Serialized Form

Package org.expasy.jpl.commons.base

Class org.expasy.jpl.commons.base.AbstractDecorator extends Object implements Serializable

serialVersionUID: 6157547336840616630L

Serialized Fields

decoratedObject

Object decoratedObject

Class org.expasy.jpl.commons.base.CounterImpl extends Object implements Serializable

serialVersionUID: 7831797543622859629L

Serialized Fields

count

int count

Class org.expasy.jpl.commons.base.EditorException extends RuntimeException implements Serializable

serialVersionUID: 1L

Class org.expasy.jpl.commons.base.TypedDatum.IllegalDataAssignmentException extends Exception implements Serializable

serialVersionUID: -3878333178604081898L

Package org.expasy.jpl.commons.base.builder

Class org.expasy.jpl.commons.base.builder.BuilderException extends RuntimeException implements Serializable

serialVersionUID: 1L

Package org.expasy.jpl.commons.base.cond

Class org.expasy.jpl.commons.base.cond.ConditionImpl.ConditionRuntimeException extends RuntimeException implements Serializable

serialVersionUID: 1L

Package org.expasy.jpl.commons.base.cond.operator

Class org.expasy.jpl.commons.base.cond.operator.OperatorManager.InvalidOperatorException extends Exception implements Serializable

serialVersionUID: 2619370166950396830L

Class org.expasy.jpl.commons.base.cond.operator.OperatorManager.InvalidOperatorRTException extends RuntimeException implements Serializable

serialVersionUID: 7505270167210601346L

Package org.expasy.jpl.commons.base.io

Class org.expasy.jpl.commons.base.io.JPLFile extends File implements Serializable

serialVersionUID: 3173731867857806938L

Serialized Fields

dirName

String dirName

baseName

String baseName

baseNameNoExt

String baseNameNoExt

extension

String extension

Package org.expasy.jpl.commons.base.math

Class org.expasy.jpl.commons.base.math.MixedRadixNtupleFactory.BadRadixException extends Exception implements Serializable

serialVersionUID: 4576827468762428439L

Package org.expasy.jpl.commons.base.process

Class org.expasy.jpl.commons.base.process.ProcessException extends Exception implements Serializable

serialVersionUID: -9002587265333407131L

Package org.expasy.jpl.commons.base.record

Class org.expasy.jpl.commons.base.record.DataTable extends Object implements Serializable

serialVersionUID: -8082865514318464456L

Serialized Fields

id

int id

incremental id of the next Record.

records

List<E> records

table rows.

factory

DataTableFactory factory

the factory that created this instance (fields are defined there).

Class org.expasy.jpl.commons.base.record.DataTable.Record extends Object implements Serializable

serialVersionUID: 3877675591713190063L

Serialized Fields

id

int id

id (get from DataTable)

table

DataTable table

the record's container

values

Properties values

key: string field name, value: string field value

Class org.expasy.jpl.commons.base.record.DataTableFactory extends Object implements Serializable

serialVersionUID: 2423992525514039531L

Serialized Fields

fields

Map<K,V> fields

fields name associated with String to any type converter

Class org.expasy.jpl.commons.base.record.RecordsCount extends Object implements Serializable

serialVersionUID: 1934533693711477202L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream s)
                  throws IOException,
                         ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Package org.expasy.jpl.commons.base.render

Class org.expasy.jpl.commons.base.render.ImageRenderingException extends Exception implements Serializable

serialVersionUID: 1L

Package org.expasy.jpl.commons.base.string

Class org.expasy.jpl.commons.base.string.StringConverters extends Object implements Serializable

serialVersionUID: -5511811932302734965L

Class org.expasy.jpl.commons.base.string.StringConverters.StringConverter extends Object implements Serializable

serialVersionUID: -7583591561073492788L

Package org.expasy.jpl.commons.collection

Class org.expasy.jpl.commons.collection.Interval.IntervalOverlapException extends RuntimeException implements Serializable

serialVersionUID: -1907037439513935537L

Class org.expasy.jpl.commons.collection.Pool.KeyAlreadyExistException extends RuntimeException implements Serializable

serialVersionUID: -3173144664053561763L

Class org.expasy.jpl.commons.collection.Pool.ObjectAlreadyExistException extends RuntimeException implements Serializable

serialVersionUID: -3173144664053561763L

Package org.expasy.jpl.commons.collection.graph

Class org.expasy.jpl.commons.collection.graph.KPartiteGraphImpl extends edu.uci.ics.jung.graph.SparseMultigraph<V,E> implements Serializable

serialVersionUID: 7653446445107694853L

Serialized Fields

nodes

Map<K,V> nodes

predicates

Collection<E> predicates

subSets

List<E> subSets

subsets

boolean subsets

id

String id

Package org.expasy.jpl.commons.collection.sorter

Class org.expasy.jpl.commons.collection.sorter.ComparatorInverter extends AbstractDecorator<Comparator<T>> implements Serializable

serialVersionUID: 7533667406088258902L

Package org.expasy.jpl.commons.collection.stat

Class org.expasy.jpl.commons.collection.stat.HistogramDataSet.OutOfUpperBoundException extends Exception implements Serializable

serialVersionUID: 6254862093474313168L

Class org.expasy.jpl.commons.collection.stat.LaplaceGaussRandomVar extends Number implements Serializable

serialVersionUID: 6291028259485532277L

Serialized Fields

mean

double mean

mean

stdDev

double stdDev

standard deviation

frequency

double frequency

the associated frequency or weight (the density (=1) by default)

Class org.expasy.jpl.commons.collection.stat.StatisticalCategory extends Number implements Serializable

serialVersionUID: 1006653730774220432L

Serialized Fields

from

double from

to

double to

center

double center

histogram

HistogramDataSet histogram

frequency

double frequency

Package org.expasy.jpl.commons.collection.symbol

Class org.expasy.jpl.commons.collection.symbol.AbstractDataSymbolRegister extends Object implements Serializable

serialVersionUID: -6039773204711212086L

Serialized Fields

letter2data

Map<K,V> letter2data

sym2data

Map<K,V> sym2data

type

Symbol.SymbolType<T> type

the symbol type

alphabet

AlphabetImpl<T> alphabet

data symbol alphabet

Class org.expasy.jpl.commons.collection.symbol.AbstractSymbol extends Object implements Serializable

serialVersionUID: -5042441402526578891L

Serialized Fields

name

char name

the symbol character

type

Symbol.SymbolType<T> type

the symbol type

Class org.expasy.jpl.commons.collection.symbol.AbstractSymbolType extends Object implements Serializable

serialVersionUID: -4570576825644372748L

Serialized Fields

name

String name

type name

treeString

String treeString

alphabet

Alphabet<T> alphabet

Class org.expasy.jpl.commons.collection.symbol.AlphabetException extends RuntimeException implements Serializable

serialVersionUID: -5576012259901108344L

Class org.expasy.jpl.commons.collection.symbol.AlphabetImpl extends Object implements Serializable

serialVersionUID: -5097124740396112979L

Serialized Fields

map

Map<K,V> map

mapping letter -> symbol tree

type

Symbol.SymbolType<T> type

the type of alphabet defined by its symbol type

leaves

Set<E> leaves

regex

String regex

Class org.expasy.jpl.commons.collection.symbol.SymbolNotFoundException extends RuntimeException implements Serializable

serialVersionUID: -5576012259901108344L

Package org.expasy.jpl.commons.collection.symbol.seq

Class org.expasy.jpl.commons.collection.symbol.seq.SequenceOutOfBoundsException extends ArrayIndexOutOfBoundsException implements Serializable

serialVersionUID: 1L

Class org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

symbols

char[] symbols

the symbols (only for the root sequence)

symbolType

Symbol.SymbolType<T> symbolType

the symbol type

manager

DataSymbolRegister<T> manager

manage the access of symbols

ambiPos

List<E> ambiPos

store the ambiguous symbol positions

startIndexInRoot

int startIndexInRoot

the beginning and length of subsequence relative to the root

length

int length

root

SymbolSequenceImpl<E> root

the sequence root of the sequence hierarchy

parent

SymbolSequenceImpl<E> parent

the direct tree parent of the current sequence (null for root)

Package org.expasy.jpl.commons.collection.tree

Class org.expasy.jpl.commons.collection.tree.TreeNodeImpl extends Object implements Serializable

serialVersionUID: 1724526834635959445L

Serialized Fields

data

Object data

parent

TreeNode<T> parent

children

List<E> children