All Classes
| Class | Description |
|---|---|
| AbstractDialogFactory<T extends Dialog> |
A factory responsible for building
Dialogs from a supplied YAML file. |
| AbstractListBean |
Implements
ListModel event listening funtionality |
| AdjustedGORLine | |
| AdjustedGORLineIterator | |
| Argument |
A base class for all arguments.
|
| ArgumentBuilder |
Base class for all argument builders.
|
| ArgumentContent |
Class for perspective dialog argument content.
|
| ArgumentContent.Format |
Definition of argument content formats.
|
| ArgumentDescription |
Argument description class.
|
| ArgumentType |
Enumeration of argument types.
|
| BaseStreamIterator |
Iterator that is based on stream coming from the Supplier provided.
|
| BashCmd | |
| BasicBean |
Bean that provides basic support for Java beans.
|
| BatchedPipeStepIteratorAdaptor |
Created by sigmar on 05/05/2017.
|
| BatchedReadSource |
A wrapper rowSource reading the child rowSource in a thread into a buffer and offering to the main thread in batches
|
| BatchedReadSourceConfig |
Created by sigmar on 26/04/2017.
|
| BucketCreator<T extends org.gorpipe.gor.table.BucketableTableEntry> |
Helper class to create bucket files from bucket descriptions.
|
| BucketCreatorGorPipe<T extends org.gorpipe.gor.table.BucketableTableEntry> |
Helper class to create bucket file from bucket description.
|
| BucketizeCommand | |
| BucketManager<T extends org.gorpipe.gor.table.BucketableTableEntry> | |
| BucketManager.BucketPackLevel | |
| BucketManager.Builder<T extends org.gorpipe.gor.table.BucketableTableEntry> | |
| CacheCommand | |
| CalcCompiler |
CalcCompiler implements an Antlr parse tree visitor, starting on an expression node.
|
| CalcLambdaBoolean | |
| CalcLambdaDouble | |
| CalcLambdaDoubleConstant | |
| CalcLambdaInteger | |
| CalcLambdaIntegerConstant | |
| CalcLambdaLong | |
| CalcLambdaLongConstant | |
| CalcLambdaNumeric | |
| CalcLambdaString | |
| CalcLambdaStringConstant | |
| CalcLambdaVariable | |
| CdCmd | |
| ColumnGroup |
Holds a definition of columns that should be grouped together.
|
| CombinationIterator |
Iterate through all combinations (n choose k) and provide permutations representing the combinations.
|
| CommandBucketizeOptions | |
| Commands | |
| CommandsCommand | |
| Constant | |
| CreateCmd | |
| CvpBooleanLambda | |
| CvpDoubleLambda | |
| CvpIntegerLambda | |
| CvpLongLambda | |
| CvpStringLambda | |
| DateArgument |
Represents an argument that expects a date value.
|
| DateArgumentBuilder |
Responsible for building date arguments.
|
| DefCmd | |
| DeleteBucketCommand | |
| DeleteCommand | |
| Dialog |
A basic dialog implementation
|
| DialogArgumentWrapper |
A wrapper for dialog arguments.
|
| DialogDescription |
Class for describing a dialog.
|
| DialogType |
The types of dialogs currently supported
|
| DominantLogLikelihood |
Log likelihood calculator for dominant variant association.
|
| ExitCmd | |
| FileArgument |
Represents an argument that expects a file path.
|
| FileArgumentBuilder |
Responsible for building file arguments.
|
| FilteringColumnDefinition |
Interface for filtering column definition.
|
| FilterOptions | |
| FormattingOptions | |
| FreemarkerQueryUtilities |
Helper functions to parse and create reports with the freemarker parsing engine.
|
| FreemarkerReportBuilder |
Report builder class for building freemarker based reports via yml files.
|
| GavaLogLikelihood |
Log-likelihood ratio calculator for variant association.
|
| GBasicRulesCalculator |
Checks the correctness of phase of haplotypes/genotypes using basic rules.
|
| GChiSquared2by2 |
Chi-squared for 2-by-2 contingency tables.
|
| GenericGorRunner |
This class handles the most basic gor pipe execution.
|
| GenericRunnerFactory |
Factory method for creating an instance of the GenericGorRunner class.
|
| GenericSessionFactory |
Factory class for creating default/generic gor sessions.
|
| GenotypeLookupUtilities |
Genotype lookup utilities for generating vcf files from horizontal got gt data
|
| GFisherExact2by2 |
Fisher's exact test for 2-by-2 tables.
|
| GLogGamma |
Compute the log of the Gamma-function for integer values, i.e.,
compute log(n!) for n = 0,1,2,...
|
| GorBench | |
| GorCLI | |
| GorConfigDoc |
A main class to scan through the runtime classpath and find all descendants of
Config. |
| GorConstants | |
| GorJavaUtilities |
Created by sigmar on 21/12/15.
|
| GorJavaUtilities.CmdParams | |
| GorJavaUtilities.PRPRPRValue | |
| GorJavaUtilities.PRPRValue | |
| GorJavaUtilities.VCFValue | |
| GORLine |
This class merges gor lines from multiple BufferedReaders.
|
| GorLogbackUtil | |
| GorMeta |
Main class to get meta information about gor files/urls resolved through the
gor driver.
|
| GorParquetFileOut | |
| GorParquetWriter |
Writes parquet file from a stream of gor/nor rows
|
| GorParquetWriter.GorParquetBuilder | |
| GorParquetWriteSupport |
Translates a gor/nor row to corresponding format in a parquet file
|
| GorParsingError | |
| GorQueryHandler | |
| GorRowFilterFunction<T extends org.gorpipe.gor.model.Row> | |
| GorRowInferFunction |
For map-reduce type inferance, such as in SparkSQL which needs a schema
The gor type syntax, I for Int, D for Double and S for String
Two rows with types I and S are reduced to type S etc.
|
| GorRowMapFunction | |
| GorRowQueryFunction | |
| GorScriptAnalyzer | |
| GorScriptBaseListener |
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. |
| GorScriptBaseVisitor<T> |
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. |
| GorScriptLexer | |
| GorScriptListener |
This interface defines a complete listener for a parse tree produced by
GorScriptParser. |
| GorScriptParser | |
| GorScriptParser.ArgumentContext | |
| GorScriptParser.Calc_commandContext | |
| GorScriptParser.Calc_expression_listContext | |
| GorScriptParser.Calc_expressionContext | |
| GorScriptParser.Column_listContext | |
| GorScriptParser.Column_nameContext | |
| GorScriptParser.Column_numberContext | |
| GorScriptParser.Column_rangeContext | |
| GorScriptParser.Column_refContext | |
| GorScriptParser.Column_rename_ruleContext | |
| GorScriptParser.Column_selectionContext | |
| GorScriptParser.Column_wildcardContext | |
| GorScriptParser.Compare_expressionsContext | |
| GorScriptParser.Create_statementContext | |
| GorScriptParser.Def_macroContext | |
| GorScriptParser.ExpressionContext | |
| GorScriptParser.FactorContext | |
| GorScriptParser.FilenameContext | |
| GorScriptParser.Function_callContext | |
| GorScriptParser.Function_exprContext | |
| GorScriptParser.Function_nameContext | |
| GorScriptParser.Generic_commandContext | |
| GorScriptParser.Gor_expressionContext | |
| GorScriptParser.Gornor_expressionContext | |
| GorScriptParser.Hide_commandContext | |
| GorScriptParser.If_exprContext | |
| GorScriptParser.In_expressionContext | |
| GorScriptParser.Indag_expressionContext | |
| GorScriptParser.Input_sourceContext | |
| GorScriptParser.Macro_nameContext | |
| GorScriptParser.Macro_valueContext | |
| GorScriptParser.Nested_queryContext | |
| GorScriptParser.Nor_expressionContext | |
| GorScriptParser.Not_rel_exprContext | |
| GorScriptParser.NumberContext | |
| GorScriptParser.Option_valueContext | |
| GorScriptParser.Optional_power_factorContext | |
| GorScriptParser.OptionContext | |
| GorScriptParser.Options_and_argsContext | |
| GorScriptParser.Paren_exprContext | |
| GorScriptParser.Paren_rel_exprContext | |
| GorScriptParser.Pgor_expressionContext | |
| GorScriptParser.Pipe_commandContext | |
| GorScriptParser.Power_factorContext | |
| GorScriptParser.Predicate_factorContext | |
| GorScriptParser.PredicateContext | |
| GorScriptParser.Query_expressionContext | |
| GorScriptParser.Rel_exprContext | |
| GorScriptParser.Rel_termContext | |
| GorScriptParser.Rename_commandContext | |
| GorScriptParser.Replace_commandContext | |
| GorScriptParser.ScriptContext | |
| GorScriptParser.Select_commandContext | |
| GorScriptParser.Signed_factorContext | |
| GorScriptParser.String_literal_listContext | |
| GorScriptParser.String_literalContext | |
| GorScriptParser.TermContext | |
| GorScriptParser.ValueContext | |
| GorScriptParser.VariableContext | |
| GorScriptParser.Virtual_relation_nameContext | |
| GorScriptParser.Virtual_relationContext | |
| GorScriptParser.Where_commandContext | |
| GorScriptParser.XfactorContext | |
| GorScriptVisitor<T> |
This interface defines a complete generic visitor for a parse tree produced
by
GorScriptParser. |
| GorSessionCacheManager |
Class that stores the session cache on a requestId key.
|
| GorSessionFactory | |
| GorShell | |
| GorShell.Settings | |
| GorShellSessionFactory | |
| GorStreamIterator | |
| GorToolsCLI | |
| GPParser |
Utility functions for parsing genotype probability triplets.
|
| GridArgument |
Argument for selecting grids or values from grids.
|
| GridArgumentBuilder |
Builder for grid argument.
|
| GTGen |
A class for running simple joint variant calling.
|
| HelpCmd | |
| HelpCommand | |
| HelpOptions | |
| IndexCommand | |
| InfoCommand | |
| InputsCommand | |
| InsertCommand | |
| IOTestAnalyser | |
| LinearAlgebra | |
| LinearRegression | |
| ListRowAdaptor | |
| LocalFileCacheClient |
Local implementation of file cache client working directly against the file system.
|
| LogisticRegression |
This program fits a logistic regression model on a given data set.
|
| LsCmd | |
| MacrosCommand | |
| MainWindow | |
| ManagerCommand | |
| ManagerOptions | |
| MathArrayUtils |
Provides various useful functions on arrays.
|
| MultiInsertCommand | |
| NetworkTemplateLoader | |
| NoCacheFileCacheClient |
Stub implememntation of FileCache, that doesn't do any caching - for running with caching disabled.
|
| NordIterator |
Iterator to access data from a nor dictionary file.
|
| NordIteratorEntry | |
| NorStreamIterator | |
| NorToGorPipeStep |
Created by sigmar on 16/08/2016.
|
| NumberArgument |
Represents an argument that expects a numeric value.
|
| NumberArgumentBuilder |
Responsible for building number arguments.
|
| OptionEvaluator | |
| ParallelExecutor |
This class encapsulates a general execution in parallel of the pgor command when a
standard parallel query handler is not used.
|
| Perspective |
Represents a particular perspective onto data returned from a dialog query.
|
| Perspective.VIEW_TYPE |
Defines the type of view that should be selected by default when the perspective is activated.
|
| PerspectiveDialog | |
| PerspectiveDialogDisplayParams |
Class for defining a perspective dialog display parameters.
|
| PerspectiveDialogFactory | |
| PlinkAdjustAdaptor |
This analysis class collects gor or vcf lines and writes them in batches to a temporary vcf files read by plink2 process
|
| PlinkAdjustment | |
| PlinkArguments |
This class stores the phenotype file for plink vcf input header generation
Also the argument to the plink external process
|
| PlinkProcessAdaptor |
This analysis class collects gor or vcf lines and writes them in batches to a temporary vcf files read by plink2 process
|
| PlinkVcfProcessAdaptor |
This analysis class collects gor or vcf lines and writes them in batches to a temporary vcf files read by plink2 process
|
| PositionCacheCmd | |
| PowerLookupTable | |
| ProcessIteratorAdaptor |
Created by sigmar on 03/11/15.
|
| ProcessRowSource |
Created by sigmar on 12/02/16.
|
| ProcessSource |
Created by sigmar on 12/02/16.
|
| PurgeCommand | |
| PwdCmd | |
| QueryArgument |
Represents an argument that uses a gor/nor query to create the values the user can select from.
|
| QueryArgumentBuilder |
Responsible for building GOR/NOR query arguments.
|
| QueryCommand | |
| QueryEvalMethodModel | |
| QueryRunner | |
| RangedNumberFormatter |
A number formatter that can constrain values to a minimum and/or maximum value.
|
| RecessiveLogLikelihood |
Log likelihood calculator for recessive variant association.
|
| RegularLogLikelihood |
Log likelihood calculator for regular variant association.
|
| RenderCommand | |
| RenderOptions | |
| ReportCommand | |
| ReportViewer |
Report container is implemented by viewmanagers that will display Reports created from Report Forms.
|
| RequestStats | |
| RowBuffer |
An array of GOR row objects implementing iterator interface
The user class, BatchedReadSource, ensures thread safety
|
| ScriptCmd | |
| ScriptCommand | |
| SelectCommand | |
| SemanticChecker | |
| SessionBasedQueryEvaluator | |
| SetCmd | |
| SetCmd.ConfigFile | |
| SetCmd.DisplayResults | |
| SetCmd.RequestStats | |
| SetCmd.Timing | |
| SigmoidFunction |
A class which uses a lookup table to compute the sigmoid function x -> 1/(1 + e^(-x)) up to a precision of 10^(-10).
|
| SkipFirstMethodModel |
Template model that enables template writer to skip first occurence of a given argument.
|
| StatisticalAdjustment | |
| StringArgument |
Represents an argument that expects a string value.
|
| StringArgumentBuilder |
Responsible for building string arguments.
|
| SubjectLists |
Class holding information on lists and their content.
|
| SyntaxChecker | |
| TableManager |
Class to manage gor tables (dictionaries and tables).
|
| TableManager.Builder | |
| TableManagerCLI |
Command line interface for the table manager.
|
| TestCommand | |
| TestIsLockCommand | |
| TestReadLockCommand | |
| TestWriteLockCommand | |
| TouchCommand | |
| ValueFormatter | |
| VariantAssociation |
Variant association algorithm, based on the VAAST algorithm.
|
| VariantCounts |