A B C D E F G H I J K L M N O P R S T U V W X Y

A

Abstract2DChartRenderer<T> - Class in org.expasy.jpl.commons.collection.render
 
Abstract2DChartRenderer(XYItemRenderer) - Constructor for class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
Abstract2DChartRenderer(XYItemRenderer, ImageFormat, Dimension) - Constructor for class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
AbstractApplicationParameters - Class in org.expasy.jpl.commons.app
A basic command line parameter handler.
AbstractApplicationParameters(Class<?>, String, String, String[]) - Constructor for class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
AbstractDataSymbolRegister<T> - Class in org.expasy.jpl.commons.collection.symbol
Generic data symbol manager to include in jpl.
AbstractDataSymbolRegister(Symbol.SymbolType<T>) - Constructor for class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
AbstractDecorator<T> - Class in org.expasy.jpl.commons.base
A Decorator is a design pattern allowing new behaviour or responsabilities to be added to an existing T-object dynamically.
AbstractDecorator(T) - Constructor for class org.expasy.jpl.commons.base.AbstractDecorator
 
AbstractDoublesArrayIndexComparator - Class in org.expasy.jpl.commons.collection.sorter
Abstract class for comparator of array of doubles.
AbstractDoublesArrayIndexComparator() - Constructor for class org.expasy.jpl.commons.collection.sorter.AbstractDoublesArrayIndexComparator
 
AbstractIntsArrayIndexComparator - Class in org.expasy.jpl.commons.collection.sorter
Abstract class for comparator of array of ints.
AbstractIntsArrayIndexComparator() - Constructor for class org.expasy.jpl.commons.collection.sorter.AbstractIntsArrayIndexComparator
 
AbstractListIndexComparator<T> - Class in org.expasy.jpl.commons.collection.sorter
Generic abstract class for comparator of list of Objects.
AbstractListIndexComparator() - Constructor for class org.expasy.jpl.commons.collection.sorter.AbstractListIndexComparator
 
AbstractObjectsArrayIndexComparator<T> - Class in org.expasy.jpl.commons.collection.sorter
Generic abstract class for comparator of array of Objects.
AbstractObjectsArrayIndexComparator() - Constructor for class org.expasy.jpl.commons.collection.sorter.AbstractObjectsArrayIndexComparator
 
AbstractOperator<U,V> - Class in org.expasy.jpl.commons.base.cond.operator.api
Abstract class to derivate by concrete Operators.
AbstractOperator() - Constructor for class org.expasy.jpl.commons.base.cond.operator.api.AbstractOperator
 
AbstractSequencePositioner<T> - Class in org.expasy.jpl.commons.collection.symbol.seq
This class provides a skeletal implementation of the PositionIterable interface, to minimize the effort required to implement this interface.
AbstractSequencePositioner() - Constructor for class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner
 
AbstractSequencePositioner.Iterator - Class in org.expasy.jpl.commons.collection.symbol.seq
This inner class provides implementations for next() and hasNext() needed from Iterator interface.
AbstractSequencePositioner.Iterator() - Constructor for class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner.Iterator
 
AbstractStringBasedComparator<T,V> - Class in org.expasy.jpl.commons.collection.sorter
The base class for {@code StringBasedC
AbstractStringBasedComparator(Transformer<T, V>) - Constructor for class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
AbstractStringBasedComparator(AbstractStringBasedComparator.OrderType, Transformer<T, V>) - Constructor for class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
AbstractStringBasedComparator(String, Transformer<T, V>) - Constructor for class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
AbstractStringBasedComparator.OrderType - Enum in org.expasy.jpl.commons.collection.sorter
 
AbstractSymbol<T> - Class in org.expasy.jpl.commons.collection.symbol
The basic symbol class.
AbstractSymbol() - Constructor for class org.expasy.jpl.commons.collection.symbol.AbstractSymbol
for serialization only
AbstractSymbol(char, Symbol.SymbolType<T>) - Constructor for class org.expasy.jpl.commons.collection.symbol.AbstractSymbol
 
AbstractSymbolType<T> - Class in org.expasy.jpl.commons.collection.symbol
 
AbstractSymbolType(String, Class<? extends Symbol<T>>, String) - Constructor for class org.expasy.jpl.commons.collection.symbol.AbstractSymbolType
 
accessor(Transformer<T, ?>) - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl.Builder
set the path from T to ?
add(Transformer<T, T>) - Method in class org.expasy.jpl.commons.base.process.SequenceTransformer
Add a transformer.
add(IntegerSequence) - Method in class org.expasy.jpl.commons.collection.IntegerSequenceWithGap
 
addAll(List<Transformer<T, T>>) - Method in class org.expasy.jpl.commons.base.process.SequenceTransformer
Add a list of transformers.
addAlphabet(AlphabetImpl<T>) - Method in class org.expasy.jpl.commons.collection.symbol.SymbolTable
 
addAnnotInDefaultSeries(XYTextAnnotation) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
addCategory(XYSeries) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
addChild(TreeNode<T>) - Method in interface org.expasy.jpl.commons.collection.tree.TreeNode
Add the given child to the node.
addChild(TreeNode<T>) - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
addColumnName(String) - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
Add a column name
addComparator(Comparator<T>) - Method in class org.expasy.jpl.commons.collection.sorter.ChainedComparator
 
addData(Collection<TypedDatum>) - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
addDataInSeries(int, double, double) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
addDataSet(T, String) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
addDataSet(HistogramDataSet, String) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Add the statistical data set (default colors: 1st serie (blue), 2nd serie (red)).
addDataSet(HistogramDataSet, String, Color) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Add the statistical data set.
addDatum(String, TypedDatum.Type, Object) - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
addDatum(TypedDatum<T>) - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
addEdge(E, V, V) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
addEdge(E, V, V, EdgeType) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
addField(String, DataTableFactory.TypeManager.IType) - Method in class org.expasy.jpl.commons.base.record.DataTableFactory.Builder
Add a new field defined by its name and a string-value to ?-value converter.
addField(String) - Method in class org.expasy.jpl.commons.base.record.DataTableFactory.Builder
Add a new field defined by its name and a string-typed value.
addMultiDataSet(T) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
addNewRecord(Properties) - Method in class org.expasy.jpl.commons.base.record.DataTable
Create and add a new instance of internal class Record with values.
addProperty(String, T) - Method in class org.expasy.jpl.commons.base.GenericProperties
Add a new property with a name and a value.
addSettings(Properties) - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
addToCurrentDataSeries(double, double) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
addTransformer(Transformer<U1, U2>) - Method in class org.expasy.jpl.commons.base.process.U2VSequenceTransformer
 
addType(Class<T>, Transformer<String, T>) - Method in class org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager
 
addValue(double) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Add value.
addValueColumn(List<Double>) - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
Add a value array
addValueRow(List<Double>) - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
 
addValues(double[]) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Add values.
addValuesFromDist(DiscreteDistribution, int) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Add values from discrete distribution.
addValuesFromDist(ContinuousDistribution, int) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Add values from continuous distribution.
addVertex(V) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
addWeight(double) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Add weight value.
addWeights(double[]) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Add weights.
allowAmbiguity() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl.Builder
 
alphabet - Variable in class org.expasy.jpl.commons.collection.symbol.AbstractSymbolType
 
Alphabet<T> - Interface in org.expasy.jpl.commons.collection.symbol
This Alphabet interface is implemented by any alphabet.
AlphabetException - Exception in org.expasy.jpl.commons.collection.symbol
 
AlphabetException() - Constructor for exception org.expasy.jpl.commons.collection.symbol.AlphabetException
 
AlphabetException(String) - Constructor for exception org.expasy.jpl.commons.collection.symbol.AlphabetException
 
AlphabetException(Throwable) - Constructor for exception org.expasy.jpl.commons.collection.symbol.AlphabetException
 
AlphabetException(String, Throwable) - Constructor for exception org.expasy.jpl.commons.collection.symbol.AlphabetException
 
AlphabetImpl<T> - Class in org.expasy.jpl.commons.collection.symbol
An alphabet is a finite set of symbols.
alphabets - Variable in class org.expasy.jpl.commons.collection.symbol.SymbolTable
 
AlphabetView<T> - Interface in org.expasy.jpl.commons.collection.symbol
This AlphabetView interface is implemented by any read-only alphabet.
ambiguityEnabled() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl.Builder
 
aminoAcidMotifPattern - Variable in class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher
Motif searched on SymbolSequenceImpl object
ArrayIndexComparator - Interface in org.expasy.jpl.commons.collection.sorter
Objects implementing this interface can compare two arguments values for order, via the method to implement int compare(Integer o1, Integer o2), found at given indices of a given array.
ArrayIndexSorter - Class in org.expasy.jpl.commons.collection.sorter
This class sort indices of an array object given an index comparator.
ArrayIndexSorter(Object, ArrayIndexComparator) - Constructor for class org.expasy.jpl.commons.collection.sorter.ArrayIndexSorter
Default constructor
ArraySorter<T> - Interface in org.expasy.jpl.commons.collection.sorter
A ArraySorter interface have to be implemented by any object that sort arrays.
ArraySorterImpl<T extends Comparable<T>> - Class in org.expasy.jpl.commons.collection.sorter
ArraySorter can sort any generic arrays or get sorted indices.
asIntList(int[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Convert ints to List of Integers.
asList(T[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Convert arrays of Ts to List of Ts.
asSet(T...) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
Create a new instance of HashSet from a list of elements.
assign(String) - Method in class org.expasy.jpl.commons.base.TypedDatum
 
assign(T) - Method in class org.expasy.jpl.commons.base.TypedDatum
 
assignDatum(String, Object) - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
asTreeSet(T...) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
Create a new instance of TreeSet from a list of elements.

B

BarChartRenderer - Interface in org.expasy.jpl.commons.base.render
A bar chart renderer is a chart renderer with configurable bar width.
BarCode - Class in org.expasy.jpl.commons.collection
TODO:
BarCode() - Constructor for class org.expasy.jpl.commons.collection.BarCode
 
BarCodeRenderer<T extends Number> - Class in org.expasy.jpl.commons.collection.render
TODO: This object renders BarCode objects.
binNumber(int) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Set the number of bins.
binWidth() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
binWidth(double) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Set the width of each bin.
BOOLEAN - Static variable in class org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager
 
build() - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl.Builder
 
build() - Method in interface org.expasy.jpl.commons.base.builder.InstanceBuilder
Build an instance of T-type object.
build() - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl.Builder
Build an instance of ConditionImpl after checking everything is ok
build() - Method in class org.expasy.jpl.commons.base.record.DataTableFactory.Builder
Build an instance of DataTableFactory.
build() - Method in class org.expasy.jpl.commons.collection.graph.GraphExporter.Builder
 
build() - Method in class org.expasy.jpl.commons.collection.IntegerSequence.Builder
 
build() - Method in class org.expasy.jpl.commons.collection.Interval.Builder
 
build() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Build an instance of BinnedPeakListImpl.
build() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl.Builder
 
BuilderBasedParser<CT,BT extends InstanceBuilder<?>> - Interface in org.expasy.jpl.commons.base.io
Implementers of this interface are CT-typed parsers transmitting parsed data into a BT-typed builder.
BuilderException - Exception in org.expasy.jpl.commons.base.builder
This exception is thrown by a Builder when an object cannot been correctly built.
BuilderException() - Constructor for exception org.expasy.jpl.commons.base.builder.BuilderException
Empty constructor.
BuilderException(String) - Constructor for exception org.expasy.jpl.commons.base.builder.BuilderException
Constructs a new BuilderException object.
BuilderException(Throwable) - Constructor for exception org.expasy.jpl.commons.base.builder.BuilderException
 
BuilderException(String, Throwable) - Constructor for exception org.expasy.jpl.commons.base.builder.BuilderException
 
by(int) - Method in class org.expasy.jpl.commons.collection.IntegerSequence.Builder
 
byteArrayToInt(byte[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Convert an array of bytes into integer value.

C

Cachable - Interface in org.expasy.jpl.commons.collection
 
cache() - Method in class org.expasy.jpl.commons.collection.Interval.Builder
 
calcIQR(List<Double>) - Static method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates inter quartile range (IQR) of all values
calcMaximum(List<Double>) - Static method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates maximum of all values
calcMean(List<Double>) - Static method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates mean of all values
calcMinimum(List<Double>) - Static method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates minimum of all values
calcPercentile(List<Double>, double) - Static method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates quantile value of all values
calcScoreBinParamsFromData() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calc score bins from the provided lists of scores
calcScoreBins() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates the mids of the score bins
calcVariance(List<Double>) - Static method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates sample variance of all values
ChainedComparator<T> - Class in org.expasy.jpl.commons.collection.sorter
A generic comparator that sorts Ts considering multiple criteria.
ChainedStringCodedComparator<T> - Class in org.expasy.jpl.commons.collection.sorter
This class is a chained StringCodedComparator as it is a ChainedComparator where each comparators are instanciate from string.
charAt(int) - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SymbolSequence
 
charAt(int) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
 
ChartRenderer - Interface in org.expasy.jpl.commons.base.render
All chart renderers will have to implements these methods.
checkBounds(int) - Method in class org.expasy.jpl.commons.collection.PartitionList
Get the indices of T-objects int the ith partition.
clear() - Method in class org.expasy.jpl.commons.base.process.SequenceTransformer
Remove all transformers.
clear() - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
clear() - Method in class org.expasy.jpl.commons.collection.PoolImpl
Clear the register.
clear() - Method in interface org.expasy.jpl.commons.collection.Register
Clear the register.
clear() - Method in class org.expasy.jpl.commons.collection.sorter.ChainedComparator
 
clearDataSet() - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Empty data set.
clearDataSet() - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Empty data set.
clone() - Method in class org.expasy.jpl.commons.base.CounterImpl
Creates and returns a copy of this CounterImpl.
clone() - Method in interface org.expasy.jpl.commons.base.ExplicitlyCloneable
duplicate the object
clone() - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
clone(Graph<V, E>) - Method in class org.expasy.jpl.commons.collection.graph.GraphCloner
 
clone() - Method in class org.expasy.jpl.commons.collection.Interval
 
clone() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
 
collapse(Graph<V, E>, Graph<V, E>) - Method in class org.expasy.jpl.commons.collection.graph.GraphCollapser
 
CollectionUtils - Class in org.expasy.jpl.commons.collection
Provides static utility method for Collections.
CollectionUtils() - Constructor for class org.expasy.jpl.commons.collection.CollectionUtils
 
CombinationFactory - Class in org.expasy.jpl.commons.base.math
Generate all combinations of p things among n.
CombinationFactory() - Constructor for class org.expasy.jpl.commons.base.math.CombinationFactory
 
comparator - Variable in class org.expasy.jpl.commons.collection.sorter.ArrayIndexSorter
a Comparator of values found for a couple of index
ComparatorInverter<T> - Class in org.expasy.jpl.commons.collection.sorter
A comparator inverter.
compare(Double, Double) - Method in class org.expasy.jpl.commons.base.math.DoubleComparator
 
compare(Object, Object) - Method in class org.expasy.jpl.commons.collection.graph.GraphExporter.ObjectComparator
 
compare(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.IntervalComparator
 
compare(Integer, Integer) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractDoublesArrayIndexComparator
 
compare(Integer, Integer) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractIntsArrayIndexComparator
 
compare(Integer, Integer) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractListIndexComparator
 
compare(Integer, Integer) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractObjectsArrayIndexComparator
 
compare(T, T) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
compare(T, T) - Method in class org.expasy.jpl.commons.collection.sorter.ChainedComparator
 
compare(T, T) - Method in class org.expasy.jpl.commons.collection.sorter.ChainedStringCodedComparator
 
compare(T, T) - Method in class org.expasy.jpl.commons.collection.sorter.ComparatorInverter
 
compare(T, T) - Method in class org.expasy.jpl.commons.collection.sorter.NumberStringBasedComparator
 
compare(T, T) - Method in class org.expasy.jpl.commons.collection.sorter.StringStringBasedComparator
 
computeCombNumber(int, int) - Static method in class org.expasy.jpl.commons.base.math.CombinationFactory
Compute the number of all the combinations of p elements among n.
computeSize(Interval, int, boolean) - Static method in class org.expasy.jpl.commons.collection.IntegerSequence
Compute the number of integers in the sequence form an interval.
computeSize(double, double, double) - Static method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Compute the number of bins.
computeTupleNumber(int[]) - Static method in class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory
Compute the number of all the t-uples given the radices.
Condition<T> - Interface in org.expasy.jpl.commons.base.cond
The Condition interface should be implemented by any condition that have to be tested on any T-object.
ConditionBasedFilterReady<T> - Interface in org.expasy.jpl.commons.base.cond
All object containing filters based on Condition have to implement this interface.
ConditionImpl<T,V> - Class in org.expasy.jpl.commons.base.cond
Conditional statement where a T-object may meet the condition on a V-value given an operator.
ConditionImpl.Builder<T,V> - Class in org.expasy.jpl.commons.base.cond
A builder to ease the construction of conditions
ConditionImpl.Builder(V) - Constructor for class org.expasy.jpl.commons.base.cond.ConditionImpl.Builder
 
ConditionImpl.ConditionRuntimeException - Exception in org.expasy.jpl.commons.base.cond
Thrown when condition problem met.
ConditionImpl.ConditionRuntimeException() - Constructor for exception org.expasy.jpl.commons.base.cond.ConditionImpl.ConditionRuntimeException
 
ConditionImpl.ConditionRuntimeException(String) - Constructor for exception org.expasy.jpl.commons.base.cond.ConditionImpl.ConditionRuntimeException
 
ConditionImpl.ConditionRuntimeException(String, Throwable) - Constructor for exception org.expasy.jpl.commons.base.cond.ConditionImpl.ConditionRuntimeException
 
ConditionImpl.ConditionRuntimeException(Throwable) - Constructor for exception org.expasy.jpl.commons.base.cond.ConditionImpl.ConditionRuntimeException
 
ConditionInterpreter<T> - Class in org.expasy.jpl.commons.base.cond
ConditionInterpreter translates condition type expressions into Condition.
contains(T) - Method in interface org.expasy.jpl.commons.base.DomainOfDefinition
 
contains(Number) - Method in class org.expasy.jpl.commons.collection.Interval
Return true if the given number is found in this interval.
convert(String) - Static method in class org.expasy.jpl.commons.base.io.FilenameValidator
 
convert2ints(Object[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Convert objects to ints.
convertDecimal2Tuple(int, int) - Static method in class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory
Convert decimal to t-uple of given radix.
convertDecimal2Tuple(int, int, int) - Static method in class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory
Convert decimal to t-uple of given radix.
convertString2Tuple(String) - Static method in class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory
Convert string to t-uple.
convertTuple2Decimal(int[], int) - Static method in class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory
Convert a tuple from radix to radix 10 (decimal).
copy(File, File) - Static method in class org.expasy.jpl.commons.base.io.JPLFile
 
CountableRecords<T> - Interface in org.expasy.jpl.commons.base.record
This interface should be implemented by classes that want to store T objects and keep counts.
Counter - Interface in org.expasy.jpl.commons.base
A Counter interface should be implemented by any counters that handle objects counting.
CounterImpl - Class in org.expasy.jpl.commons.base
CounterImpl is a simple counter and a better alternative than Integer as a new instance is created each time you want to set the value.
createAppOptions() - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
add the app specific options
createBaseSettings() - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
createDataMap() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
createDataMap() - Method in interface org.expasy.jpl.commons.collection.symbol.DataSymbolRegister
 
createFromString(String) - Method in interface org.expasy.jpl.commons.base.builder.StringBasedFactory
Create an instance of T-type object from string if code is null or empty, T will have to be have an default status
createFromString(String) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
createFromString(String) - Method in class org.expasy.jpl.commons.collection.sorter.ChainedStringCodedComparator
 
createFromString(String) - Method in class org.expasy.jpl.commons.collection.sorter.NumberStringBasedComparator
 
createFromString(String) - Method in class org.expasy.jpl.commons.collection.sorter.StringCodedComparatorFactory
 
createFromString(String) - Method in class org.expasy.jpl.commons.collection.sorter.StringStringBasedComparator
 

D

DataRecord - Interface in org.expasy.jpl.commons.base.record
A data record is a set of typed field and values.
dataset - Variable in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
DataSymbolRegister<T> - Interface in org.expasy.jpl.commons.collection.symbol
A symbol manager makes the link between symbols and T-typed data.
DataTable - Class in org.expasy.jpl.commons.base.record
DataTable is a kind of naive relational database table.
DataTable.Record - Class in org.expasy.jpl.commons.base.record
Data table record internal class (immutable).
DataTableFactory - Class in org.expasy.jpl.commons.base.record
This factory creates instance of DataTable defined by their description of fields (or columns) composed by a name and an associated type (String by default).
DataTableFactory(DataTableFactory.Builder) - Constructor for class org.expasy.jpl.commons.base.record.DataTableFactory
The builder-based constructor.
DataTableFactory.Builder - Class in org.expasy.jpl.commons.base.record
The builder class that builds DataTableFactory.
DataTableFactory.Builder() - Constructor for class org.expasy.jpl.commons.base.record.DataTableFactory.Builder
Constructor
DataTableFactory.TypeManager - Class in org.expasy.jpl.commons.base.record
 
DataTableFactory.TypeManager.IType - Interface in org.expasy.jpl.commons.base.record
 
DecimalFormatFactory - Class in org.expasy.jpl.commons.base.io
Create an instance of Locale.US DecimalFormats through static factory methods.
DecimalFormatFactory() - Constructor for class org.expasy.jpl.commons.base.io.DecimalFormatFactory
 
decoratedObject - Variable in class org.expasy.jpl.commons.base.AbstractDecorator
 
decrement() - Method in interface org.expasy.jpl.commons.base.Counter
Decrement counter by 1.
decrement(int) - Method in interface org.expasy.jpl.commons.base.Counter
Decrement counter by dec.
decrement() - Method in class org.expasy.jpl.commons.base.CounterImpl
Decrement counter by 1.
decrement(int) - Method in class org.expasy.jpl.commons.base.CounterImpl
Decrement counter by dec.
deepSizeOf(Object) - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
Returns deep size of object, recursively iterating over its fields and superclasses.
DEFAULT_BIN_WIDTH - Static variable in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
default bin width
DEFAULT_DIMENSION - Static variable in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
DEFAULT_EPSILON - Static variable in class org.expasy.jpl.commons.base.math.DoubleComparator
 
DEFAULT_IMAGE_FORMAT - Static variable in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
DEFAULT_ORDER_TYPE - Static variable in class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
DEFAULT_PRECISION - Static variable in class org.expasy.jpl.commons.base.io.DecimalFormatFactory
exponent value
DEFAULT_SMOOTHING_WINDOW_WIDTH - Static variable in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
default window width
defaultInput(String) - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl.Builder
 
depthSearchFirst(E, Set<E>, boolean) - Static method in class org.expasy.jpl.commons.collection.tree.TreeViewImpl
Recursive depth search first.
deserialize(String) - Method in class org.expasy.jpl.commons.base.io.Serializer
 
deserialize(byte[]) - Method in class org.expasy.jpl.commons.base.io.Serializer
Deserializes a T-object from an array of bytes.
deserialize(ByteBuffer) - Method in class org.expasy.jpl.commons.base.io.Serializer
Deserializes a T-object from a ByteBuffer.
disableBinRenderMode() - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
All the values will be rendered (slow down rendering if lots of data).
DomainOfDefinition<T> - Interface in org.expasy.jpl.commons.base
The DomainOfDefinition interface has to be implemented by all class that defines specific domain of definition.
doReadHeader() - Method in class org.expasy.jpl.commons.base.io.TabFileReader
Ask whether header line is read
DOUBLE - Static variable in class org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager
 
DoubleComparator - Class in org.expasy.jpl.commons.base.math
 
doubles2Doubles(double[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Convert array of doubles to array of Doubles.
doubleValue() - Method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
doubleValue() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
drop(T) - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
Drop the given record
drop(T) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
during(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The "d" relation
duringInverse(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The "di" relation

E

Edge - Interface in org.expasy.jpl.commons.collection.graph
 
edgeValueTransformer(Transformer<E, String>) - Method in class org.expasy.jpl.commons.collection.graph.GraphExporter.Builder
 
edit() - Method in interface org.expasy.jpl.commons.base.Editor
Edit an instance of T-type object.
Editor<T> - Interface in org.expasy.jpl.commons.base
The Editor interface should be implemented by any object editing T type instance.
EditorException - Exception in org.expasy.jpl.commons.base
This exception is thrown by a Editor when an object cannot been correctly edited.
EditorException() - Constructor for exception org.expasy.jpl.commons.base.EditorException
Empty constructor.
EditorException(String) - Constructor for exception org.expasy.jpl.commons.base.EditorException
Constructs a new EditorException object.
EditorException(Throwable) - Constructor for exception org.expasy.jpl.commons.base.EditorException
 
EditorException(String, Throwable) - Constructor for exception org.expasy.jpl.commons.base.EditorException
 
emptyInstance() - Static method in class org.expasy.jpl.commons.collection.IntegerSequence
 
emptyInstance() - Static method in class org.expasy.jpl.commons.collection.Interval
 
enableBinRenderMode() - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
The values of all bins will be added for rendering (quick rendering).
enableMemoryTest(boolean) - Method in interface org.expasy.jpl.commons.base.mem.MemoryEstimatorReady
en/disable the memory test
enablePlug(boolean) - Method in interface org.expasy.jpl.commons.base.Pluggable
En/Disable plugged object
enableProgressBar(boolean) - Method in interface org.expasy.jpl.commons.base.task.ProgressBarReady
Deprecated. En/Disable progress bar utility
equals(Object) - Method in class org.expasy.jpl.commons.base.CounterImpl
 
equals(Object) - Method in class org.expasy.jpl.commons.base.record.DataTable.Record
 
equals(Object) - Method in class org.expasy.jpl.commons.base.record.DataTableFactory
 
equals(Object) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
equals(Object) - Method in interface org.expasy.jpl.commons.collection.Mappable
 
equals(Object) - Method in class org.expasy.jpl.commons.collection.symbol.AbstractSymbol
 
equals(Object) - Method in class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher
equal instances have equal patterns.
equals(Object) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
Return true if 2 aa sequences are identical
equals(Object) - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
eval(U, V) - Method in interface org.expasy.jpl.commons.base.cond.operator.api.Operator
evaluate the operation
eval(Boolean, Boolean) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorAnd
 
eval(T, T) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorApproxEquals
 
eval(T, Set<T>) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongs
 
eval(T, DomainOfDefinition<T>) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongsToDoD
 
eval(Set<T>, T) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorContains
 
eval(Object, Object) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorEquals
 
eval(T, T) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorGreaterThan
 
eval(Set<T>, Set<T>) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorInter
 
eval(T, T) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorLowerThan
 
eval(T, T) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorMulti
 
eval(Boolean, Boolean) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorOr
 
eval() - Method in interface org.expasy.jpl.commons.base.Evaluable
evaluation of the Evaluable object
eval(CountableRecords<T>) - Static method in class org.expasy.jpl.commons.base.record.RecordsCountUtils
 
eval(List<T>) - Static method in class org.expasy.jpl.commons.base.record.RecordsCountUtils
 
Evaluable - Interface in org.expasy.jpl.commons.base
Any class that can be evaluate as a double needs to implement this interface.
evaluate(TypedDataContainer) - Method in interface org.expasy.jpl.commons.base.cond.Condition
 
evaluate(T) - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl
Test if this condition is valid for the given object
evaluate(TypedDataContainer) - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl
 
evaluate(T) - Method in class org.expasy.jpl.commons.collection.graph.GraphPredicate.GraphInstancePredicate
 
evaluate(T) - Method in class org.expasy.jpl.commons.collection.graph.GraphPredicate.ValuePredicate
 
evaluate(T) - Method in class org.expasy.jpl.commons.collection.graph.GraphPredicate.VertexPatternPredicate
 
evaluate(T) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl.PredicateImpl
 
excludeLowerBound() - Method in class org.expasy.jpl.commons.collection.Interval.Builder
 
exitPattern(Pattern) - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl.Builder
 
expand(Graph<V, E>, Graph<V, E>) - Method in class org.expasy.jpl.commons.collection.graph.GraphCollapser
 
ExplicitlyCloneable - Interface in org.expasy.jpl.commons.base
The ExplicitlyCloneable interface should be implemented by any object that may be duplicated.
export(Graph<V, E>, Transformer<Graph<V, E>, String>) - Method in class org.expasy.jpl.commons.collection.graph.GraphExporter
 
export(double[], String) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
export(HistogramDataSet, String) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
exportBinDisabled() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
exportBinEnabled() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
exportBinStatus(boolean) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
exportChart(String) - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
create an image file
exportChart(String) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Export a chart (prerequisite: data sets have already been entered via addDataSet method).
exportChart(StatisticalSerie<T>, String, String) - Method in class org.expasy.jpl.commons.collection.render.BarCodeRenderer
Export as image file.
exportChart(String, String) - Method in class org.expasy.jpl.commons.collection.render.BarCodeRenderer
Export a chart (prerequisite: data sets have already been entered via addDataSet method).
exportChart(HistogramDataSet, String, String) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Export as image file.
exportChart(String) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Export a chart (prerequisite: data sets have already been entered via addDataSet method).
exportChart(StatisticalSerie<T>, String, String) - Method in class org.expasy.jpl.commons.collection.render.StatisticalSerieRenderer
Export as image file.
exportChart(String, String) - Method in class org.expasy.jpl.commons.collection.render.StatisticalSerieRenderer
Export a chart (prerequisite: data sets have already been entered via addDataSet method).
exportKPGraph(KPartiteGraphImpl<V, E>) - Method in class org.expasy.jpl.commons.collection.graph.GraphExporter
 
ExtraIterable<T> - Interface in org.expasy.jpl.commons.collection
ExtraIterable inherits from Iterable and adds the functionality of returning its next elements into a list.
ExtraIterable.AbstractExtraIterator<T> - Class in org.expasy.jpl.commons.collection
Abstract inner class with default implementation of nextToList methods.
ExtraIterable.AbstractExtraIterator() - Constructor for class org.expasy.jpl.commons.collection.ExtraIterable.AbstractExtraIterator
 

F

FactorialCalculator - Class in org.expasy.jpl.commons.base.math
A simple factorial calculator.
FileFinder - Class in org.expasy.jpl.commons.base.io
Class to find all files matching a regular expression in a directory tree.
FileFinder() - Constructor for class org.expasy.jpl.commons.base.io.FileFinder
 
FilenameValidator - Class in org.expasy.jpl.commons.base.io
This object validates file names and may convert any names.
FilenameValidator() - Constructor for class org.expasy.jpl.commons.base.io.FilenameValidator
 
filter(Collection<String>) - Method in class org.expasy.jpl.commons.base.TypedDataContainer
Get a new instance of JPLVariableContainer containing Variables that match the collection of given names.
finishes(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The "f" relation
finishesInverse(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The "fi" relation
floats2doubles(float[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
 
floatValue() - Method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
floatValue() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
flushInFile(String) - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
flush output in file
flushInStdout() - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
flush output in standard output stream
follows(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The > relation
foundNextPosition() - Method in class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner.Iterator
This function will have to set nextPosition to its value and will return true if a valid position is found otherwise false.
foundNextPosition() - Method in class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher.Iterator
 
freeData() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Delete data.
from(int) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl.Builder
 
fromIntegers(int[], int) - Static method in class org.expasy.jpl.commons.collection.IntegerSequenceWithGap
Build integer intervals
fromSymbols(Symbol.SymbolType<T>, TreeView<? extends Symbol<T>>) - Static method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
Create an alphabet from the tree of symbols (mapping name -> symbol tree).

G

GenericProperties<T> - Class in org.expasy.jpl.commons.base
A simple generic properties object.
get(int) - Method in class org.expasy.jpl.commons.collection.IntegerSequenceWithGap
 
get(int) - Method in class org.expasy.jpl.commons.collection.PartitionList
 
getAllHisto() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates and returns the histogram of the whole distribution
getAllScores() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Get list of all scores (positive and negative)
getAlphabet() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractSymbolType
 
getAlphabet() - Method in interface org.expasy.jpl.commons.collection.symbol.Symbol.SymbolType
the alphabet
getAlphabet(Symbol.SymbolType<T>) - Method in class org.expasy.jpl.commons.collection.symbol.SymbolTable
 
getArray() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractDoublesArrayIndexComparator
 
getArray() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractIntsArrayIndexComparator
 
getArray() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractListIndexComparator
 
getArray() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractObjectsArrayIndexComparator
 
getArray() - Method in interface org.expasy.jpl.commons.collection.sorter.ArrayIndexComparator
get the array to sort
getArraySize() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractDoublesArrayIndexComparator
 
getArraySize() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractIntsArrayIndexComparator
 
getArraySize() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractListIndexComparator
 
getArraySize() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractObjectsArrayIndexComparator
 
getArraySize() - Method in interface org.expasy.jpl.commons.collection.sorter.ArrayIndexComparator
the number of values to sort
getAvgSizeOfObject() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
getBaseName() - Method in class org.expasy.jpl.commons.base.io.JPLFile
 
getBaseName(String) - Static method in class org.expasy.jpl.commons.base.io.JPLFile
 
getBaseNameNoExt() - Method in class org.expasy.jpl.commons.base.io.JPLFile
 
getBaseNameNoExt(String) - Static method in class org.expasy.jpl.commons.base.io.JPLFile
 
getBinIndex(double, Interval, double) - Static method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
Get the index of bin containing the given value.
getBinIndex(double) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
Get the index of bin containing the given value.
getBins() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getBinWidth() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Get bin width for statistical score calculation
getBinWidth() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getBoundIndicesAtBin(int) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
Get bounds indices
getBuilder() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
 
getBy() - Method in class org.expasy.jpl.commons.collection.IntegerSequence
 
getCenter() - Method in class org.expasy.jpl.commons.collection.Interval
Get the center value.
getCenter() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
getChartColor(int) - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
get the color of ith chart
getChartColor(int) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
getChartColor(int) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
 
getChildAt(int) - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
getChildAt(int) - Method in interface org.expasy.jpl.commons.collection.tree.TreeView
 
getChildAt(int) - Method in class org.expasy.jpl.commons.collection.tree.TreeViewImpl
getChildren() - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
getChildren() - Method in interface org.expasy.jpl.commons.collection.tree.TreeView
 
getChildren() - Method in class org.expasy.jpl.commons.collection.tree.TreeViewImpl
getClusterGraph(Graph<V, E>, Collection<? extends V>) - Method in class org.expasy.jpl.commons.collection.graph.GraphCollapser
 
getColomnNames() - Method in class org.expasy.jpl.commons.base.io.TabFileReader
Get column names.
getCommandLine() - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
getCondition(String) - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
Get the condition given its name.
getConfigFile() - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
getConnectedNodes(Graph<V, E>, V) - Static method in class org.expasy.jpl.commons.collection.graph.GraphFilterer
Get the set of nodes connected to init node in the graph.
getConverter() - Method in interface org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager.IType
 
getCount() - Method in interface org.expasy.jpl.commons.base.Counter
 
getCount() - Method in class org.expasy.jpl.commons.base.CounterImpl
 
getCount(T) - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
 
getCount() - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
 
getCount(T) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
getCount() - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
getData() - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
getData(Collection<String>) - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
getData() - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
getData() - Method in interface org.expasy.jpl.commons.collection.tree.TreeView
 
getData() - Method in class org.expasy.jpl.commons.collection.tree.TreeViewImpl
getDataClass() - Method in class org.expasy.jpl.commons.base.TypedDatum.Type
 
getDataSymbolManager() - Method in interface org.expasy.jpl.commons.collection.symbol.Symbol.SymbolType
the manager maps symbols with the corresponding T-typed data
getDatum(String) - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
getDefaultInput() - Method in interface org.expasy.jpl.commons.app.InteractiveInputScanner
 
getDefaultInput() - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl
 
getDefaultInstance() - Static method in class org.expasy.jpl.commons.base.math.DoubleComparator
 
getDefaultMemoryRatio() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
getDefaultPrecision() - Static method in class org.expasy.jpl.commons.base.io.DecimalFormatFactory
 
getDelta() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorApproxEquals
 
getDensityAtStdDev(int) - Static method in class org.expasy.jpl.commons.collection.stat.ProbDistLGUtils
 
getDensityAtStdDevBin(int) - Static method in class org.expasy.jpl.commons.collection.stat.ProbDistLGUtils
Get the density over the curve in the interval [stdev-stdev+1[
getDependentVariables() - Method in interface org.expasy.jpl.commons.base.cond.Condition
 
getDependentVariables() - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl
 
getDirName() - Method in class org.expasy.jpl.commons.base.io.JPLFile
 
getDirName(String) - Static method in class org.expasy.jpl.commons.base.io.JPLFile
 
getEdgeCount(Predicate<V>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getEdgeCount(Collection<Predicate<V>>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getEdges(Predicate<E>) - Method in class org.expasy.jpl.commons.collection.graph.GraphFilterer
Get the edges that satisfy the predicate.
getEdges(Predicate<V>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getEdges(Collection<Predicate<V>>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getExitPattern() - Method in interface org.expasy.jpl.commons.app.InteractiveInputScanner
Get the pattern matching the interruption
getExitPattern() - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl
 
getExtension() - Method in class org.expasy.jpl.commons.base.io.JPLFile
 
getExtension(String) - Static method in class org.expasy.jpl.commons.base.io.JPLFile
 
getFDR() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates and returns the false discovery rate
getFields() - Method in interface org.expasy.jpl.commons.base.record.DataRecord
 
getFields() - Method in class org.expasy.jpl.commons.base.record.DataTable
Get the field names of this table.
getFields() - Method in class org.expasy.jpl.commons.base.record.DataTable.Record
 
getFields() - Method in class org.expasy.jpl.commons.base.record.DataTableFactory
Get the fields of the table this factory can create.
getFieldType(String) - Method in interface org.expasy.jpl.commons.base.record.DataRecord
Return the type of the given field.
getFieldType(String) - Method in class org.expasy.jpl.commons.base.record.DataTable
Get the field type of the given field of this table.
getFieldType(String) - Method in class org.expasy.jpl.commons.base.record.DataTable.Record
 
getFieldType(String) - Method in class org.expasy.jpl.commons.base.record.DataTableFactory
Get the type associated to the table field.
getFiles(String, String) - Static method in class org.expasy.jpl.commons.base.io.FileFinder
 
getFiles(String, String, boolean) - Static method in class org.expasy.jpl.commons.base.io.FileFinder
Find all files in the directory sub-tree under root
getFiles(String, Pattern) - Static method in class org.expasy.jpl.commons.base.io.FileFinder
 
getFiles(String, Pattern, boolean) - Static method in class org.expasy.jpl.commons.base.io.FileFinder
Find all files in the directory sub-tree under root
getFitOffset() - Method in class org.expasy.jpl.commons.base.math.StraightLineFitter
Gets offset of fitted straight line
getFitSlope() - Method in class org.expasy.jpl.commons.base.math.StraightLineFitter
Gets slope of fitted straight line
getFittedValues() - Method in class org.expasy.jpl.commons.base.math.StraightLineFitter
Returns the values of the fitted straight line at xValues
getFormat() - Method in class org.expasy.jpl.commons.base.TypedDatum.Type
 
getFreeMemoryRatio() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
getFrequency() - Method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
getFrequency() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
getFrequency(T) - Method in interface org.expasy.jpl.commons.collection.stat.StatisticalSerie
 
getFrequency(Integer) - Method in class org.expasy.jpl.commons.collection.stat.StatisticalSerieDiscreteDataSet
 
getFrom() - Method in class org.expasy.jpl.commons.collection.IntegerSequence
 
getId() - Method in class org.expasy.jpl.commons.base.record.DataTable.Record
 
getId() - Method in interface org.expasy.jpl.commons.base.Registrable
 
getId() - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getImageFormat() - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
get the image format (jpg, png, ...)
getImageFormat() - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Get image format.
getImageFormat() - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Get image format.
getIncidentEdges(V, Collection<Predicate<V>>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getIncidentEdges(V, Predicate<V>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getIndexRange(double[], double, double) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Get the index range of values where each is contained in the given interval.
getIndexRange(double[], Interval) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Get an interval of index in sorted values.
getIndices(int) - Method in class org.expasy.jpl.commons.collection.PartitionList
Get the indices of T-objects of partition i.
getIndices(Symbol<T>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
Return the list of indices of specified symbol
getIndices(Set<Symbol<T>>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
 
getInputPattern() - Method in interface org.expasy.jpl.commons.app.InteractiveInputScanner
Get the pattern matching the input
getInputPattern() - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl
 
getInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorAnd
 
getInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorOr
 
getInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.OperatorManager
 
getInstance() - Static method in class org.expasy.jpl.commons.base.io.DecimalFormatFactory
 
getInstance() - Static method in class org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager
 
getInstance() - Static method in class org.expasy.jpl.commons.collection.Interval.IntervalComparator
 
getInstance() - Static method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
 
getInterval(int) - Method in class org.expasy.jpl.commons.collection.PartitionList
Get the indices of T-objects of partition i.
getInterval() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
getIntervalAreaAtStdev(double, int) - Static method in class org.expasy.jpl.commons.collection.stat.ProbDistLGUtils
 
getIntervalAreas(double) - Static method in class org.expasy.jpl.commons.collection.stat.ProbDistLGUtils
Return a list of areas for 12 sigma intervals from [-6, -5[ to [5, 6[.
getIntervalBinAt(int) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getIntervalOfDefinition() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getKeys() - Method in interface org.expasy.jpl.commons.collection.Pool
Get keys of all stored objects.
getKeys() - Method in class org.expasy.jpl.commons.collection.PoolImpl
Get keys of all stored objects.
getLeaves() - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
getLeaves() - Method in interface org.expasy.jpl.commons.collection.tree.TreeView
 
getLeaves() - Method in class org.expasy.jpl.commons.collection.tree.TreeViewImpl
getLetters() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
getLetters() - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
getLetters() - Method in interface org.expasy.jpl.commons.collection.symbol.AlphabetView
 
getList() - Method in class org.expasy.jpl.commons.collection.PartitionList
 
getLoadedValuesIndices() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getLogProbRatio(boolean) - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates and returns the logarithm of probability ratios
getLowerBound() - Method in class org.expasy.jpl.commons.collection.IntegerSequenceWithGap
 
getLowerBound() - Method in class org.expasy.jpl.commons.collection.Interval
Get the lower bound number (included).
getMaxBucketCapacity() - Method in class org.expasy.jpl.commons.collection.PartitionList
 
getMaxObjectNumber() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
getMaxScore() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Get maximal score for statistical score calculation
getMaxValue() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getMean() - Method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
getMemoryCalculator() - Method in interface org.expasy.jpl.commons.base.mem.MemoryEstimatorReady
get the memory estimator
getMemoryCap() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
getMergedSequence() - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SequenceMerger
get the merged sequence.
getMergedSequence() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolMergerImpl
get the merged sequence.
getMinMemoryForEstimation() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
getMinScore() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Get minimal score for statistical score calculation
getMinValue() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getName() - Method in interface org.expasy.jpl.commons.base.cond.Condition
the name (have to respect the file name convention)
getName() - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl
 
getName() - Method in interface org.expasy.jpl.commons.base.cond.operator.api.Operator
get the name (respecting the file name convention)
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorAnd
 
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorApproxEquals
 
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongs
 
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongsToDoD
 
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorContains
 
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorEquals
 
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorGreaterThan
 
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorInter
 
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorLowerThan
 
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorMulti
 
getName() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorOr
 
getName() - Method in class org.expasy.jpl.commons.base.TypedDatum
 
getName() - Method in class org.expasy.jpl.commons.base.TypedDatum.Type
 
getName() - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl.PredicateImpl
 
getName() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractSymbol
getName() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractSymbolType
 
getName() - Method in interface org.expasy.jpl.commons.collection.symbol.Symbol
 
getName() - Method in interface org.expasy.jpl.commons.collection.symbol.Symbol.SymbolType
the name of symbol type
getNames() - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
getNegativeHisto() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates and returns the histogram of the negative distribution
getNegativeScores() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Get list of scores for the negative distribution
getNeighbors(V, Collection<Predicate<V>>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getNeighbors(V, Predicate<V>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getNextConditionName() - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
 
getNodes() - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
getNodes() - Method in interface org.expasy.jpl.commons.collection.tree.TreeView
 
getNodes() - Method in class org.expasy.jpl.commons.collection.tree.TreeViewImpl
getNormalizedValue() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getNrBins() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Get the number of bins (array size)
getNrFractDecDigits() - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
Get number of fractional decimal digits
getNthHighestElement(double[], int) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
 
getNumberOfChildren() - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
getNumberOfChildren() - Method in interface org.expasy.jpl.commons.collection.tree.TreeView
 
getNumberOfChildren() - Method in class org.expasy.jpl.commons.collection.tree.TreeViewImpl
getNumberOfSites() - Method in class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner
 
getNumberOfSites() - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SequenceIterable
get number of positions
getNumOfCondition() - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
 
getNumOfInts() - Method in class org.expasy.jpl.commons.collection.IntegerSequenceWithGap
 
getOperator() - Method in interface org.expasy.jpl.commons.base.cond.Condition
 
getOperator() - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl
getOperator(String) - Method in class org.expasy.jpl.commons.base.cond.operator.OperatorManager
 
getOperatorPosInCondition(String) - Method in class org.expasy.jpl.commons.base.cond.operator.OperatorManager
 
getOriginalGraph() - Method in class org.expasy.jpl.commons.collection.graph.GraphFilterer
 
getParameters() - Method in interface org.expasy.jpl.commons.app.JPLTerminalApplication
 
getParamInfos() - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
getParent() - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
getParent() - Method in interface org.expasy.jpl.commons.collection.tree.TreeView
 
getParent() - Method in class org.expasy.jpl.commons.collection.tree.TreeViewImpl
getPartialGraph(Predicate<E>, boolean) - Method in class org.expasy.jpl.commons.collection.graph.GraphFilterer
Get the partial graph of edges that satisfy the predicate.
getPartialGraph(Collection<E>, boolean) - Method in class org.expasy.jpl.commons.collection.graph.GraphFilterer
 
getPartitionIndex(Predicate<V>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getPartitionIndex(V) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
Look for the partition of the given vertex.
getPartitions() - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getPattern() - Method in class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher
 
getPositiveHisto() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates and returns the histogram of the positive distribution
getPositiveScores() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Get list of scores for the positive distribution
getPpm() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getPrecision() - Method in class org.expasy.jpl.commons.collection.Interval
 
getPrompt() - Method in interface org.expasy.jpl.commons.app.InteractiveInputScanner
Get the command-line prompt
getPrompt() - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl
 
getProperty(String) - Method in class org.expasy.jpl.commons.base.GenericProperties
 
getPropertyNames() - Method in class org.expasy.jpl.commons.base.GenericProperties
 
getRange() - Method in class org.expasy.jpl.commons.collection.Interval
 
getRecord(int) - Method in class org.expasy.jpl.commons.base.record.DataTable
Get the record identified by the given id.
getRecords() - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
 
getRecords() - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
getRegEx() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
getRegEx() - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
getRegEx() - Method in interface org.expasy.jpl.commons.collection.symbol.AlphabetView
 
getRelativeFrequency(T) - Method in interface org.expasy.jpl.commons.collection.stat.StatisticalSerie
 
getRelativeFrequency(Integer) - Method in class org.expasy.jpl.commons.collection.stat.StatisticalSerieDiscreteDataSet
 
getRenderingInfo() - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Retrieve rendering info (for interactive graphs).
getRenderingInfo() - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Retrieve rendering info (for interactive graphs).
getROperand() - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl
 
getRvalueOpLvalue(String) - Method in class org.expasy.jpl.commons.base.cond.operator.OperatorManager
 
getSampleSize() - Method in interface org.expasy.jpl.commons.collection.stat.StatisticalSerie
 
getSampleSize() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalSerieDiscreteDataSet
 
getSampleValues() - Method in interface org.expasy.jpl.commons.collection.stat.StatisticalSerie
 
getSampleValues() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalSerieDiscreteDataSet
 
getScoreBins() - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Get the mids of the score bins
getSeparator() - Method in class org.expasy.jpl.commons.base.io.TabFileReader
Get separator
getSeparator() - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
Get separator
getSeqLen() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl.Builder
 
getSequencePattern(Symbol.SymbolType<E>) - Static method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
 
getSpecificParamInfos() - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
getStackCommands(ConditionImpl<T, V>, V) - Static method in class org.expasy.jpl.commons.base.cond.ConditionImpl
 
getStdDev() - Method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
getStdError() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getStringTypeInstance() - Static method in class org.expasy.jpl.commons.base.TypedDatum.Type
 
getStringValues() - Method in interface org.expasy.jpl.commons.collection.graph.Edge
Get the string representation
getSubArray(double[], int, int) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
 
getSubGraph(Collection<V>, boolean) - Method in class org.expasy.jpl.commons.collection.graph.GraphFilterer
Get the subgraph from given nodes (all interconnected nodes will be added if enabled).
getSubGraphWithPred(Predicate<V>, boolean) - Method in class org.expasy.jpl.commons.collection.graph.GraphFilterer
Get the subgraph of nodes that satisfy the predicate extended to all interconnected nodes if enabled.
getSubGraphWithPreds(Collection<Predicate<V>>, boolean) - Method in class org.expasy.jpl.commons.collection.graph.GraphFilterer
Get the subgraph of nodes that satisfy one of the predicate extended to all connected nodes.
getSymbolAt(int) - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SymbolSequence
 
getSymbolAt(int) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
Returns the symbol character at position i.
getSymbolLeaves() - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
getSymbolNumber() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
getSymbolNumber() - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
getSymbolNumber() - Method in interface org.expasy.jpl.commons.collection.symbol.AlphabetView
 
getSymbolNumber() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
 
getSymbolNumber(Set<Symbol<T>>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
 
getSymbolNumber(Symbol<T>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
Return the number of occurrences for the specified symbol.
getSymbolNumber() - Method in class org.expasy.jpl.commons.collection.symbol.SymbolTable
 
getSymbols() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
 
getSymbolType() - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
getSymbolType() - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SymbolSequence
 
getSymbolType() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
 
getTo() - Method in class org.expasy.jpl.commons.collection.IntegerSequence
 
getToken() - Method in interface org.expasy.jpl.commons.base.cond.operator.api.Operator
get the operator
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorAnd
 
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorApproxEquals
 
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongs
 
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongsToDoD
 
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorContains
 
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorEquals
 
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorGreaterThan
 
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorInter
 
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorLowerThan
 
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorMulti
 
getToken() - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorOr
 
getTotalFreeMemory() - Static method in class org.expasy.jpl.commons.base.mem.RunTimeMemoryEstimator
 
getTransformer() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
getTransformers() - Method in class org.expasy.jpl.commons.base.process.SequenceTransformer
Get object processors.
getType(Class<?>) - Method in class org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager
 
getType() - Method in class org.expasy.jpl.commons.base.TypedDatum
 
getType() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
getType() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractSymbol
getType() - Method in interface org.expasy.jpl.commons.collection.symbol.Symbol
 
getTypeAccessor(String) - Method in class org.expasy.jpl.commons.base.record.DataTable
Access field String value from Record.
getTypeClass() - Method in interface org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager.IType
get the type class
getTypedVariable(String, TypedDatum.Type<T>) - Method in interface org.expasy.jpl.commons.collection.graph.Edge
 
getUpperBound() - Method in class org.expasy.jpl.commons.collection.IntegerSequenceWithGap
 
getUpperBound() - Method in class org.expasy.jpl.commons.collection.Interval
Get the upper bound number (excluded).
getUsedMemory() - Static method in class org.expasy.jpl.commons.base.mem.RunTimeMemoryEstimator
 
getUsedMemorySize() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
getValue(int) - Static method in class org.expasy.jpl.commons.base.math.FactorialCalculator
 
getValue(String) - Method in interface org.expasy.jpl.commons.base.record.DataRecord
 
getValue(String) - Method in class org.expasy.jpl.commons.base.record.DataTable.Record
Get the typed field value.
getValue() - Method in class org.expasy.jpl.commons.base.TypedDatum
 
getValue() - Method in enum org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator.OrderType
 
getValues() - Method in class org.expasy.jpl.commons.base.io.TabFileReader
Get values
getValues() - Method in interface org.expasy.jpl.commons.collection.Pool
Get values of all stored objects.
getValues() - Method in class org.expasy.jpl.commons.collection.PoolImpl
Get values of all stored objects.
getValues() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getValues(LaplaceGaussRandomVar) - Static method in class org.expasy.jpl.commons.collection.stat.ProbDistLGUtils
 
getValues() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
getValues() - Method in interface org.expasy.jpl.commons.collection.stat.StatisticalSerie
 
getValues() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalSerieDiscreteDataSet
 
getValuesAtBin(int) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getValuesAtInterval(Interval) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getValuesAtStdev(LaplaceGaussRandomVar, int) - Static method in class org.expasy.jpl.commons.collection.stat.ProbDistLGUtils
 
getValuesIndicesAtInterval(Interval) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getVariable(String) - Method in interface org.expasy.jpl.commons.collection.graph.Edge
 
getVersion() - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
getVertex(String) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getVertexCount(Predicate<V>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getVertexCount(Collection<Predicate<V>>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getVertices(Predicate<V>) - Method in class org.expasy.jpl.commons.collection.graph.GraphFilterer
Get the nodes that satisfy the predicate.
getVertices(Collection<Predicate<V>>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getVertices(Predicate<V>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getVerticesId() - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
getWeighAtBin(int) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getWeighAtInterval(Interval) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getWeights() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
getXAt(int) - Method in class org.expasy.jpl.commons.collection.stat.StatisticalSerieDiscreteDataSet
 
getXLegend() - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
getXLegend() - Method in class org.expasy.jpl.commons.collection.render.BarCodeRenderer
 
getXLegend() - Method in class org.expasy.jpl.commons.collection.render.StatisticalSerieRenderer
 
getXValues() - Method in class org.expasy.jpl.commons.base.math.StraightLineFitter
Get the x-values of the data points
getYLegend() - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
getYLegend() - Method in class org.expasy.jpl.commons.collection.render.BarCodeRenderer
 
getYLegend() - Method in class org.expasy.jpl.commons.collection.render.StatisticalSerieRenderer
 
getYValues() - Method in class org.expasy.jpl.commons.base.math.StraightLineFitter
Get the y-values of the data points
getYVariance() - Method in class org.expasy.jpl.commons.base.math.StraightLineFitter
Get y-variance of data points
GraphCloner<V,E> - Class in org.expasy.jpl.commons.collection.graph
This object clones graphs.
GraphCollapser<V,E> - Class in org.expasy.jpl.commons.collection.graph
This object comes from jung.
GraphCollapser(Graph<V, E>) - Constructor for class org.expasy.jpl.commons.collection.graph.GraphCollapser
 
GraphExporter<V,E> - Class in org.expasy.jpl.commons.collection.graph
This object exports graphs.
GraphExporter.Builder<V,E> - Class in org.expasy.jpl.commons.collection.graph
 
GraphExporter.Builder() - Constructor for class org.expasy.jpl.commons.collection.graph.GraphExporter.Builder
 
GraphExporter.DotTransformer<V,E> - Class in org.expasy.jpl.commons.collection.graph
 
GraphExporter.DotTransformer() - Constructor for class org.expasy.jpl.commons.collection.graph.GraphExporter.DotTransformer
 
GraphExporter.ObjectComparator - Class in org.expasy.jpl.commons.collection.graph
 
GraphExporter.ObjectComparator() - Constructor for class org.expasy.jpl.commons.collection.graph.GraphExporter.ObjectComparator
 
GraphFilterer<V,E> - Class in org.expasy.jpl.commons.collection.graph
This object search a graph based on predicate on nodes or edges
GraphPredicate - Class in org.expasy.jpl.commons.collection.graph
A simple Graph node predicate (needed for collapsable graph).
GraphPredicate() - Constructor for class org.expasy.jpl.commons.collection.graph.GraphPredicate
 
GraphPredicate.GraphInstancePredicate<T> - Class in org.expasy.jpl.commons.collection.graph
 
GraphPredicate.GraphInstancePredicate() - Constructor for class org.expasy.jpl.commons.collection.graph.GraphPredicate.GraphInstancePredicate
 
GraphPredicate.ValuePredicate<T extends Number> - Class in org.expasy.jpl.commons.collection.graph
 
GraphPredicate.ValuePredicate(T) - Constructor for class org.expasy.jpl.commons.collection.graph.GraphPredicate.ValuePredicate
 
GraphPredicate.VertexPatternPredicate<T> - Class in org.expasy.jpl.commons.collection.graph
 
GraphPredicate.VertexPatternPredicate(Pattern) - Constructor for class org.expasy.jpl.commons.collection.graph.GraphPredicate.VertexPatternPredicate
 
GREATER_EQUALS - Static variable in class org.expasy.jpl.commons.base.cond.operator.OperatorManager
 

H

hasBin(double) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
hasCommonInterval(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
 
hasData() - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
hasDatum(String) - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
hasExtension() - Method in class org.expasy.jpl.commons.base.io.JPLFile
 
hasExtension(String) - Static method in class org.expasy.jpl.commons.base.io.JPLFile
 
hasField(String) - Method in interface org.expasy.jpl.commons.base.record.DataRecord
Return true if the given field exists.
hasField(String) - Method in class org.expasy.jpl.commons.base.record.DataTable
Return true if this table has the given field.
hasField(String) - Method in class org.expasy.jpl.commons.base.record.DataTable.Record
 
hasField(String) - Method in class org.expasy.jpl.commons.base.record.DataTableFactory
Is the given field exists in the table's signature that the factory creates ?
hashCode() - Method in class org.expasy.jpl.commons.base.CounterImpl
 
hashCode() - Method in class org.expasy.jpl.commons.base.record.DataTable.Record
 
hashCode() - Method in interface org.expasy.jpl.commons.collection.Mappable
 
hashCode() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractSymbol
 
hashCode() - Method in class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher
 
hashCode() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
Same length JPLAASequence have the same hash code.
hashCode() - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
hasNext() - Method in class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner.Iterator
Has found next match ? [method implemented to respect Iterator contract].
hasOverlap(Interval) - Method in class org.expasy.jpl.commons.collection.Interval
 
hasProperty(String) - Method in class org.expasy.jpl.commons.base.GenericProperties
 
hasRecord() - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
 
hasRecord(T) - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
 
hasRecord(T) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
hasRecord() - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
hasSymbol(char) - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
hasSymbol(char) - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
hasSymbol(char) - Method in interface org.expasy.jpl.commons.collection.symbol.AlphabetView
 
hasSymbol(Symbol<T>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
 
hasValue(String) - Method in interface org.expasy.jpl.commons.base.record.DataRecord
 
hasValue(String) - Method in class org.expasy.jpl.commons.base.record.DataTable.Record
 
HistogramDataSet - Class in org.expasy.jpl.commons.collection.stat
In statistics, a histogram is a graphical representation, showing a visual impression of the distribution of data.
HistogramDataSet(HistogramDataSet.Builder) - Constructor for class org.expasy.jpl.commons.collection.stat.HistogramDataSet
Create a binned peak list from a builder.
HistogramDataSet.Builder - Class in org.expasy.jpl.commons.collection.stat
Build a binned peak list with binNumber bins, the bins precision is deduced.
HistogramDataSet.Builder() - Constructor for class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
 
HistogramDataSet.Builder(double[], Interval) - Constructor for class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
 
HistogramDataSet.OutOfUpperBoundException - Exception in org.expasy.jpl.commons.collection.stat
 
HistogramDataSetExporter - Class in org.expasy.jpl.commons.collection.stat
This object exports HistogramDataSets into files or convert into other objects (for rendering for example).
HistogramDataSetRenderer - Class in org.expasy.jpl.commons.collection.render
This object renders HistogramDataSet objects.

I

ImageFormat - Enum in org.expasy.jpl.commons.base.render
Image format.
ImageRenderingException - Exception in org.expasy.jpl.commons.base.render
Thrown when image processing problem met.
ImageRenderingException() - Constructor for exception org.expasy.jpl.commons.base.render.ImageRenderingException
 
ImageRenderingException(String) - Constructor for exception org.expasy.jpl.commons.base.render.ImageRenderingException
 
ImageRenderingException(String, Throwable) - Constructor for exception org.expasy.jpl.commons.base.render.ImageRenderingException
 
ImageRenderingException(Throwable) - Constructor for exception org.expasy.jpl.commons.base.render.ImageRenderingException
 
includeUpperBound() - Method in class org.expasy.jpl.commons.collection.Interval.Builder
 
increment() - Method in interface org.expasy.jpl.commons.base.Counter
Increment counter by 1.
increment(int) - Method in interface org.expasy.jpl.commons.base.Counter
Increment counter by inc.
increment() - Method in class org.expasy.jpl.commons.base.CounterImpl
Increment counter by 1.
increment(int) - Method in class org.expasy.jpl.commons.base.CounterImpl
Increment counter by inc.
indeterminate() - Static method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
 
IndexIterable - Interface in org.expasy.jpl.commons.collection
This interfaces allow the manipulation of iterator over indices ( Integer).
IndexIterable.Iterator - Class in org.expasy.jpl.commons.collection
Abstract inner class that iterates over list of Integer.
IndexIterable.Iterator() - Constructor for class org.expasy.jpl.commons.collection.IndexIterable.Iterator
 
indexOf(PartitionList<T>, Object) - Method in interface org.expasy.jpl.commons.collection.PartitionList.IndexingAlgo
 
indexOf(Object) - Method in class org.expasy.jpl.commons.collection.PartitionList
 
indexOf(Object, PartitionList.IndexingAlgo<T>) - Method in class org.expasy.jpl.commons.collection.PartitionList
 
indices - Variable in class org.expasy.jpl.commons.collection.sorter.ArrayIndexSorter
the sorted indices of the array object handled by the comparator
indicesOf(String, String) - Static method in class org.expasy.jpl.commons.base.string.StringUtils
Return the indices of a motif found within a target string.
init() - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
init() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
initDataset() - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
initDataset() - Method in class org.expasy.jpl.commons.collection.render.BarCodeRenderer
 
initDataset() - Method in class org.expasy.jpl.commons.collection.render.StatisticalSerieRenderer
 
initGraph(Graph<V, E>) - Method in class org.expasy.jpl.commons.collection.graph.GraphCollapser
 
initGraph(Graph<V, E>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl.Collapser
 
inputPattern(Pattern) - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl.Builder
 
inputStream(InputStream) - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl.Builder
 
INSTANCE - Static variable in class org.expasy.jpl.commons.base.math.DoubleComparator
 
InstanceBuilder<T> - Interface in org.expasy.jpl.commons.base.builder
The InstanceBuilder interface should be implemented by any builder building T type instance.
INTEGER - Static variable in class org.expasy.jpl.commons.base.io.RegexConstants
integer expression
INTEGER - Static variable in class org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager
 
IntegerSequence - Class in org.expasy.jpl.commons.collection
A IntegerSequence in mathematics is a sequence (i.e., an ordered list) of integers.
IntegerSequence(IntegerSequence.Builder) - Constructor for class org.expasy.jpl.commons.collection.IntegerSequence
 
IntegerSequence.Builder - Class in org.expasy.jpl.commons.collection
 
IntegerSequence.Builder(int, int) - Constructor for class org.expasy.jpl.commons.collection.IntegerSequence.Builder
 
IntegerSequence.Builder(Interval) - Constructor for class org.expasy.jpl.commons.collection.IntegerSequence.Builder
Alternative builder Convert double interval to integer interval: a, b -> floor(1), ceil(b)
IntegerSequenceWithGap - Class in org.expasy.jpl.commons.collection
This object is IntegerSequenceWithGap with gaps defining a sequence of integers with missing integers at some intervals.
InteractiveInputScanner - Interface in org.expasy.jpl.commons.app
InteractiveInputScanner interactively reads input stream.
InteractiveInputScannerImpl - Class in org.expasy.jpl.commons.app
 
InteractiveInputScannerImpl(InteractiveInputScannerImpl.Builder) - Constructor for class org.expasy.jpl.commons.app.InteractiveInputScannerImpl
 
InteractiveInputScannerImpl.Builder - Class in org.expasy.jpl.commons.app
 
InteractiveInputScannerImpl.Builder() - Constructor for class org.expasy.jpl.commons.app.InteractiveInputScannerImpl.Builder
 
Interpreter<T> - Interface in org.expasy.jpl.commons.base.builder
The Interpreter interface should be implemented by any interpreter building T type instance from String.
intersection(Set<T>, Set<T>) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
Compute the intersection between the 2 given sets.
Interval - Class in org.expasy.jpl.commons.collection
An interval is a set of numbers with the property that any number that lies between two numbers is included in the set.
interval(Interval) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Set the interval to make bins.
Interval.Builder - Class in org.expasy.jpl.commons.collection
 
Interval.Builder(double, double) - Constructor for class org.expasy.jpl.commons.collection.Interval.Builder
 
Interval.IntervalComparator - Class in org.expasy.jpl.commons.collection
 
Interval.IntervalOverlapException - Exception in org.expasy.jpl.commons.collection
 
Interval.IntervalOverlapException() - Constructor for exception org.expasy.jpl.commons.collection.Interval.IntervalOverlapException
 
Interval.IntervalOverlapException(String) - Constructor for exception org.expasy.jpl.commons.collection.Interval.IntervalOverlapException
 
Interval.OverlapFinder - Class in org.expasy.jpl.commons.collection
 
ints2Integers(int[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Convert ints to array of Integers.
intToByteArray(int) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Convert an integer to an array of bytes.
intValue() - Method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
intValue() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
isAmbiguous() - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SymbolSequence
 
isAmbiguous() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
 
isBeyondMemoryCap(long) - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
Test if memory is sufficient to store all.
isBinExport() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
isCompatibleOperands(Object, Object) - Method in class org.expasy.jpl.commons.base.cond.operator.api.AbstractOperator
 
isCompatibleOperands(Object, Object) - Method in interface org.expasy.jpl.commons.base.cond.operator.api.Operator
return true if operands are compatible
isCompatibleOperands(Object, Object) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongs
 
isCompatibleOperands(Object, Object) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongsToDoD
 
isCompatibleOperands(Object, Object) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorContains
 
isCompatibleOperands(Object, Object) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorEquals
 
isCompatibleOperands(Object, Object) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorInter
 
isCompatibleOperands(Object, Object) - Method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorMulti
 
isConditionContainsOperator(String) - Method in class org.expasy.jpl.commons.base.cond.operator.OperatorManager
 
isDataNormalized() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
isEmpty() - Method in class org.expasy.jpl.commons.collection.IntegerSequence
 
isEmpty() - Method in class org.expasy.jpl.commons.collection.Interval
 
isEmpty() - Method in class org.expasy.jpl.commons.collection.PartitionList
 
isIndeterminate() - Method in class org.expasy.jpl.commons.base.task.JProgressBarAdapter
 
isIndeterminate() - Method in interface org.expasy.jpl.commons.base.task.ProgressBar
Return true if indeterminate
isIndeterminate() - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
 
isLeave() - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
isLeave() - Method in interface org.expasy.jpl.commons.collection.tree.TreeView
 
isLeave() - Method in class org.expasy.jpl.commons.collection.tree.TreeViewImpl
isLoadCenterBin() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
isLowerBoundIncluded() - Method in class org.expasy.jpl.commons.collection.Interval
 
isNormalizedSum() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
isNotCondition() - Method in interface org.expasy.jpl.commons.base.cond.Condition
 
isNotCondition() - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl
isPlugEnabled() - Method in interface org.expasy.jpl.commons.base.Pluggable
Return true if enabled
isProgressBarEnabled() - Method in interface org.expasy.jpl.commons.base.task.ProgressBarReady
Deprecated. Return true if activated
isRegistered(T) - Method in interface org.expasy.jpl.commons.collection.Pool
Return true if object exists in pool.
isRegistered(String) - Method in class org.expasy.jpl.commons.collection.PoolImpl
isRegistered(T) - Method in class org.expasy.jpl.commons.collection.PoolImpl
Return true if object exists in pool.
isRegistered(String) - Method in interface org.expasy.jpl.commons.collection.Register
 
isRoot() - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
isRoot() - Method in interface org.expasy.jpl.commons.collection.tree.TreeView
 
isRoot() - Method in class org.expasy.jpl.commons.collection.tree.TreeViewImpl
isSharedFlyweight(Object) - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
Returns true if this is a well-known shared flyweight.
isSufficientDataForEstimation() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
isTerminalSymbol(Symbol<T>) - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
isUpperBoundIncluded(Interval, int) - Static method in class org.expasy.jpl.commons.collection.IntegerSequence
 
isUpperBoundIncluded() - Method in class org.expasy.jpl.commons.collection.Interval
 
isValidated(String) - Static method in class org.expasy.jpl.commons.base.io.FilenameValidator
http://www.med.nyu.edu/rcr/rcr/nyu_vms/unixfileanddirectorynames.htm
isValidType(Object) - Method in class org.expasy.jpl.commons.base.TypedDatum.Type
 
isValidTypeString(String) - Method in class org.expasy.jpl.commons.base.TypedDatum.Type
 
isVerbose() - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
iterator() - Method in class org.expasy.jpl.commons.base.record.DataTable
Get an iterator over the records.
iterator() - Method in interface org.expasy.jpl.commons.collection.ExtraIterable
Returns a JPL iterator over a set of elements of type T.
iterator() - Method in interface org.expasy.jpl.commons.collection.IndexIterable
Returns a JPL iterator over a list of Integer.
iterator(SymbolSequence<T>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner
 
iterator() - Method in class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher
 
iterator(SymbolSequence<T>) - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SequenceIterable
coupling sequence with iterator

J

join(Iterable<String>, String) - Static method in class org.expasy.jpl.commons.base.string.StringUtils
 
JPLFile - Class in org.expasy.jpl.commons.base.io
A File that supports localized paths Also adds basename/dirname functionality.
JPLFile(String) - Constructor for class org.expasy.jpl.commons.base.io.JPLFile
 
JPLTerminalApplication - Interface in org.expasy.jpl.commons.app
All JPL applications launched from the terminal will have to implements these methods.
JProgressBarAdapter - Class in org.expasy.jpl.commons.base.task
A simple adapter of JProgressBar to interface ProgressBar

K

keepTrack() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
KPartiteGraphImpl<V,E> - Class in org.expasy.jpl.commons.collection.graph
A simple implementation of KPartiteGraph.
KPartiteGraphImpl() - Constructor for class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
KPartiteGraphImpl.Collapser<V,E> - Class in org.expasy.jpl.commons.collection.graph
 
KPartiteGraphImpl.Collapser(KPartiteGraphImpl<V, E>) - Constructor for class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl.Collapser
 
KPartiteGraphImpl.PredicateImpl<T> - Class in org.expasy.jpl.commons.collection.graph
 

L

LaplaceGaussRandomVar - Class in org.expasy.jpl.commons.collection.stat
A random variable that follow the Laplace-Gauss (Normal) Probability Distribution N(mean, variance).
lastIndexOf(PartitionList<T>, Object) - Method in interface org.expasy.jpl.commons.collection.PartitionList.LastIndexingAlgo
 
lastIndexOf(Object) - Method in class org.expasy.jpl.commons.collection.PartitionList
 
lastIndexOf(Object, PartitionList.LastIndexingAlgo<T>) - Method in class org.expasy.jpl.commons.collection.PartitionList
 
length() - Method in interface org.expasy.jpl.commons.collection.symbol.seq.Sequence
 
length() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
 
LESS_EQUALS - Static variable in class org.expasy.jpl.commons.base.cond.operator.OperatorManager
 
LINE_DELIMITOR - Static variable in class org.expasy.jpl.commons.base.io.RegexConstants
About new lines, sources at http://en.wikipedia.org/wiki/Newline: Systems based on ASCII or a compatible character set use either LF (Line feed, '\n', 0x0A, 10 in decimal) or CR (Carriage return, '\r', 0x0D, 13 in decimal) individually, or CR followed by LF (CR+LF, 0x0D 0x0A).
link(Symbol<T>, T) - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
link(Symbol<T>, T) - Method in interface org.expasy.jpl.commons.collection.symbol.DataSymbolRegister
link a symbol to its data
loadArray(T, Transformer<T, double[]>, double[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Copy array of doubles accessible from T-object in a given copy array.
loadBinCenter() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
loadBinLowerBound() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
loadDataInSerie(Number) - Method in interface org.expasy.jpl.commons.collection.stat.StatisticalSerie
load a value in the statistical serie
loadDataInSerie(Number) - Method in class org.expasy.jpl.commons.collection.stat.StatisticalSerieDiscreteDataSet
 
loadSerie(List<? extends Number>) - Method in interface org.expasy.jpl.commons.collection.stat.StatisticalSerie
load values in the statistical serie
loadSerie(List<? extends Number>) - Method in class org.expasy.jpl.commons.collection.stat.StatisticalSerieDiscreteDataSet
 
longValue() - Method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
longValue() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
lookup(String) - Method in class org.expasy.jpl.commons.collection.PoolImpl
lookup(String) - Method in interface org.expasy.jpl.commons.collection.Register
 
lookupData(Symbol<T>) - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
lookupData(char) - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
lookupData(Symbol<T>) - Method in interface org.expasy.jpl.commons.collection.symbol.DataSymbolRegister
 
lookupData(char) - Method in interface org.expasy.jpl.commons.collection.symbol.DataSymbolRegister
 
lookupSymbol(char) - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
lookupSymbol(char) - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
lookupSymbol(char) - Method in interface org.expasy.jpl.commons.collection.symbol.AlphabetView
 
lookUpSymbol(char, Symbol.SymbolType<T>) - Method in class org.expasy.jpl.commons.collection.symbol.SymbolTable
 
lookupSymbolNode(char) - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
lookupSymbolNode(char) - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
lookupSymbolNode(char) - Method in interface org.expasy.jpl.commons.collection.symbol.AlphabetView
 
lookUpSymbolNode(char, Symbol.SymbolType<T>) - Method in class org.expasy.jpl.commons.collection.symbol.SymbolTable
 
lvarName(String) - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl.Builder
the lvalue

M

MAP - Static variable in class org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager
 
map - Variable in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
mapping letter -> symbol tree
Mappable - Interface in org.expasy.jpl.commons.collection
The Mappable interface has to be implemented by all object that can be keyed in hash maps.
mapping(Object[], int[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Map the objects found at given indices.
mapping(int[], int[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Map the integers found at given indices.
mapping(double[], int[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Map the doubles found at given indices.
mapping(double[], int, int) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Map the values found in the given interval.
matcher - Variable in class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher.Iterator
 
maxMemoryBlock(long) - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
meets(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The "m" relation
meetsInverse(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The "mi" relation
MemoryAgent - Class in org.expasy.jpl.commons.base.mem
This agent trace sizeof of running objects.
MemoryAgent() - Constructor for class org.expasy.jpl.commons.base.mem.MemoryAgent
 
MemoryEstimatorReady - Interface in org.expasy.jpl.commons.base.mem
This interface has to be implemented by classes that want to estimate the memory space.
merge(RecordsCount<T>, RecordsCount.Operator) - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
Update n T-records given an operator
merge(RecordsCount<T>, RecordsCount.Operator) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
mergeUp(double[], double[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Merge two sorted arrays (ascending or up) in one
minus(T, int) - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
Remove n T-records.
minus(RecordsCount<T>) - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
Remove all given records from this.
minus(T, int) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
minus(Collection<? extends T>) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
minus(RecordsCount<T>) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
minus(Set<T>, Set<T>) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
Compute s1 - s2.
minusminus(T) - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
Remove one record
minusminus(T) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
MixedRadixNtupleFactory - Class in org.expasy.jpl.commons.base.math
This class generates generalized n-tuples.
MixedRadixNtupleFactory.BadRadixException - Exception in org.expasy.jpl.commons.base.math
 
MixedRadixNtupleFactory.BadRadixException(int) - Constructor for exception org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory.BadRadixException
 
MixedRadixNtupleFactory.BadRadixException(int, Throwable) - Constructor for exception org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory.BadRadixException
 
MotifMatcher<T> - Class in org.expasy.jpl.commons.collection.symbol.seq
This class allows to search a regular expression pattern all over a symbol sequence and store positions in its inner Iterator.
MotifMatcher(String) - Constructor for class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher
Create an instance for a given pattern.
MotifMatcher.Iterator - Class in org.expasy.jpl.commons.collection.symbol.seq
Inner iterator over pattern matching sequence positions.
MotifMatcher.Iterator() - Constructor for class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher.Iterator
 

N

name(String) - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl.Builder
 
name - Variable in class org.expasy.jpl.commons.collection.symbol.AbstractSymbol
the symbol character
name - Variable in class org.expasy.jpl.commons.collection.symbol.AbstractSymbolType
type name
newInstance() - Static method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
 
newInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorApproxEquals
 
newInstance(double) - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorApproxEquals
 
newInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongs
 
newInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongsToDoD
 
newInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorContains
 
newInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorEquals
 
newInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorGreaterThan
 
newInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorInter
 
newInstance() - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorLowerThan
 
newInstance(List<? extends AbstractOperator<T, T>>) - Static method in class org.expasy.jpl.commons.base.cond.operator.impl.OperatorMulti
 
newInstance() - Static method in class org.expasy.jpl.commons.base.CounterImpl
A basic static factory method.
newInstance() - Static method in class org.expasy.jpl.commons.base.GenericProperties
the static factory method to get a new instance
newInstance() - Static method in class org.expasy.jpl.commons.base.io.Serializer
 
newInstance() - Static method in class org.expasy.jpl.commons.base.io.TabFileReader
retrieve new instance
newInstance() - Static method in class org.expasy.jpl.commons.base.io.TabFileWriter
 
newInstance() - Static method in class org.expasy.jpl.commons.base.math.CombinationFactory
 
newInstance(double) - Static method in class org.expasy.jpl.commons.base.math.DoubleComparator
 
newInstance() - Static method in class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory
Generate all tuples considering the given strict limits (excluded).
newInstance(int) - Static method in class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory
 
newInstance() - Static method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
newInstance() - Static method in class org.expasy.jpl.commons.base.process.SequenceTransformer
 
newInstance() - Static method in class org.expasy.jpl.commons.base.process.U2VSequenceTransformer
 
newInstance() - Static method in class org.expasy.jpl.commons.base.record.RecordsCount
 
newInstance(int, int) - Static method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
 
newInstance() - Static method in class org.expasy.jpl.commons.base.TypedDataContainer
 
newInstance(String, TypedDatum.Type<T>) - Static method in class org.expasy.jpl.commons.base.TypedDatum
 
newInstance(String, Transformer<String, T>, Pattern, Class<T>) - Static method in class org.expasy.jpl.commons.base.TypedDatum.Type
Create a new instance of Type.
newInstance() - Static method in class org.expasy.jpl.commons.collection.graph.GraphCloner
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.graph.GraphExporter
 
newInstance(Graph<V, E>) - Static method in class org.expasy.jpl.commons.collection.graph.GraphFilterer
 
newInstance(List<Predicate<V>>, boolean) - Static method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
newInstance(String, Predicate<T>) - Static method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl.PredicateImpl
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.IntegerSequenceWithGap
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.PoolImpl
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.render.BarCodeRenderer
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.render.StatisticalSerieRenderer
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.sorter.ArraySorterImpl
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.sorter.ChainedComparator
 
newInstance(Comparator<T>...) - Static method in class org.expasy.jpl.commons.collection.sorter.ChainedComparator
Make an instance of ChainedComparator.
newInstance(List<Comparator<T>>) - Static method in class org.expasy.jpl.commons.collection.sorter.ChainedComparator
 
newInstance(String, StringCodedComparatorFactory<T>) - Static method in class org.expasy.jpl.commons.collection.sorter.ChainedStringCodedComparator
 
newInstance(Comparator<T>) - Static method in class org.expasy.jpl.commons.collection.sorter.ComparatorInverter
 
newInstance(Transformer<T, Double>) - Static method in class org.expasy.jpl.commons.collection.sorter.NumberStringBasedComparator
 
newInstance(AbstractStringBasedComparator.OrderType, Transformer<T, Double>) - Static method in class org.expasy.jpl.commons.collection.sorter.NumberStringBasedComparator
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.sorter.StringCodedComparatorFactory
 
newInstance(Transformer<T, String>) - Static method in class org.expasy.jpl.commons.collection.sorter.StringStringBasedComparator
 
newInstance(AbstractStringBasedComparator.OrderType, Transformer<T, String>) - Static method in class org.expasy.jpl.commons.collection.sorter.StringStringBasedComparator
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.stat.StatisticalSerieDiscreteDataSet
 
newInstance(Symbol.SymbolType<T>) - Static method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
newInstance(String) - Static method in class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
 
newInstance() - Static method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolMergerImpl
Build a new merger.
newNode(T, TreeNode<T>) - Static method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
newRoot(T) - Static method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
newSymbolInstance(Class<? extends Symbol<T>>, Symbol.SymbolType<T>, char) - Static method in class org.expasy.jpl.commons.collection.symbol.AbstractSymbol
 
newTable() - Method in class org.expasy.jpl.commons.base.record.DataTableFactory
 
next() - Method in class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner.Iterator
Returns the next Integer element [method implemented to respect Iterator contract].
nextPosition - Variable in class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner.Iterator
 
nextToList(int) - Method in class org.expasy.jpl.commons.collection.ExtraIterable.AbstractExtraIterator
Return a list with the next elements up to nValues.
nextToList() - Method in class org.expasy.jpl.commons.collection.ExtraIterable.AbstractExtraIterator
Returns all elements into a list.
Node - Interface in org.expasy.jpl.commons.collection.graph
 
noOverlapping() - Static method in class org.expasy.jpl.commons.collection.Interval.IntervalComparator
 
normalizedSum(double) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Set the normalized sum value.
not() - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl.Builder
 
numberOfPositions - Variable in class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner
 
NumberStringBasedComparator<T> - Class in org.expasy.jpl.commons.collection.sorter
 
numOfString(String, String) - Static method in class org.expasy.jpl.commons.base.string.StringUtils
Return the number of time a motif is found within a target string.

O

ObjectSizeEstimator - Class in org.expasy.jpl.commons.base.mem
Estimate the average memory (in bytes) used to store an object from a collection of objects.
operator(Operator) - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl.Builder
 
Operator<U,V> - Interface in org.expasy.jpl.commons.base.cond.operator.api
The Operator interface should be implemented by any operator.
OperatorAnd - Class in org.expasy.jpl.commons.base.cond.operator.impl
 
OperatorApproxEquals<T extends Number> - Class in org.expasy.jpl.commons.base.cond.operator.impl
This operator evaluates the equality of two numbers in a given interval of uncertainty.
OperatorBelongs<T> - Class in org.expasy.jpl.commons.base.cond.operator.impl
This operator evaluates the membership of T-element in set.
OperatorBelongs() - Constructor for class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongs
 
OperatorBelongsToDoD<T> - Class in org.expasy.jpl.commons.base.cond.operator.impl
This operator evaluates the existence of elements that satisfy the set of conditions defined in the DomainOfDefinition.
OperatorBelongsToDoD() - Constructor for class org.expasy.jpl.commons.base.cond.operator.impl.OperatorBelongsToDoD
 
OperatorContains<T> - Class in org.expasy.jpl.commons.base.cond.operator.impl
This operator evaluates the existence of T-element in set.
OperatorContains() - Constructor for class org.expasy.jpl.commons.base.cond.operator.impl.OperatorContains
 
OperatorEquals<T> - Class in org.expasy.jpl.commons.base.cond.operator.impl
This operator evaluates the strict equality of two numbers .
OperatorEquals() - Constructor for class org.expasy.jpl.commons.base.cond.operator.impl.OperatorEquals
 
OperatorGreaterThan<T extends Number> - Class in org.expasy.jpl.commons.base.cond.operator.impl
This operator evaluates T1 is > T2.
OperatorInter<T> - Class in org.expasy.jpl.commons.base.cond.operator.impl
This operator evaluates the intersection of sets.
OperatorInter() - Constructor for class org.expasy.jpl.commons.base.cond.operator.impl.OperatorInter
 
OperatorLowerThan<T extends Number> - Class in org.expasy.jpl.commons.base.cond.operator.impl
This operator evaluates T1 is < T2.
OperatorManager - Class in org.expasy.jpl.commons.base.cond.operator
This manager stores all Operators and provides an access by name.
OperatorManager() - Constructor for class org.expasy.jpl.commons.base.cond.operator.OperatorManager
 
OperatorManager.InvalidOperatorException - Exception in org.expasy.jpl.commons.base.cond.operator
 
OperatorManager.InvalidOperatorException(String) - Constructor for exception org.expasy.jpl.commons.base.cond.operator.OperatorManager.InvalidOperatorException
 
OperatorManager.InvalidOperatorRTException - Exception in org.expasy.jpl.commons.base.cond.operator
Exception thrown when AbstractOperator is not well configured or adapted to the operand types.
OperatorManager.InvalidOperatorRTException(String) - Constructor for exception org.expasy.jpl.commons.base.cond.operator.OperatorManager.InvalidOperatorRTException
 
OperatorMulti<T> - Class in org.expasy.jpl.commons.base.cond.operator.impl
This operator evaluates the all collection of operators.
OperatorOr - Class in org.expasy.jpl.commons.base.cond.operator.impl
 
org.expasy.jpl.commons.app - package org.expasy.jpl.commons.app
Provides classes and interfaces to build JPL terminal applications.
org.expasy.jpl.commons.base - package org.expasy.jpl.commons.base
Provides JPL base objects and interfaces.
org.expasy.jpl.commons.base.builder - package org.expasy.jpl.commons.base.builder
Provides builder objects and interfaces.
org.expasy.jpl.commons.base.cond - package org.expasy.jpl.commons.base.cond
Provides generic condition and expression classes that may be tested on any object.
org.expasy.jpl.commons.base.cond.operator - package org.expasy.jpl.commons.base.cond.operator
Provides operators for conditions.
org.expasy.jpl.commons.base.cond.operator.api - package org.expasy.jpl.commons.base.cond.operator.api
Provides api for condition operators.
org.expasy.jpl.commons.base.cond.operator.impl - package org.expasy.jpl.commons.base.cond.operator.impl
Provides implementations of condition operators.
org.expasy.jpl.commons.base.io - package org.expasy.jpl.commons.base.io
Provides interfaces for I/O.
org.expasy.jpl.commons.base.math - package org.expasy.jpl.commons.base.math
Provides algorithms and objects for mathematics and statistics computations.
org.expasy.jpl.commons.base.mem - package org.expasy.jpl.commons.base.mem
Provides classes to evaluate and measure memory.
org.expasy.jpl.commons.base.process - package org.expasy.jpl.commons.base.process
Provides interfaces and objects for data processing.
org.expasy.jpl.commons.base.record - package org.expasy.jpl.commons.base.record
Provides data records.
org.expasy.jpl.commons.base.render - package org.expasy.jpl.commons.base.render
Provides interfaces for image rendering.
org.expasy.jpl.commons.base.string - package org.expasy.jpl.commons.base.string
Provides strings services.
org.expasy.jpl.commons.base.task - package org.expasy.jpl.commons.base.task
Provides objects and interface about task description and monitoring.
org.expasy.jpl.commons.collection - package org.expasy.jpl.commons.collection
Provides JPL collection objects.
org.expasy.jpl.commons.collection.graph - package org.expasy.jpl.commons.collection.graph
Provides higher structured graphs object and interface (based on jung2 library).
org.expasy.jpl.commons.collection.render - package org.expasy.jpl.commons.collection.render
Provides interfaces and renderers for image rendering of collections.
org.expasy.jpl.commons.collection.sorter - package org.expasy.jpl.commons.collection.sorter
Provides sorters for arrays of primitives and generic collections of objects.
org.expasy.jpl.commons.collection.stat - package org.expasy.jpl.commons.collection.stat
Provides interfaces and objects for statistical data.
org.expasy.jpl.commons.collection.symbol - package org.expasy.jpl.commons.collection.symbol
Provides symbols and alphabets.
org.expasy.jpl.commons.collection.symbol.seq - package org.expasy.jpl.commons.collection.symbol.seq
Provides generic symbol sequence and associated tools.
org.expasy.jpl.commons.collection.tree - package org.expasy.jpl.commons.collection.tree
Provides tree objects.
originalGraph - Variable in class org.expasy.jpl.commons.collection.graph.GraphCollapser
 
originalGraph - Variable in class org.expasy.jpl.commons.collection.graph.GraphFilterer
 
outputStream(OutputStream) - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl.Builder
 
overlaps(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The "o" relation
overlapsInverse(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The "oi" relation

P

parse(CT, BT) - Method in interface org.expasy.jpl.commons.base.io.BuilderBasedParser
parses the content and transmit infos to builder.
parse(T) - Method in interface org.expasy.jpl.commons.base.io.Parser
parse the content
parse(File) - Method in class org.expasy.jpl.commons.base.io.TabFileReader
 
parseArguments(List<String>) - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
parseDoubleList(String) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
 
parseIntList(String) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
 
parseList(String, Transformer<String, E>) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
Convert a string to a List.
Parser<T> - Interface in org.expasy.jpl.commons.base.io
The Parser interface should be implemented by any parsers intending to parse T type content.
parseSpecificOptions(Options, Properties, CommandLine) - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
parseStringList(String) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
 
parseTreeString(String, Class<? extends Symbol<T>>, Symbol.SymbolType<T>) - Static method in class org.expasy.jpl.commons.collection.symbol.AbstractSymbolType
 
PartitionList<T> - Class in org.expasy.jpl.commons.collection
This object is a partition of a List that proposes a view of smaller split Lists.
PartitionList.IndexingAlgo<T> - Interface in org.expasy.jpl.commons.collection
 
PartitionList.LastIndexingAlgo<T> - Interface in org.expasy.jpl.commons.collection
 
plug(T) - Method in interface org.expasy.jpl.commons.base.Pluggable
Plug object
Pluggable<T> - Interface in org.expasy.jpl.commons.base
The Pluggable interface should be implemented by any object that can plug a T type instance.
plus(T, int) - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
Add n T-records.
plus(RecordsCount<T>) - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
Add all given records to this
plus(T, int) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
plus(Collection<? extends T>) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
plus(RecordsCount<T>) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
plusplus(T) - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
Add one record
plusplus(T) - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
Ponderable - Interface in org.expasy.jpl.commons.collection.stat
 
Pool<T extends Cachable> - Interface in org.expasy.jpl.commons.collection
A Pool interface should be implemented by any pool that handles unique objects.
Pool.KeyAlreadyExistException - Exception in org.expasy.jpl.commons.collection
Exception thrown when key already already reference an object in the pool.
Pool.KeyAlreadyExistException(String) - Constructor for exception org.expasy.jpl.commons.collection.Pool.KeyAlreadyExistException
 
Pool.ObjectAlreadyExistException - Exception in org.expasy.jpl.commons.collection
Exception thrown when object already exists in the pool.
Pool.ObjectAlreadyExistException(T) - Constructor for exception org.expasy.jpl.commons.collection.Pool.ObjectAlreadyExistException
 
PoolImpl<T extends Cachable> - Class in org.expasy.jpl.commons.collection
This pool stores unique and immutable objects.
populateData(T) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Add T-object data set
populateData(StatisticalSerie<T>) - Method in class org.expasy.jpl.commons.collection.render.BarCodeRenderer
Add the statistical data set (default colors: 1st serie (blue), 2nd serie (red)).
populateData(StatisticalSerie<T>) - Method in class org.expasy.jpl.commons.collection.render.StatisticalSerieRenderer
Add the statistical data set (default colors: 1st serie (blue), 2nd serie (red)).
ppm(double) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Set the ppm value.
precedes(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The < relation
precision(int) - Method in class org.expasy.jpl.commons.collection.Interval.Builder
 
predicate(Predicate<V>) - Method in class org.expasy.jpl.commons.collection.graph.GraphExporter.Builder
 
premain(String, Instrumentation) - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
Initializes agent
prettyByteDisabled() - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
 
prettyByteEnabled() - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
 
PrimitiveArrayUtils - Class in org.expasy.jpl.commons.collection
Provides static generic methods on primitive arrays.
PrimitiveArrayUtils() - Constructor for class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
 
printStackCommands() - Method in interface org.expasy.jpl.commons.base.cond.Condition
simply print the commands
printStackCommands() - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl
Trace tree expression stack status
printStream(PrintStream) - Method in class org.expasy.jpl.commons.collection.graph.GraphExporter.Builder
 
ProbDistLGUtils - Class in org.expasy.jpl.commons.collection.stat
 
ProbDistLGUtils() - Constructor for class org.expasy.jpl.commons.collection.stat.ProbDistLGUtils
 
process(int, int) - Method in class org.expasy.jpl.commons.base.math.CombinationFactory
Generate all combinations of p elements among n.
process(T) - Method in interface org.expasy.jpl.commons.base.process.Processor
Process the given T-object
process(SymbolSequence<T>, SymbolSequence<T>) - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SequenceMerger
concatenate two sequences.
process(Collection<SymbolSequence<T>>) - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SequenceMerger
concatenate many sequences.
process(SymbolSequence<T>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
Compute all the occurrences of a sequence of symbols.
process(List<SymbolSequence<T>>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
Compute all the occurrences of symbol for a list of symbol sequences
process(SymbolSequence<T>...) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
 
process(SymbolSequence<T>, SymbolSequence<T>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolMergerImpl
concatenate two sequences.
process(Collection<SymbolSequence<T>>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolMergerImpl
Concatenate all sequences.
ProcessException - Exception in org.expasy.jpl.commons.base.process
ProcessException signals that an error has been reached while processing an object.
ProcessException(String) - Constructor for exception org.expasy.jpl.commons.base.process.ProcessException
 
ProcessException(String, Throwable) - Constructor for exception org.expasy.jpl.commons.base.process.ProcessException
 
Processor<T> - Interface in org.expasy.jpl.commons.base.process
The Processor process a given data object.
ProgressBar - Interface in org.expasy.jpl.commons.base.task
All progress bar classes will have to implements these methods.
ProgressBarReady - Interface in org.expasy.jpl.commons.base.task
Deprecated. 
prompt(String) - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl.Builder
 

R

readHistosFromFile(String, String) - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Reads statistical histograms from file
REAL - Static variable in class org.expasy.jpl.commons.base.io.RegexConstants
float expression
RecordsCount<T> - Class in org.expasy.jpl.commons.base.record
This object handles counters on T-types records.
RecordsCount.Operator - Enum in org.expasy.jpl.commons.base.record
a count operator
RecordsCountUtils - Class in org.expasy.jpl.commons.base.record
 
RecordsCountUtils() - Constructor for class org.expasy.jpl.commons.base.record.RecordsCountUtils
 
RegexConstants - Class in org.expasy.jpl.commons.base.io
A list of static regular expressions.
RegexConstants() - Constructor for class org.expasy.jpl.commons.base.io.RegexConstants
 
register(String, Condition<T>) - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
Add a named condition in the condition table.
register(Condition<T>) - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
Add anonymous condition instance in the condition table.
register(String, String) - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
 
register(String) - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
Add anonymous condition.
register(T) - Method in class org.expasy.jpl.commons.collection.PoolImpl
 
Register<T extends Registrable> - Interface in org.expasy.jpl.commons.collection
A recording of T-objects.
register(T) - Method in interface org.expasy.jpl.commons.collection.Register
 
register(String, StringBasedFactory<Comparator<T>>) - Method in class org.expasy.jpl.commons.collection.sorter.StringCodedComparatorFactory
 
registerAllSymbolNodes(TreeView<? extends Symbol<T>>) - Method in interface org.expasy.jpl.commons.collection.symbol.Alphabet
Add all nodes including the given tree root in the symbol table
registerAllSymbolNodes(TreeView<? extends Symbol<T>>) - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
registerAllSymbolNodes(TreeView<? extends Symbol<T>>) - Method in class org.expasy.jpl.commons.collection.symbol.SymbolTable
 
registerSymbolNode(TreeView<? extends Symbol<T>>) - Method in interface org.expasy.jpl.commons.collection.symbol.Alphabet
Add the given node in the symbol table
registerSymbolNode(TreeView<? extends Symbol<T>>) - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
registerSymbolNode(TreeView<? extends Symbol<T>>) - Method in class org.expasy.jpl.commons.collection.symbol.SymbolTable
 
Registrable - Interface in org.expasy.jpl.commons.base
All Registrable objects have to be identifiable.
remove() - Method in class org.expasy.jpl.commons.collection.ExtraIterable.AbstractExtraIterator
remove is not supported.
removeAllConditions() - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
Remove all conditions.
removeCondition(String) - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
Remove the condition.
removeDatum(String) - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
removeEdge(E) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
removeVertex(V) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
render() - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
render the chart
render() - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Create an image (prerequisite: data sets have already been entered via addDataSet method).
render(HistogramDataSet, String) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Create an image corresponding to the given MS spectrum.
render() - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Create an image (prerequisite: data sets have already been entered via addDataSet method).
reset() - Method in class org.expasy.jpl.commons.base.CounterImpl
 
reset() - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
Clears column names and values and resets parameters to default
reset() - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
reset() - Method in interface org.expasy.jpl.commons.base.Resetable
reinitialising object
Resetable - Interface in org.expasy.jpl.commons.base
The Resetable interface should be implemented by any mutable object that can be reused principally for performance reasons.
reverse(int[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
simply reverse the array
revert() - Method in class org.expasy.jpl.commons.collection.IntegerSequence.Builder
 
run() - Method in interface org.expasy.jpl.commons.app.JPLTerminalApplication
run the application
RunTimeMemoryEstimator - Class in org.expasy.jpl.commons.base.mem
This class evaluates the amount of memory used, free and total.
RunTimeMemoryEstimator() - Constructor for class org.expasy.jpl.commons.base.mem.RunTimeMemoryEstimator
 

S

searchIndices(double[], double[], double) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Search the given query intervals into the target values.
searchIndices(double[], double[], double, int) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Search the given query intervals into the target values.
select(Condition<DataTable.Record>) - Method in class org.expasy.jpl.commons.base.record.DataTable
Select every Records that satisfy the given condition.
select(Set<Integer>, int, int) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
Keep all integers that belong to the interval.
select(Set<Integer>, Interval) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
Keep all integers that belong to the interval.
sequence - Variable in class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner
Iterator will iterate over found positions on this sequence.
Sequence<T> - Interface in org.expasy.jpl.commons.collection.symbol.seq
This interface is the generic version of CharSequence for any object.
SequenceIterable<T> - Interface in org.expasy.jpl.commons.collection.symbol.seq
This interface allows the manipulation of iterator over T-sequence indices.
SequenceMerger<T> - Interface in org.expasy.jpl.commons.collection.symbol.seq
All concrete subclasses of this interface will have to provides implementations for the processing of concatenation and access to the merged symbol sequence.
SequenceOutOfBoundsException - Exception in org.expasy.jpl.commons.collection.symbol.seq
 
SequenceOutOfBoundsException() - Constructor for exception org.expasy.jpl.commons.collection.symbol.seq.SequenceOutOfBoundsException
 
SequenceOutOfBoundsException(String) - Constructor for exception org.expasy.jpl.commons.collection.symbol.seq.SequenceOutOfBoundsException
 
SequenceSymbolCounter<T> - Class in org.expasy.jpl.commons.collection.symbol.seq
This object calculates the number of symbols in SymbolSequence[s].
SequenceSymbolMergerImpl<T> - Class in org.expasy.jpl.commons.collection.symbol.seq
This class simply concatenates SymbolSequences in a new SymbolSequence.
SequenceTransformer<T> - Class in org.expasy.jpl.commons.base.process
Manager that handles list of Transformer<T> and transform all.
SerialIdentifiable - Interface in org.expasy.jpl.commons.base
The SerialIdentifiable interface has to be implemented by all class that can be serialized and identified.
serialize(T, String) - Method in class org.expasy.jpl.commons.base.io.Serializer
 
serialize(T) - Method in class org.expasy.jpl.commons.base.io.Serializer
Serializes a T-object.
Serializer<T extends Serializable> - Class in org.expasy.jpl.commons.base.io
The serializer just handles (de)serialization of objects T.
Serializer() - Constructor for class org.expasy.jpl.commons.base.io.Serializer
 
setArray(Object) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractDoublesArrayIndexComparator
 
setArray(Object) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractIntsArrayIndexComparator
 
setArray(Object) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractListIndexComparator
 
setArray(Object) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractObjectsArrayIndexComparator
 
setArray(Object) - Method in interface org.expasy.jpl.commons.collection.sorter.ArrayIndexComparator
set the array to sort
setBackgroundColor(Paint) - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
set the background color
setBackgroundColor(Paint) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Set plot background color.
setBackgroundColor(Paint) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Set plot background color.
setBarLength(int) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
Set the progress bar length.
setBarWidth(double) - Method in interface org.expasy.jpl.commons.base.render.BarChartRenderer
set the bar width
setBarWidth(double) - Method in class org.expasy.jpl.commons.collection.render.BarCodeRenderer
 
setBarWidth(double) - Method in class org.expasy.jpl.commons.collection.render.StatisticalSerieRenderer
 
setBinExport(boolean) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSetExporter
 
setBlockMemoryLimit(long) - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
Set the memory limit.
setChartColor(int, Paint) - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
set the color of ith chart
setChartColor(int, Paint) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
setChartColor(int, Paint) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
 
setColumnNames(List<String>) - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
Add a column names
setCompatibleOperands(Class<U>, Class<V>) - Method in class org.expasy.jpl.commons.base.cond.operator.api.AbstractOperator
 
setCompatibleOperands(Set<Class<U>>, Set<Class<V>>) - Method in class org.expasy.jpl.commons.base.cond.operator.api.AbstractOperator
 
setCompatibleOperands(Set<Class<U>>, Set<Class<V>>) - Method in interface org.expasy.jpl.commons.base.cond.operator.api.Operator
 
setCondition(Condition<T>) - Method in interface org.expasy.jpl.commons.base.cond.ConditionBasedFilterReady
Set a condition for all parsed T-objects
setData(T) - Method in interface org.expasy.jpl.commons.collection.tree.TreeNode
Set the data to this node.
setData(T) - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
setDefaultOrderType() - Method in class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
setDimension(Dimension) - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
set chart dimension
setDimension(Dimension) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Set image dimension.
setDimension(Dimension) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Set image dimension.
setDoneMessage(String) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
 
setFrequency(double) - Method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
setHeader(String) - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
 
setId(String) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
setImageFormat(ImageFormat) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Set image format.
setImageFormat(ImageFormat) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Set image format.
setIncompleteMessage(String) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
 
setIndeterminate(boolean) - Method in class org.expasy.jpl.commons.base.task.JProgressBarAdapter
 
setIndeterminate(boolean) - Method in interface org.expasy.jpl.commons.base.task.ProgressBar
Sets the indeterminate property of the progress bar which determines whether the progress bar is in determinate or indeterminate mode.
setIndeterminate(boolean) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
 
setInputStream(InputStream) - Method in interface org.expasy.jpl.commons.app.InteractiveInputScanner
Set input stream from where input is find (stdin by default)
setInputStream(InputStream) - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl
 
setLeftMarginLength(int) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
Set the left margin length (with completion infos).
setMaximum(int) - Method in class org.expasy.jpl.commons.base.task.JProgressBarAdapter
 
setMaximum(int) - Method in interface org.expasy.jpl.commons.base.task.ProgressBar
Sets the progress bar's minimum value to n
setMaximum(int) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
 
setMaxMemoryRatio(double) - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
Set the max free memory ratio.
setMaxWeight(double) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Update the maximum weight value and normalize others.
setMemoryCalculator(ObjectSizeEstimator) - Method in interface org.expasy.jpl.commons.base.mem.MemoryEstimatorReady
set the memory estimator
setMinimum(int) - Method in class org.expasy.jpl.commons.base.task.JProgressBarAdapter
 
setMinimum(int) - Method in interface org.expasy.jpl.commons.base.task.ProgressBar
Sets the progress bar's maximum value to n
setMinimum(int) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
 
setNegativeAllScores(List<Double>, List<Double>) - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Set list of scores for the positive distribution
setNrFractDecDigits(int) - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
Set number of fractional decimal digits
setOrderType(String) - Method in class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
setOriGraph(KPartiteGraphImpl<V, E>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl.Collapser
 
setOutputStream(OutputStream) - Method in interface org.expasy.jpl.commons.app.InteractiveInputScanner
Set output stream to where prompt flushed (stdout by default)
setOutputStream(OutputStream) - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl
 
setParent(TreeNode<T>) - Method in interface org.expasy.jpl.commons.collection.tree.TreeNode
Set the parent node.
setParent(TreeNode<T>) - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
setPartitions(Collection<Predicate<V>>) - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
setPonderation(double) - Method in interface org.expasy.jpl.commons.collection.stat.Ponderable
 
setPositiveAllScores(List<Double>, List<Double>) - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Set list of scores for the positive distribution
setPositiveNegativeScores(List<Double>, List<Double>) - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Set list of scores for the positive distribution
setPrintStream(PrintStream) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
Set the print stream for bar display.
setProgressBar(ProgressBar) - Method in interface org.expasy.jpl.commons.base.task.ProgressBarReady
Deprecated. Bound progress bar
setPropertyValues() - Method in class org.expasy.jpl.commons.app.AbstractApplicationParameters
This method handles all setting/conversions of parameter values to the correct type.
setReadHeader(boolean) - Method in class org.expasy.jpl.commons.base.io.TabFileReader
Set flag that defines whether to read heather
setRefreshBarPeriod(int) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
Set the period of bar animation refresh while the bar is in indeterminate mode.
setScoreBinParams(double, double, double) - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Set parameters for creating the score bins
setScoreBinParams(double, double, int) - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Set parameters for creating the score bins
setSegmentLength(int) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
Set the length of segment constantly animated in indeterminate mode.
setSeparator(String) - Method in class org.expasy.jpl.commons.base.io.TabFileReader
Set separator
setSeparator(String) - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
Set separator
setSequence(SymbolSequence<T>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner
Set the sequence for future searches.
setSequence(SymbolSequence<T>) - Method in class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher
Override setSequence() to convert byte sequence representation to String in order to use Java Regular Expression.
setSequence(SymbolSequence<T>) - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SequenceIterable
sequence over which positions will be retrieved.
setTaskName(String) - Method in class org.expasy.jpl.commons.base.task.JProgressBarAdapter
 
setTaskName(String) - Method in interface org.expasy.jpl.commons.base.task.ProgressBar
Set the task name (displayed in left margin)
setTaskName(String) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
 
settings - Variable in class org.expasy.jpl.commons.app.AbstractApplicationParameters
the parameters
setTransformer(Transformer<T, String>) - Method in class org.expasy.jpl.commons.collection.graph.GraphPredicate.VertexPatternPredicate
 
setTransformers(List<Transformer<T, T>>) - Method in class org.expasy.jpl.commons.base.process.SequenceTransformer
Set processors.
setValue(int) - Method in class org.expasy.jpl.commons.base.task.JProgressBarAdapter
 
setValue(int) - Method in interface org.expasy.jpl.commons.base.task.ProgressBar
Sets the progress bar's current value to n
setValue(int) - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
 
setValues(List<List<Double>>) - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
Set all values
setXAxisDefaultInterval() - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
 
setXAxisDefaultInterval() - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
setXAxisDefaultInterval() - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
 
setXAxisInterval(double, double) - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
set the x-axis interval to render
setXAxisInterval(double, double) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
 
setXAxisInterval(double, double) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
 
setXAxisLegend(String) - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
set x axis legend
setXAxisLegend(String) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Set the legend for the m/z axis.
setXAxisLegend(String) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Set the legend for the var axis.
setXYValues(ArrayList<Double>, ArrayList<Double>) - Method in class org.expasy.jpl.commons.base.math.StraightLineFitter
Sets x-,y-values.
setXYValues(ArrayList<Double>, ArrayList<Double>, ArrayList<Double>) - Method in class org.expasy.jpl.commons.base.math.StraightLineFitter
Sets x-,y- and variance values
setYAxisLegend(String) - Method in interface org.expasy.jpl.commons.base.render.ChartRenderer
set y axis legend
setYAxisLegend(String) - Method in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
Set the legend for the intensity axis.
setYAxisLegend(String) - Method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Set the legend for the frequency axis.
size() - Method in class org.expasy.jpl.commons.base.GenericProperties
 
size() - Method in class org.expasy.jpl.commons.base.process.SequenceTransformer
 
size() - Method in interface org.expasy.jpl.commons.base.record.CountableRecords
 
size() - Method in class org.expasy.jpl.commons.base.record.DataTable
 
size() - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
size() - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
size() - Method in class org.expasy.jpl.commons.collection.IntegerSequence
 
size() - Method in class org.expasy.jpl.commons.collection.IntegerSequenceWithGap
 
size() - Method in class org.expasy.jpl.commons.collection.PartitionList
 
size() - Method in class org.expasy.jpl.commons.collection.PoolImpl
size() - Method in interface org.expasy.jpl.commons.collection.Register
 
size() - Method in class org.expasy.jpl.commons.collection.sorter.ChainedComparator
 
size() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
sizeOf(Object) - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
Returns object size.
smoothHisto(HistogramDataSet) - Static method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
smoothHisto(HistogramDataSet, int) - Static method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
A local smoothing by medians, of given window size is applied to the given histogram.
sort() - Method in class org.expasy.jpl.commons.collection.sorter.ArrayIndexSorter
Sort the indices of array's object
sort(T[]) - Method in interface org.expasy.jpl.commons.collection.sorter.ArraySorter
sort array of T-objects
sort(T[], int, int) - Method in interface org.expasy.jpl.commons.collection.sorter.ArraySorter
sort array of T-objects between from and to
sort(T[]) - Method in class org.expasy.jpl.commons.collection.sorter.ArraySorterImpl
 
sort(T[], int, int) - Method in class org.expasy.jpl.commons.collection.sorter.ArraySorterImpl
Reimplementation of quicksort for performance gain.
sortDown(int[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Sort int values in descending order.
sortDown(double[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Sort double values in descending order.
sortIndexesDown(int[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Sort int value indices in descending order.
sortIndexesDown(double[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
 
sortIndexesUp(int[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Sort int value indices in ascending order.
sortIndexesUp(double[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
 
sortIndices(double[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
 
sortIndices(double[], int[], int, int) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Reimplementation of quicksort for performance gain.
sortIndices(T[]) - Method in interface org.expasy.jpl.commons.collection.sorter.ArraySorter
sort indinces of array of T-objects
sortIndices(T[]) - Method in class org.expasy.jpl.commons.collection.sorter.ArraySorterImpl
 
sortUp(int[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Sort int values in ascending order.
sortUp(double[]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Sort double values in ascending order.
sortUpArrraysOnFirst(double[][]) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
sort (increasing) the list of arrays based on the values contained in the first one (think of masses, intensities...)
sortValues() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
 
start() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
Init the memory size estimation.
start() - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
Initialize progress bar (mandatory to restart bar in Indeterminate mode)
starts(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The "s" relation
startsInverse(Interval, Interval) - Method in class org.expasy.jpl.commons.collection.Interval.OverlapFinder
The "si" relation
StatisticalCategory - Class in org.expasy.jpl.commons.collection.stat
A statistical category or class is an interval of values where data lie.
StatisticalCategory(HistogramDataSet, Interval) - Constructor for class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
StatisticalCategory(HistogramDataSet, double, double) - Constructor for class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
StatisticalSerie<T extends Number> - Interface in org.expasy.jpl.commons.collection.stat
The StatisticalSerie interface should be implemented by any 1-Dimension statistical serie concerning samples with one measured variable.
StatisticalSerieDiscreteDataSet - Class in org.expasy.jpl.commons.collection.stat
A StatisticalSerieDiscreteVar contains only integer values.
StatisticalSerieRenderer<T extends Number> - Class in org.expasy.jpl.commons.collection.render
This object renders StatisticalSerie objects.
StatScoreCalculator - Class in org.expasy.jpl.commons.base.math
Class to calculate false discovery rate (FDR), and the log-ratio log(p(score|+)/p(score|-)) (logProbRatio) for a given lists of positive and negative scores.
StatScoreCalculator() - Constructor for class org.expasy.jpl.commons.base.math.StatScoreCalculator
 
stdError(double) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet.Builder
Set the standard error value.
stop(int) - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
Stop the current memory size estimation.
stop() - Method in class org.expasy.jpl.commons.base.task.TerminalProgressBar
Interrupt the task (mandatory to complete Inderminate mode)
STR_2_BOOL - Static variable in class org.expasy.jpl.commons.base.string.StringConverters
String -> Boolean
STR_2_DBL - Static variable in class org.expasy.jpl.commons.base.string.StringConverters
String -> Double
STR_2_INT - Static variable in class org.expasy.jpl.commons.base.string.StringConverters
String -> Integer
STR_2_MAP - Static variable in class org.expasy.jpl.commons.base.string.StringConverters
String -> Map
STR_2_NBR - Static variable in class org.expasy.jpl.commons.base.string.StringConverters
String -> Number
STR_2_STR - Static variable in class org.expasy.jpl.commons.base.string.StringConverters
String -> String
StraightLineFitter - Class in org.expasy.jpl.commons.base.math
Class to fit straight line to a set of 2D data points.
StraightLineFitter(ArrayList<Double>, ArrayList<Double>) - Constructor for class org.expasy.jpl.commons.base.math.StraightLineFitter
Constructor : y-variance is set to 1 for all data points
StraightLineFitter(ArrayList<Double>, ArrayList<Double>, ArrayList<Double>) - Constructor for class org.expasy.jpl.commons.base.math.StraightLineFitter
Constructor
STRING - Static variable in class org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager
 
StringBasedFactory<T> - Interface in org.expasy.jpl.commons.base.builder
The StringBasedFactory interface should be implemented by any factory building T type instance from a given string.
StringCodedComparatorFactory<T> - Class in org.expasy.jpl.commons.collection.sorter
This object is a factory that create Comparator<T>s based on String (comparator-id:comparator-logic).
StringConverters - Class in org.expasy.jpl.commons.base.string
StringConverters simply provides converter from string into specific values.
StringConverters() - Constructor for class org.expasy.jpl.commons.base.string.StringConverters
 
StringConverters.StringConverter<T> - Class in org.expasy.jpl.commons.base.string
 
StringConverters.StringConverter() - Constructor for class org.expasy.jpl.commons.base.string.StringConverters.StringConverter
 
StringStringBasedComparator<T> - Class in org.expasy.jpl.commons.collection.sorter
 
StringUtils - Class in org.expasy.jpl.commons.base.string
 
StringUtils() - Constructor for class org.expasy.jpl.commons.base.string.StringUtils
 
subSequence(int, int) - Method in interface org.expasy.jpl.commons.collection.symbol.seq.Sequence
 
subSequence(int, int) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
Warning: [start, end[
sumLogProbRatios(int, double, List<Double>) - Method in class org.expasy.jpl.commons.base.math.StatScoreCalculator
Calculates the logProbRatios for a set of statistically independent scores.
switchFlyweightProfilingOff() - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
 
switchFlyweightProfilingOn() - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
 
sym2data - Variable in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
Symbol<T> - Interface in org.expasy.jpl.commons.collection.symbol
The Symbol interface should be implemented by any symbol class defined by a character id and a SymbolType<T>.
Symbol.SymbolType<T> - Interface in org.expasy.jpl.commons.collection.symbol
A symbol type is defined by a name and an alphabet
SymbolNotFoundException - Exception in org.expasy.jpl.commons.collection.symbol
 
SymbolNotFoundException() - Constructor for exception org.expasy.jpl.commons.collection.symbol.SymbolNotFoundException
 
SymbolNotFoundException(String) - Constructor for exception org.expasy.jpl.commons.collection.symbol.SymbolNotFoundException
 
SymbolNotFoundException(Throwable) - Constructor for exception org.expasy.jpl.commons.collection.symbol.SymbolNotFoundException
 
SymbolNotFoundException(String, Throwable) - Constructor for exception org.expasy.jpl.commons.collection.symbol.SymbolNotFoundException
 
symbolSequence - Variable in class org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher
String representation of SymbolSequenceImpl
SymbolSequence<T> - Interface in org.expasy.jpl.commons.collection.symbol.seq
The SymbolSequence interface should be implemented by any concrete class that deals with sequence of symbols.
SymbolSequenceImpl<E> - Class in org.expasy.jpl.commons.collection.symbol.seq
A sequence of symbol letters defined by an alphabet.
SymbolSequenceImpl() - Constructor for class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
for serialization only
SymbolSequenceImpl(SymbolSequenceImpl.Builder<E>) - Constructor for class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
The only constructor that build an instance of JPLAASequence.
SymbolSequenceImpl.Builder<E> - Class in org.expasy.jpl.commons.collection.symbol.seq
This builder builds an instance of JPLAASequence given a numerous number of possible parameters.
SymbolSequenceImpl.Builder(String, Symbol.SymbolType<E>) - Constructor for class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl.Builder
The main builder constructor.
SymbolSequenceImpl.Builder(SymbolSequenceImpl<E>) - Constructor for class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl.Builder
An alternative builder constructor.
SymbolTable<T> - Class in org.expasy.jpl.commons.collection.symbol
A table that stores symbols grouped by alphabet type.
SymbolTable() - Constructor for class org.expasy.jpl.commons.collection.symbol.SymbolTable
 

T

TabFileReader - Class in org.expasy.jpl.commons.base.io
 
TabFileReader() - Constructor for class org.expasy.jpl.commons.base.io.TabFileReader
Constructor
TabFileWriter - Class in org.expasy.jpl.commons.base.io
Class to write tabular files
TabFileWriter() - Constructor for class org.expasy.jpl.commons.base.io.TabFileWriter
 
TerminalProgressBar - Class in org.expasy.jpl.commons.base.task
A simple terminal progress bar.
to(int) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl.Builder
 
toCategory(int) - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
toDoubleArray(List<Double>) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Convert a list of Doubles to an array of doubles.
toHistogram(LaplaceGaussRandomVar) - Static method in class org.expasy.jpl.commons.collection.stat.ProbDistLGUtils
 
toIntArray(List<Integer>) - Static method in class org.expasy.jpl.commons.collection.PrimitiveArrayUtils
Convert a list of Integers to an array of ints.
toInts() - Method in class org.expasy.jpl.commons.collection.IntegerSequence
 
toInts() - Method in class org.expasy.jpl.commons.collection.IntegerSequenceWithGap
 
toList(CountableRecords<T>) - Static method in class org.expasy.jpl.commons.base.record.RecordsCount
Convert to list of Ts.
toString() - Method in class org.expasy.jpl.commons.base.AbstractDecorator
 
toString() - Method in exception org.expasy.jpl.commons.base.builder.BuilderException
 
toString() - Method in class org.expasy.jpl.commons.base.cond.ConditionImpl
 
toString() - Method in class org.expasy.jpl.commons.base.cond.operator.api.AbstractOperator
 
toString() - Method in class org.expasy.jpl.commons.base.cond.operator.OperatorManager
 
toString() - Method in class org.expasy.jpl.commons.base.CounterImpl
 
toString() - Method in class org.expasy.jpl.commons.base.GenericProperties
 
toString() - Method in class org.expasy.jpl.commons.base.io.JPLFile
 
toString(List<int[]>) - Static method in class org.expasy.jpl.commons.base.math.CombinationFactory
 
toString(List<int[]>) - Static method in class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory
A simple string converter for n-tuples.
toString() - Method in class org.expasy.jpl.commons.base.mem.ObjectSizeEstimator
 
toString() - Method in class org.expasy.jpl.commons.base.record.DataTable.Record
 
toString() - Method in class org.expasy.jpl.commons.base.record.DataTable
 
toString() - Method in class org.expasy.jpl.commons.base.record.DataTableFactory
 
toString() - Method in class org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager
 
toString() - Method in class org.expasy.jpl.commons.base.record.RecordsCount
 
toString() - Method in class org.expasy.jpl.commons.base.TypedDataContainer
 
toString() - Method in class org.expasy.jpl.commons.base.TypedDatum
 
toString() - Method in class org.expasy.jpl.commons.base.TypedDatum.Type
 
toString() - Method in class org.expasy.jpl.commons.collection.graph.GraphPredicate.GraphInstancePredicate
 
toString() - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl.PredicateImpl
 
toString() - Method in class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl
 
toString() - Method in class org.expasy.jpl.commons.collection.IntegerSequence
 
toString() - Method in class org.expasy.jpl.commons.collection.IntegerSequenceWithGap
 
toString() - Method in class org.expasy.jpl.commons.collection.Interval
 
toString() - Method in class org.expasy.jpl.commons.collection.PoolImpl
 
toString() - Method in class org.expasy.jpl.commons.collection.sorter.ChainedComparator
 
toString() - Method in class org.expasy.jpl.commons.collection.sorter.ChainedStringCodedComparator
 
toString() - Method in class org.expasy.jpl.commons.collection.stat.HistogramDataSet
 
toString() - Method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
toString() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalCategory
 
toString() - Method in class org.expasy.jpl.commons.collection.stat.StatisticalSerieDiscreteDataSet
 
toString() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister
 
toString() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractSymbol
 
toString() - Method in class org.expasy.jpl.commons.collection.symbol.AbstractSymbolType
 
toString() - Method in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
 
toString() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SequenceSymbolCounter
 
toString() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
 
toString() - Method in class org.expasy.jpl.commons.collection.symbol.SymbolTable
 
toString() - Method in class org.expasy.jpl.commons.collection.tree.TreeNodeImpl
 
toSymbolString() - Method in interface org.expasy.jpl.commons.collection.symbol.seq.SymbolSequence
 
toSymbolString() - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
 
toXYDataset(HistogramDataSetExporter, String, HistogramDataSet) - Static method in class org.expasy.jpl.commons.collection.render.HistogramDataSetRenderer
Convert the histogram for jfreechart display (add values and weights).
traceDisabled() - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
 
traceEnabled() - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
trace enabled/disabled
traceInternalConditions() - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
Display the internal content of defined conditions variables.
traceMemory() - Static method in class org.expasy.jpl.commons.base.mem.RunTimeMemoryEstimator
 
traceSizesOf(Object) - Static method in class org.expasy.jpl.commons.base.mem.MemoryAgent
 
transform(int[]) - Method in class org.expasy.jpl.commons.base.math.CombinationFactory
 
transform(int, int) - Method in class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory
This algorithm generate all n-tuples with same radix for any positions.
transform(int[]) - Method in class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory
This algorithm generate all n-tuples where each ai have different upper limit li.
transform(T) - Method in class org.expasy.jpl.commons.base.process.SequenceTransformer
Successively process object by all processors.
transform(U) - Method in class org.expasy.jpl.commons.base.process.U2VSequenceTransformer
 
transform(String) - Method in interface org.expasy.jpl.commons.base.record.DataTableFactory.TypeManager.IType
convert a String value into the type
transform(String) - Method in class org.expasy.jpl.commons.base.string.StringConverters.StringConverter
 
transform(String) - Method in class org.expasy.jpl.commons.base.TypedDatum.Type
 
transform(Graph<V, E>) - Method in class org.expasy.jpl.commons.collection.graph.GraphExporter.DotTransformer
 
transformer - Variable in class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
transformers - Variable in class org.expasy.jpl.commons.base.process.SequenceTransformer
the list of object processors
translate(String) - Method in interface org.expasy.jpl.commons.base.builder.Interpreter
translate String in T
translate(String) - Method in class org.expasy.jpl.commons.base.cond.ConditionInterpreter
Parse expression and return a tree conditional expression.
TreeNode<T> - Interface in org.expasy.jpl.commons.collection.tree
A TreeNode interface should be implemented by any tree like structured node.
TreeNodeImpl<T> - Class in org.expasy.jpl.commons.collection.tree
Naive tree node.
treeString - Variable in class org.expasy.jpl.commons.collection.symbol.AbstractSymbolType
 
TreeView<T> - Interface in org.expasy.jpl.commons.collection.tree
A TreeView interface should be implemented by any tree like structured read-only node.
TreeViewImpl<T> - Class in org.expasy.jpl.commons.collection.tree
A read-only tree view.
TreeViewImpl(TreeNode<T>) - Constructor for class org.expasy.jpl.commons.collection.tree.TreeViewImpl
 
type - Variable in class org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator
 
type - Variable in class org.expasy.jpl.commons.collection.symbol.AbstractSymbol
the symbol type
type - Variable in class org.expasy.jpl.commons.collection.symbol.AlphabetImpl
the type of alphabet defined by its symbol type
TypedDataContainer - Class in org.expasy.jpl.commons.base
This object is a container for TypedDatas.
TypedDatum<T> - Class in org.expasy.jpl.commons.base
Typed data object.
TypedDatum.IllegalDataAssignmentException - Exception in org.expasy.jpl.commons.base
Exception thrown when an assignment imply incompatible types.
TypedDatum.IllegalDataAssignmentException(Throwable) - Constructor for exception org.expasy.jpl.commons.base.TypedDatum.IllegalDataAssignmentException
 
TypedDatum.IllegalDataAssignmentException(String, Throwable) - Constructor for exception org.expasy.jpl.commons.base.TypedDatum.IllegalDataAssignmentException
 
TypedDatum.Type<T> - Class in org.expasy.jpl.commons.base
A simple data type with wrapped string-to-T conversion with control type.

U

U2VSequenceTransformer<U,V> - Class in org.expasy.jpl.commons.base.process
A sequence of Transformers.
union(Set<T>...) - Static method in class org.expasy.jpl.commons.collection.CollectionUtils
Compute the union of many sets.
unregister(String) - Method in class org.expasy.jpl.commons.collection.PoolImpl
 
unregister(String) - Method in interface org.expasy.jpl.commons.collection.Register
 
updateFrequency(double) - Method in class org.expasy.jpl.commons.collection.stat.StatisticalCategory
Add the given value in this category.
usage - Variable in class org.expasy.jpl.commons.app.AbstractApplicationParameters
usage

V

valueAt(int) - Method in interface org.expasy.jpl.commons.collection.symbol.seq.Sequence
 
valueAt(int) - Method in class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl
 
valueOf(String, String, String) - Static method in class org.expasy.jpl.commons.base.cond.ConditionImpl
Factory method for numerical condition types.
valueOf(String, String) - Static method in class org.expasy.jpl.commons.base.cond.ConditionImpl
 
valueOf(String) - Static method in class org.expasy.jpl.commons.base.cond.ConditionImpl
Factory method for numerical condition types.
valueOf(int) - Static method in class org.expasy.jpl.commons.base.CounterImpl
A type-conversion static factory method.
valueOf(String) - Static method in class org.expasy.jpl.commons.base.io.DecimalFormatFactory
 
valueOf(int) - Static method in class org.expasy.jpl.commons.base.io.DecimalFormatFactory
 
valueOf(int, int) - Static method in class org.expasy.jpl.commons.base.io.DecimalFormatFactory
 
valueOf(String) - Static method in enum org.expasy.jpl.commons.base.record.RecordsCount.Operator
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in class org.expasy.jpl.commons.base.record.RecordsCount
Parse the given string and create an instance of RecordsCount over Strings.
valueOf(String, Transformer<String, T>) - Static method in class org.expasy.jpl.commons.base.record.RecordsCount
Parse the given string and create a generic instance of RecordsCount over Ts.
valueOf(String) - Static method in enum org.expasy.jpl.commons.base.render.ImageFormat
Returns the enum constant of this type with the specified name.
valueOf(Collection<TypedDatum>) - Static method in class org.expasy.jpl.commons.base.TypedDataContainer
 
valueOf(String) - Static method in enum org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator.OrderType
Returns the enum constant of this type with the specified name.
valueOf(String, Transformer<T, Double>) - Static method in class org.expasy.jpl.commons.collection.sorter.NumberStringBasedComparator
 
valueOf(String, Transformer<T, String>) - Static method in class org.expasy.jpl.commons.collection.sorter.StringStringBasedComparator
 
values() - Static method in enum org.expasy.jpl.commons.base.record.RecordsCount.Operator
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.expasy.jpl.commons.base.render.ImageFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.expasy.jpl.commons.collection.sorter.AbstractStringBasedComparator.OrderType
Returns an array containing the constants of this enum type, in the order they are declared.

W

waitInput() - Method in interface org.expasy.jpl.commons.app.InteractiveInputScanner
Read input stream
waitInput() - Method in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl
 
withBucketCapacity(List<T>, int) - Static method in class org.expasy.jpl.commons.collection.PartitionList
Make a partition from a given list and a partition capacity.
withBucketNumber(List<T>, int) - Static method in class org.expasy.jpl.commons.collection.PartitionList
Make a partition from a given list and a bucket number.
withPPM(double, double) - Static method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
withStdDev(double, double) - Static method in class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar
 
write(String, boolean) - Method in class org.expasy.jpl.commons.base.io.TabFileWriter
Write data to tabular file

X

xAxisInterval - Variable in class org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer
the x-axis interval

Y

YES_NO_PATTERN - Static variable in class org.expasy.jpl.commons.app.InteractiveInputScannerImpl
 

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Copyright (c) 2012 Swiss Institute of Bioinformatics. All rights reserved.