All Classes and Interfaces
Class
Description
A factory responsible for building
Dialogs from a supplied YAML file.Implements
ListModel event listening funtionalityA base class for all arguments.
Base class for all argument builders.
Class for perspective dialog argument content.
Definition of argument content formats.
Argument description class.
Enumeration of argument types.
Iterator that is based on stream coming from the Supplier provided.
Bean that provides basic support for Java beans.
Created by sigmar on 05/05/2017.
A wrapper rowSource reading the child rowSource in a thread into a buffer and offering to the main thread in batches
Created by sigmar on 26/04/2017.
BucketCreator<T extends org.gorpipe.gor.table.dictionary.DictionaryEntry>
Helper class to create bucket files from bucket descriptions.
BucketCreatorGorPipe<T extends org.gorpipe.gor.table.dictionary.DictionaryEntry>
Helper class to create bucket file from bucket description.
BucketManager<T extends org.gorpipe.gor.table.dictionary.DictionaryEntry>
BucketManager.Builder<T extends org.gorpipe.gor.table.dictionary.DictionaryEntry>
CalcCompiler implements an Antlr parse tree visitor, starting on an expression node.
Holds a definition of columns that should be grouped together.
Iterate through all combinations (n choose k) and provide permutations representing the combinations.
Represents an argument that expects a date value.
Responsible for building date arguments.
A basic dialog implementation
A wrapper for dialog arguments.
Class for describing a dialog.
The types of dialogs currently supported
LinkTable consist of a link and the the actual data.
Log likelihood calculator for dominant variant association.
Represents an argument that expects a file path.
Responsible for building file arguments.
Table class representing file (gor/gorz/nor/tsv etc)
The internal data is stored in temp files.
Interface for filtering column definition.
Helper functions to parse and create reports with the freemarker parsing engine.
Report builder class for building freemarker based reports via yml files.
Log-likelihood ratio calculator for variant association.
Checks the correctness of phase of haplotypes/genotypes using basic rules.
Chi-squared for 2-by-2 contingency tables.
This class handles the most basic gor pipe execution.
Factory method for creating an instance of the GenericGorRunner class.
Factory class for creating default/generic gor sessions.
Genotype lookup utilities for generating vcf files from horizontal got gt data
Fisher's exact test for 2-by-2 tables.
Compute the log of the Gamma-function for integer values, i.e.,
compute log(n!) for n = 0,1,2,...
Created by sigmar on 21/12/15.
This class merges gor lines from multiple BufferedReaders.
Writes parquet file from a stream of gor/nor rows
Translates a gor/nor row to corresponding format in a parquet file
GorRowFilterFunction<T extends org.gorpipe.gor.model.Row>
This class provides an empty implementation of
GorScriptListener,
which can be extended to create a listener which only needs to handle a subset
of the available methods.This class provides an empty implementation of
GorScriptVisitor,
which can be extended to create a visitor which only needs to handle a subset
of the available methods.This interface defines a complete listener for a parse tree produced by
GorScriptParser.This interface defines a complete generic visitor for a parse tree produced
by
GorScriptParser.Class that stores the session cache on a requestId key.
Table class representing gor file (gor/gorz)
The internal data is stored in temp files.
Utility functions for parsing genotype probability triplets.
Argument for selecting grids or values from grids.
Builder for grid argument.
A class for running simple joint variant calling.
Local implementation of file cache client working directly against the file system.
This program fits a logistic regression model on a given data set.
Provides various useful functions on arrays.
Stub implememntation of FileCache, that doesn't do any caching - for running with caching disabled.
Iterator to access data from a nor dictionary file.
Table class representing nor file.
Created by sigmar on 16/08/2016.
Represents an argument that expects a numeric value.
Responsible for building number arguments.
This class encapsulates a general execution in parallel of the pgor command when a
standard parallel query handler is not used.
Represents a particular perspective onto data returned from a dialog query.
Defines the type of view that should be selected by default when the perspective is activated.
Class for defining a perspective dialog display parameters.
This analysis class collects gor or vcf lines and writes them in batches to a temporary vcf files read by plink2 process
This class stores the phenotype file for plink vcf input header generation
Also the argument to the plink external process
This analysis class collects gor or vcf lines and writes them in batches to a temporary vcf files read by plink2 process
This analysis class collects gor or vcf lines and writes them in batches to a temporary vcf files read by plink2 process
Created by sigmar on 03/11/15.
Created by sigmar on 12/02/16.
Created by sigmar on 12/02/16.
Represents an argument that uses a gor/nor query to create the values the user can select from.
Responsible for building GOR/NOR query arguments.
A number formatter that can constrain values to a minimum and/or maximum value.
Log likelihood calculator for recessive variant association.
Log likelihood calculator for regular variant association.
Report container is implemented by viewmanagers that will display Reports created from Report Forms.
An array of GOR row objects implementing iterator interface
The user class, BatchedReadSource, ensures thread safety
A class which uses a lookup table to compute the sigmoid function x -> 1/(1 + e^(-x)) up to a precision of 10^(-10).
Template model that enables template writer to skip first occurence of a given argument.
Represents an argument that expects a string value.
Responsible for building string arguments.
Class holding information on lists and their content.
Class to manage gor tables (dictionaries and tables).
Variant association algorithm, based on the VAAST algorithm.