Serialized Form

Package gorsat

Package gorsat.parser

Class gorsat.parser.ColumnInfo extends java.lang.Object implements Serializable

Serialized Fields

dataType

java.lang.String dataType

name

java.lang.String name

Class gorsat.parser.ColumnInfo$ extends scala.runtime.AbstractFunction2<java.lang.String,java.lang.String,gorsat.parser.ColumnInfo> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.parser.FixedSizeIteratorCvp extends java.lang.Object implements Serializable

Serialized Fields

curIndex

int curIndex

cvp

org.gorpipe.gor.model.ColumnValueProvider cvp

itemSize

int itemSize

source

java.lang.String source

start

int start

Class gorsat.parser.FixedSizeIteratorCvp$ extends scala.runtime.AbstractFunction3<org.gorpipe.gor.model.ColumnValueProvider,java.lang.String,java.lang.Object,gorsat.parser.FixedSizeIteratorCvp> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.parser.FunctionWrapper extends java.lang.Object implements Serializable

Serialized Fields

bitmap$0

byte bitmap$0

expectedArgs

scala.collection.immutable.List<java.lang.String> expectedArgs

mangledName

java.lang.String mangledName

myFunction

java.lang.Object myFunction

name

java.lang.String name

ReducerSet$module

gorsat.parser.FunctionWrapper.ReducerSet$ ReducerSet$module

returnType

java.lang.String returnType

signature

java.lang.String signature

Class gorsat.parser.FunctionWrapper$ extends scala.runtime.AbstractFunction3<java.lang.String,java.lang.String,java.lang.Object,gorsat.parser.FunctionWrapper> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.parser.IteratorCvp extends java.lang.Object implements Serializable

Serialized Fields

curEnd

int curEnd

curIndex

int curIndex

curStart

int curStart

cvp

org.gorpipe.gor.model.ColumnValueProvider cvp

delimiter

java.lang.String delimiter

next

scala.Function0<scala.runtime.BoxedUnit> next

singleCharDelimiter

char singleCharDelimiter

source

java.lang.String source

start

int start

Class gorsat.parser.IteratorCvp$ extends scala.runtime.AbstractFunction3<org.gorpipe.gor.model.ColumnValueProvider,java.lang.String,java.lang.String,gorsat.parser.IteratorCvp> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.parser.ParseArith extends java.lang.Object implements Serializable

Serialized Fields

$tilde$module

scala.util.parsing.combinator.Parsers.$tilde$ $tilde$module

calcLambda

TypedCalcLambda calcLambda

compileAntlr

boolean compileAntlr

compileClassic

boolean compileClassic

context

org.gorpipe.gor.session.GorContext context

doubleCols

scala.collection.immutable.List<java.lang.String> doubleCols

Error$module

scala.util.parsing.combinator.Parsers.Error$ Error$module

executeNor

boolean executeNor

Failure$module

scala.util.parsing.combinator.Parsers.Failure$ Failure$module

gorsat$parser$ParseArith$$columnNames

java.lang.String[] gorsat$parser$ParseArith$$columnNames

gorsat$parser$ParseArith$$columns

scala.collection.immutable.Map<java.lang.String,gorsat.parser.ColumnInfo> gorsat$parser$ParseArith$$columns

gorsat$parser$ParseArith$$doubleVariableMap

scala.collection.immutable.Map<java.lang.String,java.lang.Object> gorsat$parser$ParseArith$$doubleVariableMap

gorsat$parser$ParseArith$$intVariableMap

scala.collection.immutable.Map<java.lang.String,java.lang.Object> gorsat$parser$ParseArith$$intVariableMap

gorsat$parser$ParseArith$$longVariableMap

scala.collection.immutable.Map<java.lang.String,java.lang.Object> gorsat$parser$ParseArith$$longVariableMap

intCols

scala.collection.immutable.List<java.lang.String> intCols

NoSuccess$module

scala.util.parsing.combinator.Parsers.NoSuccess$ NoSuccess$module

orgColNames

java.lang.String[] orgColNames

orgColTypes

java.lang.String[] orgColTypes

outputType

java.lang.String outputType

refSeq

org.gorpipe.model.gor.iterators.RefSeq refSeq

rs

org.gorpipe.gor.model.GenomicIterator rs

runAntlr

boolean runAntlr

runClassic

boolean runClassic

stringCols

scala.collection.immutable.List<java.lang.String> stringCols

stringVariableMap

scala.collection.immutable.Map<java.lang.String,java.lang.Object> stringVariableMap

subFilters

java.util.ArrayList<gorsat.parser.ParseArith> subFilters

Success$module

scala.util.parsing.combinator.Parsers.Success$ Success$module

whiteSpace

scala.util.matching.Regex whiteSpace

Class gorsat.parser.ParseArith$ extends java.lang.Object implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.parser.ReplaceCvp extends java.lang.Object implements Serializable

Serialized Fields

cvp

org.gorpipe.gor.model.ColumnValueProvider cvp

replaceCol

int replaceCol

Class gorsat.parser.ReplaceCvp$ extends scala.runtime.AbstractFunction1<org.gorpipe.gor.model.ColumnValueProvider,gorsat.parser.ReplaceCvp> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.parser.TypedExpression extends java.lang.Object implements Serializable

Serialized Fields

expression

java.lang.Object expression

expressionType

java.lang.String expressionType

Class gorsat.parser.TypedExpression$ extends scala.runtime.AbstractFunction2<java.lang.String,java.lang.Object,gorsat.parser.TypedExpression> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Package gorsat.process

Class gorsat.process.ProcessIteratorAdaptor extends org.gorpipe.gor.model.GenomicIteratorBase implements Serializable

Serialized Fields

allowerror

boolean allowerror

breader

java.io.BufferedReader breader

errorStr

java.lang.StringBuilder errorStr

is

java.io.InputStream is

line

java.lang.String line

mustReCheck

boolean mustReCheck

myHasNext

boolean myHasNext

nor

boolean nor

outThread

gorsat.process.ProcessIteratorAdaptor.OutThread outThread

proc

java.lang.Process proc

processName

java.lang.String processName

rowSource

java.util.Iterator<org.gorpipe.gor.model.Row> rowSource

skipheader

boolean skipheader

Class gorsat.process.SourceProvider extends java.lang.Object implements Serializable

Serialized Fields

context

org.gorpipe.gor.session.GorContext context

dynSource

gorsat.DynIterator.DynamicRowSource dynSource

executeNor

boolean executeNor

header

java.lang.String header

inputSource

java.lang.String inputSource

isNor

boolean isNor

iteratorCommand

java.lang.String iteratorCommand

source

org.gorpipe.gor.model.GenomicIterator source

usedFiles

java.lang.String[] usedFiles

Class gorsat.process.SourceProvider$ extends java.lang.Object implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Package gorsat.Regression

Class gorsat.Regression.LogisticRegressionFit extends java.lang.Object implements Serializable

Serialized Fields

b

breeze.linalg.DenseVector<java.lang.Object> b

converged

boolean converged

exploded

boolean exploded

fisher

scala.Option<breeze.linalg.DenseMatrix<java.lang.Object>> fisher

logLkhd

double logLkhd

nIter

int nIter

score

scala.Option<breeze.linalg.DenseVector<java.lang.Object>> score

Class gorsat.Regression.LogisticRegressionFit$ extends scala.runtime.AbstractFunction7<breeze.linalg.DenseVector<java.lang.Object>,scala.Option<breeze.linalg.DenseVector<java.lang.Object>>,scala.Option<breeze.linalg.DenseMatrix<java.lang.Object>>,java.lang.Object,java.lang.Object,java.lang.Object,java.lang.Object,gorsat.Regression.LogisticRegressionFit> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Regression.WaldStats extends java.lang.Object implements Serializable

Serialized Fields

b

breeze.linalg.DenseVector<java.lang.Object> b

p

breeze.linalg.DenseVector<java.lang.Object> p

se

breeze.linalg.DenseVector<java.lang.Object> se

z

breeze.linalg.DenseVector<java.lang.Object> z

Class gorsat.Regression.WaldStats$ extends scala.runtime.AbstractFunction4<breeze.linalg.DenseVector<java.lang.Object>,breeze.linalg.DenseVector<java.lang.Object>,breeze.linalg.DenseVector<java.lang.Object>,breeze.linalg.DenseVector<java.lang.Object>,gorsat.Regression.WaldStats> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Package gorsat.Script

Class gorsat.Script.CommandEntry extends java.lang.Object implements Serializable

Serialized Fields

batchGroupName

java.lang.String batchGroupName

cacheFile

java.lang.String cacheFile

createName

java.lang.String createName

query

java.lang.String query

Class gorsat.Script.CommandEntry$ extends scala.runtime.AbstractFunction4<java.lang.String,java.lang.String,java.lang.String,java.lang.String,gorsat.Script.CommandEntry> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Script.CommandGroup extends java.lang.Object implements Serializable

Serialized Fields

commandEntries

java.util.List<gorsat.Script.CommandEntry> commandEntries

removeFromCreate

boolean removeFromCreate

Class gorsat.Script.CommandGroup$ extends scala.runtime.AbstractFunction2<java.util.List<gorsat.Script.CommandEntry>,java.lang.Object,gorsat.Script.CommandGroup> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Script.ExecutionBatch extends java.lang.Object implements Serializable

Serialized Fields

executionBlocks

scala.collection.mutable.ListBuffer<gorsat.Script.ExecutionBlock> executionBlocks

executionCommands

scala.collection.mutable.ListBuffer<gorsat.Script.ExecutionCommand> executionCommands

level

int level

Class gorsat.Script.ExecutionBatch$ extends scala.runtime.AbstractFunction1<java.lang.Object,gorsat.Script.ExecutionBatch> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Script.ExecutionBlock extends java.lang.Object implements Serializable

Serialized Fields

batchGroupName

java.lang.String batchGroupName

cachePath

java.lang.String cachePath

dependencies

java.lang.String[] dependencies

groupName

java.lang.String groupName

hasForkWrite

boolean hasForkWrite

isDictionary

boolean isDictionary

query

java.lang.String query

signature

java.lang.String signature

Class gorsat.Script.ExecutionBlock$ extends scala.runtime.AbstractFunction8<java.lang.String,java.lang.String,java.lang.String,java.lang.String[],java.lang.String,java.lang.String,java.lang.Object,java.lang.Object,gorsat.Script.ExecutionBlock> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Script.ExecutionCommand extends java.lang.Object implements Serializable

Serialized Fields

batchGroupName

java.lang.String batchGroupName

cacheFile

java.lang.String cacheFile

createName

java.lang.String createName

query

java.lang.String query

signature

java.lang.String signature

Class gorsat.Script.ExecutionCommand$ extends scala.runtime.AbstractFunction5<java.lang.String,java.lang.String,java.lang.String,java.lang.String,java.lang.String,gorsat.Script.ExecutionCommand> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Script.ExecutionGraph extends java.lang.Object implements Serializable

Serialized Fields

blocks

java.util.Map<java.lang.String,gorsat.Script.ExecutionBlock> blocks

gorCommands

java.lang.String[] gorCommands

levels

scala.collection.immutable.List<gorsat.Script.ExecutionBlock>[] levels

remainingBlocks

java.util.Map<java.lang.String,gorsat.Script.ExecutionBlock> remainingBlocks

root

gorsat.Script.ExecutionBlock root

Class gorsat.Script.ExecutionGraph$ extends scala.runtime.AbstractFunction1<java.lang.String[],gorsat.Script.ExecutionGraph> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Script.MacroInfo extends java.lang.Object implements Serializable

Serialized Fields

commandArguments

gorsat.Commands.CommandArguments commandArguments

name

java.lang.String name

Class gorsat.Script.MacroInfo$ extends java.lang.Object implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Script.MacroParsingResult extends java.lang.Object implements Serializable

Serialized Fields

aliases

java.util.Map<java.lang.String,java.lang.String> aliases

createCommands

java.util.LinkedHashMap<java.lang.String,gorsat.Script.ExecutionBlock> createCommands

virtualFiles

scala.collection.immutable.Map<java.lang.String,java.lang.String> virtualFiles

Class gorsat.Script.MacroParsingResult$ extends scala.runtime.AbstractFunction3<java.util.LinkedHashMap<java.lang.String,gorsat.Script.ExecutionBlock>,scala.collection.immutable.Map<java.lang.String,java.lang.String>,java.util.Map<java.lang.String,java.lang.String>,gorsat.Script.MacroParsingResult> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Script.ScriptResult extends java.lang.Object implements Serializable

Serialized Fields

aliases

java.util.Map<java.lang.String,java.lang.String> aliases

createdFiles

scala.collection.immutable.Map<java.lang.String,java.lang.String> createdFiles

equivalentVirtualFiles

scala.collection.immutable.List<scala.Tuple2<java.lang.String,java.lang.String>> equivalentVirtualFiles

gorCommand

java.lang.String gorCommand

Class gorsat.Script.ScriptResult$ extends scala.runtime.AbstractFunction4<java.lang.String,scala.collection.immutable.Map<java.lang.String,java.lang.String>,scala.collection.immutable.List<scala.Tuple2<java.lang.String,java.lang.String>>,java.util.Map<java.lang.String,java.lang.String>,gorsat.Script.ScriptResult> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Script.SplitEntry extends java.lang.Object implements Serializable

Serialized Fields

chrom

java.lang.String chrom

end

int end

start

int start

tag

java.lang.String tag

Class gorsat.Script.SplitEntry$ extends scala.runtime.AbstractFunction4<java.lang.String,java.lang.Object,java.lang.Object,java.lang.String,gorsat.Script.SplitEntry> implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Class gorsat.Script.SplitManager extends java.lang.Object implements Serializable

Serialized Fields

chromosomeSplits

scala.collection.immutable.Map<java.lang.String,gorsat.Script.SplitEntry> chromosomeSplits

groupName

java.lang.String groupName

replacementPattern

java.lang.String replacementPattern

Class gorsat.Script.SplitManager$ extends java.lang.Object implements Serializable

Serialization Methods

readResolve

private java.lang.Object readResolve()

Serialized Fields

CHROM_PATTERN

java.lang.String CHROM_PATTERN

MAX_CHROM_SIZE

int MAX_CHROM_SIZE

MAXIMUM_NUMBER_OF_SPLITS

int MAXIMUM_NUMBER_OF_SPLITS

RANGETAG_PATTERN

java.lang.String RANGETAG_PATTERN

REGULAR_REPLACEMENT_PATTERN

java.lang.String REGULAR_REPLACEMENT_PATTERN

SPLIT_REPLACEMENT_PATTERN

java.lang.String SPLIT_REPLACEMENT_PATTERN

START_PATTERN

java.lang.String START_PATTERN

STOP_PATTERN

java.lang.String STOP_PATTERN

WHERE_SPLIT_WINDOW

java.lang.String WHERE_SPLIT_WINDOW

Package org.gorpipe.gor.function

Class org.gorpipe.gor.function.GorRowFilterFunction extends java.lang.Object implements Serializable

Serialized Fields

booleanFunction

scala.Function1<org.gorpipe.gor.model.ColumnValueProvider,java.lang.Object> booleanFunction

Class org.gorpipe.gor.function.GorRowInferFunction extends java.lang.Object implements Serializable

Class org.gorpipe.gor.function.GorRowMapFunction extends java.lang.Object implements Serializable

Serialized Fields

calcType

java.lang.String calcType

func

scala.Function1 func

Class org.gorpipe.gor.function.GorRowQueryFunction extends java.lang.Object implements Serializable

Serialized Fields

bufferedPipeStep

gorsat.Commands.Analysis bufferedPipeStep

header

java.lang.String header

lra

ListRowAdaptor lra

query

java.lang.String query

Package org.gorpipe.gor.util

Class org.gorpipe.gor.util.ByteTextBuilder extends java.lang.Object implements Serializable

serialVersionUID:

1L

Serialized Fields

bytes

byte[] bytes

pos

int pos

Class org.gorpipe.gor.util.DoubleArray extends java.lang.Object implements Serializable

Serialized Fields

array

double[] array

pos

int pos

Class org.gorpipe.gor.util.GLongHashMap extends java.lang.Object implements Serializable

Serialized Fields

count

int count

keys

long[] keys

lengthminusone

int lengthminusone

loadfactor

float loadfactor

used

int[] used

values

int[] values

Class org.gorpipe.gor.util.IntHashMap extends java.lang.Object implements Serializable

Serialized Fields

count

int count

keys

int[] keys

lengthminusone

int lengthminusone

loadfactor

float loadfactor

used

int[] used

values

int[] values

Package org.gorpipe.querydialogs

Class org.gorpipe.querydialogs.AbstractListBean extends BasicBean implements Serializable

Serialized Fields

listenerList

javax.swing.event.EventListenerList listenerList

Class org.gorpipe.querydialogs.Argument extends AbstractListBean implements Serializable

Serialized Fields

advanced

boolean advanced

allowedValues

java.util.List<java.lang.Object> allowedValues

argDescr

ArgumentDescription argDescr

currentOperator

java.lang.String currentOperator

defaultValue

java.lang.Object defaultValue

displayWidth

java.lang.Integer displayWidth

operators

java.util.List<java.lang.String> operators

optional

boolean optional

type

ArgumentType type

value

java.lang.Object value

valuesHeader

java.lang.String[] valuesHeader

valuesPath

java.net.URI valuesPath

Class org.gorpipe.querydialogs.BasicBean extends java.lang.Object implements Serializable

serialVersionUID:

1L

Serialized Fields

changeSupport

java.beans.PropertyChangeSupport changeSupport

Class org.gorpipe.querydialogs.Dialog extends AbstractListBean implements Serializable

Serialized Fields

advancedArgumentsVisible

boolean advancedArgumentsVisible

argumentListener

java.beans.PropertyChangeListener argumentListener

argumentMap

java.util.Map<java.lang.String,Argument> argumentMap

arguments

java.util.List<java.lang.String> arguments

attributes

java.util.Map<java.lang.String,? extends java.lang.Object> attributes

baseChartColumns

java.lang.String baseChartColumns

baseChartDF

ChartDataType baseChartDF

baseChartExec

java.lang.String baseChartExec

baseChartMd5Digest

java.lang.String baseChartMd5Digest

baseChartScript

java.lang.String baseChartScript

baseQuery

java.lang.String baseQuery

baseQueryMd5Digest

java.lang.String baseQueryMd5Digest

chartColumns

java.lang.String[] chartColumns

deferUpdates

boolean deferUpdates

DIALOG_TEMPLATE_LOADER

freemarker.cache.StringTemplateLoader DIALOG_TEMPLATE_LOADER

dialogDescription

DialogDescription dialogDescription

errorMsgTemplate

java.lang.String errorMsgTemplate

executable

boolean executable

fileResolver

org.gorpipe.gor.model.FileReader fileResolver

gitSHA

java.lang.String gitSHA

hasErrorMsgTemplate

boolean hasErrorMsgTemplate

hasLongRunningQuery

boolean hasLongRunningQuery

interpolatedChart

java.lang.String interpolatedChart

interpolatedQuery

java.lang.String interpolatedQuery

longRunningQueryTemplate

java.lang.String longRunningQueryTemplate

packageVersion

java.lang.String packageVersion

projectName

java.lang.String projectName

queryEval

org.gorpipe.gor.model.QueryEvaluator queryEval

TEMPLATE_CONFIG

freemarker.template.Configuration TEMPLATE_CONFIG

type

DialogType type

version

java.lang.String version

Class org.gorpipe.querydialogs.GridArgument extends StringArgument implements Serializable

Serialized Fields

extractValues

java.lang.Boolean extractValues

Defines whether grid values or grid name should be used in selector.

gorOnly

java.lang.Boolean gorOnly

Defines if only gor grids should be selected.

requiredColumns

java.util.List<org.gorpipe.gor.model.RequiredColumn> requiredColumns

Grid required columns.

requiredColumnsOnly

java.lang.Boolean requiredColumnsOnly

Defines if only required columns may exist in grid.

Class org.gorpipe.querydialogs.RangedNumberFormatter extends javax.swing.text.NumberFormatter implements Serializable

Package org.gorpipe.querydialogs.argument

Class org.gorpipe.querydialogs.argument.DateArgument extends Argument implements Serializable

Class org.gorpipe.querydialogs.argument.FileArgument extends Argument implements Serializable

Serialized Fields

fileFilterComponents

java.util.List<java.lang.String> fileFilterComponents

Class org.gorpipe.querydialogs.argument.NumberArgument extends Argument implements Serializable

Serialized Fields

formatter

RangedNumberFormatter formatter

maxTextFieldMinWidth

int maxTextFieldMinWidth

minTextFieldMinWidth

int minTextFieldMinWidth

valueTextFieldMinWidth

int valueTextFieldMinWidth

Class org.gorpipe.querydialogs.argument.QueryArgument extends Argument implements Serializable

Serialized Fields

query

java.lang.String query

queryEvaluator

org.gorpipe.gor.model.QueryEvaluator queryEvaluator

Class org.gorpipe.querydialogs.argument.StringArgument extends Argument implements Serializable

Serialized Fields

format

java.lang.String format

formatter

ValueFormatter formatter

helpDefinition

FilteringColumnDefinition helpDefinition

persistingValueObject

SubjectLists persistingValueObject

quoted

boolean quoted

singleSelection

boolean singleSelection

Package org.gorpipe.querydialogs.factory

Class org.gorpipe.querydialogs.factory.PerspectiveDialog extends Dialog implements Serializable

Serialized Fields

columnGroups

java.util.List<ColumnGroup> columnGroups

dialogsFilePath

java.nio.file.Path dialogsFilePath

displayParams

PerspectiveDialogDisplayParams displayParams

htmlTemplate

java.lang.String htmlTemplate

initialColumns

java.util.Set<java.lang.Object> initialColumns

perspectives

java.util.List<Perspective> perspectives

reportCommands

java.util.List<org.gorpipe.gor.model.ReportCommand> reportCommands

reportViewer

ReportViewer reportViewer

writePath

java.lang.String writePath