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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.
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