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