokenizer2

hasMoreTokens() - Method in class org.gersteinlab.act.util.StringTokenizer2

I

intersects(Interval) - Method in class org.gersteinlab.act.data.Interval

Check if this interval intersects with an input interval.

Interval - Class in org.gersteinlab.act.data

This class defines an interval of genomic locations.

Interval() - Constructor for class org.gersteinlab.act.data.Interval

Create a dummy interval.

Interval(String, long, long) - Constructor for class org.gersteinlab.act.data.Interval

Create an interval.

Interval(String, long, long, char) - Constructor for class org.gersteinlab.act.data.Interval

Create an interval.

intervalStart - Variable in class org.gersteinlab.act.io.WigFilesReader

Starting position of the last interval, 0-based, included

L

lastIsDelim - Variable in class org.gersteinlab.act.util.StringTokenizer2

Whether the last element read from st is a delimiter

M

main(String[]) - Static method in class org.gersteinlab.act.BinFileCreator

main(String[]) - Static method in class org.gersteinlab.act.CorrelationsCalculator

main(String[]) - Static method in class org.gersteinlab.act.SaturationPlotsCreator

MINUS_STRAND - Static variable in class org.gersteinlab.act.data.Interval

The official symbol for the minus strand.

N

NarrowPeakFilesReader - Class in org.gersteinlab.act.io

This class defines a reader of data files in narrowPeak format.

NarrowPeakFilesReader(Reader) - Constructor for class org.gersteinlab.act.io.NarrowPeakFilesReader

Create a new reader with source data from an input reader.

nextElement() - Method in class org.gersteinlab.act.util.StringTokenizer2

nextToken() - Method in class org.gersteinlab.act.util.StringTokenizer2

NORMALSCORE - Static variable in class org.gersteinlab.act.CorrelationsCalculator

Normal-score correlation

O

org.gersteinlab.act - package org.gersteinlab.act

org.gersteinlab.act.data - package org.gersteinlab.act.data

org.gersteinlab.act.io - package org.gersteinlab.act.io

org.gersteinlab.act.util - package org.gersteinlab.act.util

P

PEARSON - Static variable in class org.gersteinlab.act.CorrelationsCalculator

Pearson correlation

PLUS_STRAND - Static variable in class org.gersteinlab.act.data.Interval

The official symbol for the plus strand.

R

readInterval() - Method in class org.gersteinlab.act.io.BedFilesReader

Read the next interval from the reader.

readInterval() - Method in class org.gersteinlab.act.io.DataFilesReader

Read the next interval from the reader.

readInterval() - Method in class org.gersteinlab.act.io.GtfFilesReader

Read the next interval from the reader.

readInterval() - Method in class org.gersteinlab.act.io.NarrowPeakFilesReader

Read the next interval from the reader.

readInterval() - Method in class org.gersteinlab.act.io.WigFilesReader

Read the next interval from the reader.

readIntervals(Collection<Interval>) - Method in class org.gersteinlab.act.io.DataFilesReader

Read all intervals into a collection.

readIntervals(Collection<Interval>, double) - Method in class org.gersteinlab.act.io.DataFilesReader

Read the intervals that contain a given value into a collection.

readVector(File, Config) - Static method in class org.gersteinlab.act.CorrelationsCalculator

Read a vector of values from a data file.

reset() - Method in class org.gersteinlab.act.io.DataFilesReader

Reset the reader.

returnDelims - Variable in class org.gersteinlab.act.util.StringTokenizer2

Whether to return delimiters

S

SaturationPlotsCreator - Class in org.gersteinlab.act

This class produces saturation plots from a set of files, each containing a list of genomic regions.

SaturationPlotsCreator() - Constructor for class org.gersteinlab.act.SaturationPlotsCreator

SaturationPlotsCreator.DefaultBoxAndWhiskerCategoryDatasetWithNoFarOuts - Class in org.gersteinlab.act

SaturationPlotsCreator.DefaultBoxAndWhiskerCategoryDatasetWithNoFarOuts() - Constructor for class org.gersteinlab.act.SaturationPlotsCreator.DefaultBoxAndWhiskerCategoryDatasetWithNoFarOuts

seg - Variable in class org.gersteinlab.act.io.WigFilesReader

Segment of the last interval

setAttribute(String, String) - Method in class org.gersteinlab.act.data.Interval

Set the value of an attribute.

setChr(String) - Method in class org.gersteinlab.act.data.Interval

Set the chromosome of the interval.

setDoubleValue(double) - Method in class org.gersteinlab.act.data.Interval

Set the double value of the interval.

setEnd(long) - Method in class org.gersteinlab.act.data.Interval

Set the ending position of the interval.

setStart(long) - Method in class org.gersteinlab.act.data.Interval

Set the starting position of the interval.

setStrand(char) - Method in class org.gersteinlab.act.data.Interval

Set the strand of the interval.

span - Variable in class org.gersteinlab.act.io.WigFilesReader

The span of each interval

SPEARMAN - Static variable in class org.gersteinlab.act.CorrelationsCalculator

Spearman correlation

st - Variable in class org.gersteinlab.act.util.StringTokenizer2

The underlying string tokenizer

start - Variable in class org.gersteinlab.act.data.Interval

The starting position of the interval, 0-based, included.

step - Variable in class org.gersteinlab.act.io.WigFilesReader

The step size of the intervals

STEP_FIXED - Static variable in class org.gersteinlab.act.io.WigFilesReader

Fixed step format

STEP_VARIABLE - Static variable in class org.gersteinlab.act.io.WigFilesReader

Variable step format

stepType - Variable in class org.gersteinlab.act.io.WigFilesReader

The step type of intervals

strand - Variable in class org.gersteinlab.act.data.Interval

The strand of the interval.

StringTokenizer2 - Class in org.gersteinlab.act.util

This class represents a modified version of StringTokenizer that returns an empty string between two consecutive delimiters.

StringTokenizer2(String) - Constructor for class org.gersteinlab.act.util.StringTokenizer2

StringTokenizer2(String, String) - Constructor for class org.gersteinlab.act.util.StringTokenizer2

StringTokenizer2(String, String, boolean) - Constructor for class org.gersteinlab.act.util.StringTokenizer2

T

toString() - Method in class org.gersteinlab.act.data.Interval

Get a string representation of the interval.

W

WigFilesReader - Class in org.gersteinlab.act.io

This class defines a reader of data files in WIG format.

WigFilesReader(Reader) - Constructor for class org.gersteinlab.act.io.WigFilesReader

Create a new reader with source data from an input reader.

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