Serialized Form

Package gorsat

Package gorsat.parser

Class gorsat.parser.ColumnInfo

class ColumnInfo extends Object implements Serializable

Serialized Fields

dataType

String dataType

name

String name

Class gorsat.parser.ColumnInfo$

class ColumnInfo$ extends scala.runtime.AbstractFunction2<String,String,gorsat.parser.ColumnInfo> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.parser.FixedSizeIteratorCvp

class FixedSizeIteratorCvp extends Object implements Serializable

Serialized Fields

curIndex

int curIndex

cvp

org.gorpipe.gor.model.ColumnValueProvider cvp

itemSize

int itemSize

source

String source

start

int start

Class gorsat.parser.FixedSizeIteratorCvp$

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

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.parser.FunctionWrapper

class FunctionWrapper extends Object implements Serializable

Serialized Fields

bitmap$0

byte bitmap$0

expectedArgs

scala.collection.immutable.List<String> expectedArgs

mangledName

String mangledName

myFunction

Object myFunction

name

String name

ReducerSet$module

gorsat.parser.FunctionWrapper.ReducerSet$ ReducerSet$module

returnType

String returnType

signature

String signature

Class gorsat.parser.FunctionWrapper$

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

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.parser.IteratorCvp

class IteratorCvp extends Object implements Serializable

Serialized Fields

curEnd

int curEnd

curIndex

int curIndex

curStart

int curStart

cvp

org.gorpipe.gor.model.ColumnValueProvider cvp

delimiter

String delimiter

next

scala.Function0<scala.runtime.BoxedUnit> next

singleCharDelimiter

char singleCharDelimiter

source

String source

start

int start

Class gorsat.parser.IteratorCvp$

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

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.parser.ParseArith

class ParseArith extends 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<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

String[] gorsat$parser$ParseArith$$columnNames

gorsat$parser$ParseArith$$columns

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

gorsat$parser$ParseArith$$doubleVariableMap

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

gorsat$parser$ParseArith$$intVariableMap

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

gorsat$parser$ParseArith$$longVariableMap

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

intCols

scala.collection.immutable.List<String> intCols

NoSuccess$module

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

orgColNames

String[] orgColNames

orgColTypes

String[] orgColTypes

outputType

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<String> stringCols

stringVariableMap

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

subFilters

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$

class ParseArith$ extends Object implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.parser.ReplaceCvp

class ReplaceCvp extends Object implements Serializable

Serialized Fields

cvp

org.gorpipe.gor.model.ColumnValueProvider cvp

replaceCol

int replaceCol

Class gorsat.parser.ReplaceCvp$

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

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.parser.TypedExpression

class TypedExpression extends Object implements Serializable

Serialized Fields

expression

Object expression

expressionType

String expressionType

Class gorsat.parser.TypedExpression$

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

Serialization Methods

readResolve

private Object readResolve()

Package gorsat.process

Class gorsat.process.ProcessIteratorAdaptor

class ProcessIteratorAdaptor extends org.gorpipe.gor.model.GenomicIteratorBase implements Serializable

Serialized Fields

allowerror

boolean allowerror

breader

BufferedReader breader

errorStr

StringBuilder errorStr

is

InputStream is

line

String line

mustReCheck

boolean mustReCheck

myHasNext

boolean myHasNext

nor

boolean nor

outThread

gorsat.process.ProcessIteratorAdaptor.OutThread outThread

proc

Process proc

processName

String processName

rowSource

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

skipheader

boolean skipheader

Class gorsat.process.SourceProvider

class SourceProvider extends Object implements Serializable

Serialized Fields

context

org.gorpipe.gor.session.GorContext context

dynSource

gorsat.DynIterator.DynamicRowSource dynSource

executeNor

boolean executeNor

header

String header

inputSource

String inputSource

isNor

boolean isNor

iteratorCommand

String iteratorCommand

source

org.gorpipe.gor.model.GenomicIterator source

usedFiles

String[] usedFiles

Class gorsat.process.SourceProvider$

class SourceProvider$ extends Object implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Package gorsat.Regression

Class gorsat.Regression.LogisticRegressionFit

class LogisticRegressionFit extends Object implements Serializable

Serialized Fields

b

breeze.linalg.DenseVector<Object> b

converged

boolean converged

exploded

boolean exploded

fisher

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

logLkhd

double logLkhd

nIter

int nIter

score

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

Class gorsat.Regression.LogisticRegressionFit$

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

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Regression.WaldStats

class WaldStats extends Object implements Serializable

Serialized Fields

b

breeze.linalg.DenseVector<Object> b

p

breeze.linalg.DenseVector<Object> p

se

breeze.linalg.DenseVector<Object> se

z

breeze.linalg.DenseVector<Object> z

Class gorsat.Regression.WaldStats$

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

Serialization Methods

readResolve

private Object readResolve()

Package gorsat.Script

Class gorsat.Script.CommandEntry

class CommandEntry extends Object implements Serializable

Serialized Fields

batchGroupName

String batchGroupName

cacheFile

String cacheFile

createName

String createName

query

String query

Class gorsat.Script.CommandEntry$

class CommandEntry$ extends scala.runtime.AbstractFunction4<String,String,String,String,gorsat.Script.CommandEntry> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Script.CommandGroup

class CommandGroup extends Object implements Serializable

Serialized Fields

commandEntries

List<gorsat.Script.CommandEntry> commandEntries

removeFromCreate

boolean removeFromCreate

Class gorsat.Script.CommandGroup$

class CommandGroup$ extends scala.runtime.AbstractFunction2<List<gorsat.Script.CommandEntry>,Object,gorsat.Script.CommandGroup> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Script.ExecutionBatch

class ExecutionBatch extends 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$

class ExecutionBatch$ extends scala.runtime.AbstractFunction1<Object,gorsat.Script.ExecutionBatch> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Script.ExecutionBlock

class ExecutionBlock extends Object implements Serializable

Serialized Fields

batchGroupName

String batchGroupName

cachePath

String cachePath

dependencies

String[] dependencies

groupName

String groupName

hasForkWrite

boolean hasForkWrite

isDictionary

boolean isDictionary

query

String query

signature

String signature

Class gorsat.Script.ExecutionBlock$

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

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Script.ExecutionCommand

class ExecutionCommand extends Object implements Serializable

Serialized Fields

batchGroupName

String batchGroupName

cacheFile

String cacheFile

createName

String createName

query

String query

signature

String signature

Class gorsat.Script.ExecutionCommand$

class ExecutionCommand$ extends scala.runtime.AbstractFunction5<String,String,String,String,String,gorsat.Script.ExecutionCommand> implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Script.ExecutionGraph

class ExecutionGraph extends Object implements Serializable

Serialized Fields

blocks

Map<String,gorsat.Script.ExecutionBlock> blocks

gorCommands

String[] gorCommands

levels

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

remainingBlocks

Map<String,gorsat.Script.ExecutionBlock> remainingBlocks

root

gorsat.Script.ExecutionBlock root

Class gorsat.Script.ExecutionGraph$

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

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Script.MacroInfo

class MacroInfo extends Object implements Serializable

Serialized Fields

commandArguments

gorsat.Commands.CommandArguments commandArguments

name

String name

Class gorsat.Script.MacroInfo$

class MacroInfo$ extends Object implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Script.MacroParsingResult

class MacroParsingResult extends Object implements Serializable

Serialized Fields

aliases

Map<String,String> aliases

createCommands

LinkedHashMap<String,gorsat.Script.ExecutionBlock> createCommands

virtualFiles

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

Class gorsat.Script.MacroParsingResult$

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

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Script.ScriptResult

class ScriptResult extends Object implements Serializable

Serialized Fields

aliases

Map<String,String> aliases

createdFiles

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

equivalentVirtualFiles

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

gorCommand

String gorCommand

Class gorsat.Script.ScriptResult$

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

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Script.SplitEntry

class SplitEntry extends Object implements Serializable

Serialized Fields

chrom

String chrom

end

int end

start

int start

tag

String tag

Class gorsat.Script.SplitEntry$

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

Serialization Methods

readResolve

private Object readResolve()

Class gorsat.Script.SplitManager

class SplitManager extends Object implements Serializable

Serialized Fields

chromosomeSplits

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

groupName

String groupName

replacementPattern

String replacementPattern

Class gorsat.Script.SplitManager$

class SplitManager$ extends Object implements Serializable

Serialization Methods

readResolve

private Object readResolve()

Serialized Fields

CHROM_PATTERN

String CHROM_PATTERN

MAX_CHROM_SIZE

int MAX_CHROM_SIZE

MAXIMUM_NUMBER_OF_SPLITS

int MAXIMUM_NUMBER_OF_SPLITS

RANGETAG_PATTERN

String RANGETAG_PATTERN

REGULAR_REPLACEMENT_PATTERN

String REGULAR_REPLACEMENT_PATTERN

SPLIT_REPLACEMENT_PATTERN

String SPLIT_REPLACEMENT_PATTERN

START_PATTERN

String START_PATTERN

STOP_PATTERN

String STOP_PATTERN

WHERE_SPLIT_WINDOW

String WHERE_SPLIT_WINDOW

Package org.gorpipe.gor.function

Class org.gorpipe.gor.function.GorRowFilterFunction

class GorRowFilterFunction extends Object implements Serializable

Serialized Fields

booleanFunction

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

Class org.gorpipe.gor.function.GorRowInferFunction

class GorRowInferFunction extends Object implements Serializable

Class org.gorpipe.gor.function.GorRowMapFunction

class GorRowMapFunction extends Object implements Serializable

Serialized Fields

calcType

String calcType

func

scala.Function1 func

Class org.gorpipe.gor.function.GorRowQueryFunction

class GorRowQueryFunction extends Object implements Serializable

Serialized Fields

bufferedPipeStep

gorsat.Commands.Analysis bufferedPipeStep

header

String header

lra

ListRowAdaptor lra

query

String query

Package org.gorpipe.gor.util

Class org.gorpipe.gor.util.ByteTextBuilder

class ByteTextBuilder extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

bytes

byte[] bytes

pos

int pos

Class org.gorpipe.gor.util.DoubleArray

class DoubleArray extends Object implements Serializable

Serialized Fields

array

double[] array

pos

int pos

Class org.gorpipe.gor.util.GLongHashMap

class GLongHashMap extends 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

class IntHashMap extends 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

class AbstractListBean extends BasicBean implements Serializable

Serialized Fields

listenerList

EventListenerList listenerList

Class org.gorpipe.querydialogs.Argument

class Argument extends AbstractListBean implements Serializable

Serialized Fields

advanced

boolean advanced

allowedValues

List<Object> allowedValues

argDescr

ArgumentDescription argDescr

currentOperator

String currentOperator

defaultValue

Object defaultValue

displayWidth

Integer displayWidth

operators

List<String> operators

optional

boolean optional

type

ArgumentType type

value

Object value

valuesHeader

String[] valuesHeader

valuesPath

URI valuesPath

Class org.gorpipe.querydialogs.BasicBean

class BasicBean extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

changeSupport

PropertyChangeSupport changeSupport

Class org.gorpipe.querydialogs.Dialog

class Dialog extends AbstractListBean implements Serializable

Serialized Fields

advancedArgumentsVisible

boolean advancedArgumentsVisible

argumentListener

PropertyChangeListener argumentListener

argumentMap

Map<String,Argument> argumentMap

arguments

List<String> arguments

attributes

Map<String,? extends Object> attributes

baseChartColumns

String baseChartColumns

baseChartDF

ChartDataType baseChartDF

baseChartExec

String baseChartExec

baseChartMd5Digest

String baseChartMd5Digest

baseChartScript

String baseChartScript

baseQuery

String baseQuery

baseQueryMd5Digest

String baseQueryMd5Digest

chartColumns

String[] chartColumns

deferUpdates

boolean deferUpdates

DIALOG_TEMPLATE_LOADER

freemarker.cache.StringTemplateLoader DIALOG_TEMPLATE_LOADER

dialogDescription

DialogDescription dialogDescription

errorMsgTemplate

String errorMsgTemplate

executable

boolean executable

fileResolver

org.gorpipe.gor.model.FileReader fileResolver

gitSHA

String gitSHA

hasErrorMsgTemplate

boolean hasErrorMsgTemplate

hasLongRunningQuery

boolean hasLongRunningQuery

interpolatedChart

String interpolatedChart

interpolatedQuery

String interpolatedQuery

longRunningQueryTemplate

String longRunningQueryTemplate

packageVersion

String packageVersion

projectName

String projectName

queryEval

org.gorpipe.gor.model.QueryEvaluator queryEval

TEMPLATE_CONFIG

freemarker.template.Configuration TEMPLATE_CONFIG

type

DialogType type

version

String version

Class org.gorpipe.querydialogs.GridArgument

class GridArgument extends StringArgument implements Serializable

Serialized Fields

extractValues

Boolean extractValues

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

gorOnly

Boolean gorOnly

Defines if only gor grids should be selected.

requiredColumns

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

Grid required columns.

requiredColumnsOnly

Boolean requiredColumnsOnly

Defines if only required columns may exist in grid.

Class org.gorpipe.querydialogs.RangedNumberFormatter

class RangedNumberFormatter extends NumberFormatter implements Serializable

Package org.gorpipe.querydialogs.argument

Class org.gorpipe.querydialogs.argument.DateArgument

class DateArgument extends Argument implements Serializable

Class org.gorpipe.querydialogs.argument.FileArgument

class FileArgument extends Argument implements Serializable

Serialized Fields

fileFilterComponents

List<String> fileFilterComponents

Class org.gorpipe.querydialogs.argument.FormatArgument

class FormatArgument extends Argument implements Serializable

Serialized Fields

format

String format

formatter

ValueFormatter formatter

quoted

boolean quoted

Class org.gorpipe.querydialogs.argument.NumberArgument

class 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

class QueryArgument extends FormatArgument implements Serializable

Serialized Fields

query

String query

queryEvaluator

org.gorpipe.gor.model.QueryEvaluator queryEvaluator

Class org.gorpipe.querydialogs.argument.StringArgument

class StringArgument extends FormatArgument implements Serializable

Serialized Fields

helpDefinition

FilteringColumnDefinition helpDefinition

persistingValueObject

SubjectLists persistingValueObject

singleSelection

boolean singleSelection

Package org.gorpipe.querydialogs.factory

Class org.gorpipe.querydialogs.factory.PerspectiveDialog

class PerspectiveDialog extends Dialog implements Serializable

Serialized Fields

columnGroups

List<ColumnGroup> columnGroups

dialogsFilePath

Path dialogsFilePath

displayParams

PerspectiveDialogDisplayParams displayParams

htmlTemplate

String htmlTemplate

initialColumns

Set<Object> initialColumns

perspectives

List<Perspective> perspectives

reportCommands

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

reportViewer

ReportViewer reportViewer

writePath

String writePath