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

A

abortOnError - Variable in class ambit2.base.processors.ProcessorsChain

AbstractReporter<Content,Output> - Class in ambit2.base.processors

Implementation of Reporter

AbstractReporter() - Constructor for class ambit2.base.processors.AbstractReporter

accept(File) - Method in class ambit2.base.io.AmbitFileFilter

accept(File) - Method in class ambit2.base.io.MolFileFilter

add(P) - Method in class ambit2.base.data.Profile

add(Profile<P>, boolean) - Method in class ambit2.base.data.Profile

add(String, String, Class) - Method in class ambit2.base.data.Template

addElement(Property, Boolean) - Method in class ambit2.base.data.ProfileListModel

addExecutable(String, String[]) - Method in class ambit2.base.external.CommandShell

addExecutable(String, String, String[]) - Method in class ambit2.base.external.CommandShell

addExecutableLinux(String, String[]) - Method in class ambit2.base.external.CommandShell

addExecutableMac(String, String[]) - Method in class ambit2.base.external.CommandShell

addExecutableWin(String, String[]) - Method in class ambit2.base.external.CommandShell

addFields(String, String, boolean, boolean) - Method in class ambit2.base.data.Template

addProperties(Map) - Method in class ambit2.base.data.StructureRecord

addProperties(Map) - Method in interface ambit2.base.interfaces.IStructureRecord

addPropertyChangeListener(String, PropertyChangeListener) - Method in class ambit2.base.data.Profile

addPropertyChangeListener(String, PropertyChangeListener) - Method in class ambit2.base.processors.DefaultAmbitProcessor

addPropertyChangeListener(PropertyChangeListener) - Method in class ambit2.base.processors.DefaultAmbitProcessor

addPropertyChangeListener(PropertyChangeListener) - Method in class ambit2.base.processors.ProcessorsChain

addPropertyChangeListener(String, PropertyChangeListener) - Method in class ambit2.base.processors.ProcessorsChain

address - Variable in class ambit2.base.data.AmbitUser

affiliation - Variable in class ambit2.base.data.AmbitUser

afterProcessing(Target, Iterator<ItemInput>) - Method in interface ambit2.base.interfaces.IBatchProcessor

ambit2.base.config - package ambit2.base.config

ambit2.base.data - package ambit2.base.data

ambit2.base.exceptions - package ambit2.base.exceptions

ambit2.base.external - package ambit2.base.external

ambit2.base.interfaces - package ambit2.base.interfaces

ambit2.base.io - package ambit2.base.io

ambit2.base.log - package ambit2.base.log

Logging functionality

ambit2.base.processors - package ambit2.base.processors

ambit2.base.processors.batch - package ambit2.base.processors.batch

AmbitBean - Class in ambit2.base.data

AmbitBean() - Constructor for class ambit2.base.data.AmbitBean

AmbitException - Exception in ambit2.base.exceptions

AmbitException() - Constructor for exception ambit2.base.exceptions.AmbitException

AmbitException(String) - Constructor for exception ambit2.base.exceptions.AmbitException

AmbitException(Throwable) - Constructor for exception ambit2.base.exceptions.AmbitException

AmbitException(String, Throwable) - Constructor for exception ambit2.base.exceptions.AmbitException

AmbitFileFilter - Class in ambit2.base.io

Customized file filter

AmbitFileFilter() - Constructor for class ambit2.base.io.AmbitFileFilter

AmbitFileFilter(String, String) - Constructor for class ambit2.base.io.AmbitFileFilter

AmbitIOException - Exception in ambit2.base.exceptions

TODO add description

AmbitIOException() - Constructor for exception ambit2.base.exceptions.AmbitIOException

AmbitIOException(String) - Constructor for exception ambit2.base.exceptions.AmbitIOException

AmbitIOException(String, String) - Constructor for exception ambit2.base.exceptions.AmbitIOException

AmbitIOException(Throwable) - Constructor for exception ambit2.base.exceptions.AmbitIOException

AmbitIOException(Throwable, String) - Constructor for exception ambit2.base.exceptions.AmbitIOException

AmbitIOException(String, Throwable) - Constructor for exception ambit2.base.exceptions.AmbitIOException

AmbitIOException(String, Throwable, String) - Constructor for exception ambit2.base.exceptions.AmbitIOException

AmbitLogger - Class in ambit2.base.log

Logging facility

AmbitLogger() - Constructor for class ambit2.base.log.AmbitLogger

AmbitLogger(Object) - Constructor for class ambit2.base.log.AmbitLogger

Constructs a LoggingTool which produces logger lines indicating them to be for the Class of the Object.

AmbitLogger(Class) - Constructor for class ambit2.base.log.AmbitLogger

AmbitUser - Class in ambit2.base.data

Contains all information about an AMBIT database user.

AmbitUser() - Constructor for class ambit2.base.data.AmbitUser

AmbitUser(String) - Constructor for class ambit2.base.data.AmbitUser

AmbitUser(String, AmbitUser.USER_TYPE) - Constructor for class ambit2.base.data.AmbitUser

AmbitUser.USER_TYPE - Enum in ambit2.base.data

avg - Variable in class ambit2.base.data.PropertyStats

B

batch - Variable in exception ambit2.base.exceptions.BatchProcessingException

batch - Variable in class ambit2.base.processors.batch.BatchReporter

BatchProcessingException - Exception in ambit2.base.exceptions

An Exception to be used in IBatchProcessor

BatchProcessingException() - Constructor for exception ambit2.base.exceptions.BatchProcessingException

BatchProcessingException(String) - Constructor for exception ambit2.base.exceptions.BatchProcessingException

BatchProcessingException(String, IBatchProcessor) - Constructor for exception ambit2.base.exceptions.BatchProcessingException

BatchProcessingException(Throwable, IBatchProcessor) - Constructor for exception ambit2.base.exceptions.BatchProcessingException

BatchProcessingException(Throwable) - Constructor for exception ambit2.base.exceptions.BatchProcessingException

BatchProcessingException(String, Throwable) - Constructor for exception ambit2.base.exceptions.BatchProcessingException

BatchProcessingException(String, Throwable, IBatchProcessor) - Constructor for exception ambit2.base.exceptions.BatchProcessingException

BatchProcessor<INPUT,Target> - Class in ambit2.base.processors.batch

BatchProcessor() - Constructor for class ambit2.base.processors.batch.BatchProcessor

BatchProcessor(ProcessorsChain<Target, IBatchStatistics, IProcessor>) - Constructor for class ambit2.base.processors.batch.BatchProcessor

BatchReporter<Item,ItemList,Output> - Class in ambit2.base.processors.batch

Batch reporter

BatchReporter() - Constructor for class ambit2.base.processors.batch.BatchReporter

beforeProcessing(Target) - Method in interface ambit2.base.interfaces.IBatchProcessor

blank - Static variable in class ambit2.base.processors.batch.DefaultBatchStatistics

buildDocument() - Method in class ambit2.base.data.Template

C

CASProcessor - Class in ambit2.base.processors

Transform a string to CAS number format XXXXX-XX-X

CASProcessor() - Constructor for class ambit2.base.processors.CASProcessor

changeExtension(File) - Method in class ambit2.base.io.AmbitFileFilter

channelCopy2(ReadableByteChannel, WritableByteChannel) - Static method in class ambit2.base.io.DownloadTool

Channel copy method 2.

city - Variable in class ambit2.base.data.AmbitUser

ClassHolder - Class in ambit2.base.data

A place holder for class name and description, in order to allow display of light list of objects, instantiated on demand only.

ClassHolder(String, String, String, String) - Constructor for class ambit2.base.data.ClassHolder

ClassHolder(String, String, String, ImageIcon) - Constructor for class ambit2.base.data.ClassHolder

clazz - Variable in class ambit2.base.data.ClassHolder

clazz - Variable in class ambit2.base.data.Property

clear() - Method in class ambit2.base.data.Profile

clear() - Method in class ambit2.base.data.SelectionBean

clear() - Method in class ambit2.base.data.StructureRecord

clear() - Method in interface ambit2.base.interfaces.IBatchStatistics

Clears records

clear() - Method in interface ambit2.base.interfaces.IStructureRecord

clear() - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

clear() - Method in interface ambit2.base.processors.IAmbitResult

Clears te object

clearProperties() - Method in class ambit2.base.data.StructureRecord

clearProperties() - Method in interface ambit2.base.interfaces.IStructureRecord

clone() - Method in class ambit2.base.data.AmbitBean

clone() - Method in class ambit2.base.data.AmbitUser

clone() - Method in class ambit2.base.data.StructureRecord

clone() - Method in interface ambit2.base.interfaces.IStructureRecord

close() - Method in class ambit2.base.processors.ProcessorsChain

close() - Method in interface ambit2.base.processors.Reporter

closeIterator(Iterator) - Method in class ambit2.base.processors.batch.BatchProcessor

columns - Variable in class ambit2.base.data.PropertiesTableModel

Command - Class in ambit2.base.external

Command(String) - Constructor for class ambit2.base.external.Command

Command(String, String[]) - Constructor for class ambit2.base.external.Command

CommandShell<INPUT,OUTPUT> - Class in ambit2.base.external

A wrapper for an external executable (OS dependent).

CommandShell() - Constructor for class ambit2.base.external.CommandShell

compareTo(QLabel) - Method in class ambit2.base.data.QLabel

completed() - Method in interface ambit2.base.interfaces.IBatchStatistics

completed() - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

configureLog4j(boolean) - Static method in class ambit2.base.log.AmbitLogger

configureLog4j(String) - Static method in class ambit2.base.log.AmbitLogger

container - Variable in class ambit2.base.data.Profile

content - Variable in class ambit2.base.data.StructureRecord

contentsChanged(ListDataEvent) - Method in class ambit2.base.data.ProfileListModel

count - Variable in class ambit2.base.data.PropertyStats

country - Variable in class ambit2.base.data.AmbitUser

createBatch() - Method in class ambit2.base.processors.batch.BatchReporter

createBatch() - Method in class ambit2.base.processors.batch.ListReporter

D

DATABASE - Static variable in class ambit2.base.config.Preferences

debug(Object) - Method in class ambit2.base.log.AmbitLogger

Shows DEBUG output for the Object.

DEFAULT_DIR - Static variable in class ambit2.base.config.Preferences

DEFAULT_STACK_LENGTH - Variable in class ambit2.base.log.AmbitLogger

Default number of StackTraceElements to be printed by debug(Exception).

default_values - Static variable in class ambit2.base.config.Preferences

DefaultAmbitProcessor<Target,Result> - Class in ambit2.base.processors

Default (empty) implementation of IProcessor

DefaultAmbitProcessor() - Constructor for class ambit2.base.processors.DefaultAmbitProcessor

DefaultBatchStatistics - Class in ambit2.base.processors.batch

Default implementation of IBatchStatistics

DefaultBatchStatistics() - Constructor for class ambit2.base.processors.batch.DefaultBatchStatistics

description - Variable in class ambit2.base.data.ClassHolder

description - Variable in class ambit2.base.io.AmbitFileFilter

description - Variable in class ambit2.base.io.MolFileFilter

Dictionary - Class in ambit2.base.data

encapsulates pseudo ontology , defined in template and dictionary tables

Dictionary() - Constructor for class ambit2.base.data.Dictionary

Dictionary(String, String) - Constructor for class ambit2.base.data.Dictionary

Dictionary(String, String, String) - Constructor for class ambit2.base.data.Dictionary

download(URL, File) - Static method in class ambit2.base.io.DownloadTool

download(InputStream, File) - Static method in class ambit2.base.io.DownloadTool

download(InputStream, OutputStream) - Static method in class ambit2.base.io.DownloadTool

download(String, OutputStream) - Static method in class ambit2.base.io.DownloadTool

download(String, File) - Static method in class ambit2.base.io.DownloadTool

DownloadTool - Class in ambit2.base.io

DownloadTool() - Constructor for class ambit2.base.io.DownloadTool

dropFilter(int) - Method in interface ambit2.base.data.IFilteredColumns

dumpClasspath() - Method in class ambit2.base.log.AmbitLogger

Outputs the system property for java.class.path.

dumpSystemProperties() - Method in class ambit2.base.log.AmbitLogger

Outputs system properties for the operating system and the java version.

E

editable - Variable in class ambit2.base.data.LiteratureEntry

email - Variable in class ambit2.base.data.AmbitUser

enabled - Variable in class ambit2.base.data.Property

enabled - Variable in class ambit2.base.external.CommandShell

enabled - Variable in class ambit2.base.processors.DefaultAmbitProcessor

Endpoints - Class in ambit2.base.data

Endpoints() - Constructor for class ambit2.base.data.Endpoints

equals(Object) - Method in class ambit2.base.data.Dictionary

equals(Object) - Method in class ambit2.base.data.LiteratureEntry

equals(Object) - Method in class ambit2.base.data.Property

equals(Object) - Method in class ambit2.base.data.QLabel

error(SAXParseException) - Method in class ambit2.base.io.SimpleErrorHandler

error(Object) - Method in class ambit2.base.log.AmbitLogger

Shows ERROR output for the Object.

error(Object, Exception) - Method in class ambit2.base.log.AmbitLogger

executables - Variable in class ambit2.base.external.CommandShell

exitCode - Variable in class ambit2.base.external.CommandShell

exitCodeOK(int) - Method in class ambit2.base.external.CommandShell

extension - Variable in class ambit2.base.io.AmbitFileFilter

extension - Variable in class ambit2.base.io.MolFileFilter

F

FASTSMARTS - Static variable in class ambit2.base.config.Preferences

fatal(Object) - Method in class ambit2.base.log.AmbitLogger

fatalError(SAXParseException) - Method in class ambit2.base.io.SimpleErrorHandler

fields - Variable in class ambit2.base.data.ProfileListModel

filename - Static variable in class ambit2.base.config.Preferences

first() - Method in interface ambit2.base.interfaces.IRandomAccessChemObjectReader

firstName - Variable in class ambit2.base.data.AmbitUser

footer(Output, ItemList) - Method in class ambit2.base.processors.batch.BatchReporter

format - Variable in class ambit2.base.data.StructureRecord

formula - Variable in class ambit2.base.data.StructureRecord

frequency - Variable in class ambit2.base.processors.batch.DefaultBatchStatistics

G

GENERATE2D - Static variable in class ambit2.base.config.Preferences

get(String) - Method in class ambit2.base.data.Profile

get(P) - Method in class ambit2.base.data.Profile

getAdditionalFiles() - Method in class ambit2.base.external.Command

getAddress() - Method in class ambit2.base.data.AmbitUser

getAffiliation() - Method in class ambit2.base.data.AmbitUser

getAvg() - Method in class ambit2.base.data.PropertyStats

getCASInstance() - Static method in class ambit2.base.data.Property

getCASReference() - Static method in class ambit2.base.data.LiteratureEntry

getCity() - Method in class ambit2.base.data.AmbitUser

getClazz() - Method in class ambit2.base.data.ClassHolder

getClazz() - Method in class ambit2.base.data.Property

getColumnCount() - Method in class ambit2.base.data.PropertiesTableModel

getColumnName(int) - Method in class ambit2.base.data.PropertiesTableModel

getContent() - Method in class ambit2.base.data.StructureRecord

getContent() - Method in interface ambit2.base.interfaces.IStructureRecord

getCount() - Method in class ambit2.base.data.PropertyStats

getCountry() - Method in class ambit2.base.data.AmbitUser

getCurrentRecord() - Method in interface ambit2.base.interfaces.IInputOutputState

getDefault() - Static method in class ambit2.base.config.Preferences

getDescription() - Method in class ambit2.base.data.ClassHolder

getDescription() - Method in class ambit2.base.io.AmbitFileFilter

getDescription() - Method in class ambit2.base.io.MolFileFilter

getEINECSInstance() - Static method in class ambit2.base.data.Property

getEINECSReference() - Static method in class ambit2.base.data.LiteratureEntry

getElementAt(int) - Method in class ambit2.base.data.ProfileListModel

getElementAt(int) - Method in interface ambit2.base.data.TypedListModel

getEmail() - Method in class ambit2.base.data.AmbitUser

getExe() - Method in class ambit2.base.external.Command

getExecutable(String) - Method in class ambit2.base.external.CommandShell

getExecutable() - Method in class ambit2.base.external.CommandShell

invokes CommandShell.getExecutable(String) with System.getProperty("os.name") as argument

getExitCode() - Method in class ambit2.base.external.CommandShell

getExtension() - Method in class ambit2.base.io.MolFileFilter

getFirstName() - Method in class ambit2.base.data.AmbitUser

getFormat() - Method in class ambit2.base.data.StructureRecord

getFormat() - Method in interface ambit2.base.interfaces.IStructureRecord

getFormula() - Method in class ambit2.base.data.StructureRecord

getFormula() - Method in interface ambit2.base.interfaces.IChemical

getFrequency() - Method in interface ambit2.base.interfaces.IBatchStatistics

getFrequency() - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

getHash() - Method in class ambit2.base.data.StructureRecord

getHash() - Method in interface ambit2.base.interfaces.IChemical

getIcon() - Method in class ambit2.base.data.ClassHolder

getId() - Method in class ambit2.base.data.LiteratureEntry

getId() - Method in class ambit2.base.data.Property

getId() - Method in class ambit2.base.data.Template

getID() - Method in class ambit2.base.external.CommandShell

getID() - Method in interface ambit2.base.interfaces.IProcessor

getID() - Method in class ambit2.base.processors.DefaultAmbitProcessor

getID() - Method in class ambit2.base.processors.ProcessorsChain

getIdchemical() - Method in class ambit2.base.data.StructureRecord

getIdchemical() - Method in interface ambit2.base.interfaces.IChemical

getIdstructure() - Method in class ambit2.base.data.StructureRecord

getIdstructure() - Method in interface ambit2.base.interfaces.IStructureRecord

getImage() - Method in class ambit2.base.data.ClassHolder

getInchi() - Method in class ambit2.base.data.StructureRecord

getInchi() - Method in interface ambit2.base.interfaces.IChemical

getInputFile() - Method in class ambit2.base.external.CommandShell

getInstance() - Static method in class ambit2.base.data.LiteratureEntry

getInstance(String) - Static method in class ambit2.base.data.LiteratureEntry

getInstance(String, String) - Static method in class ambit2.base.data.LiteratureEntry

getInstance(String, String, int) - Static method in class ambit2.base.data.LiteratureEntry

getInstance(String, String) - Static method in class ambit2.base.data.Property

getInstance(String, LiteratureEntry) - Static method in class ambit2.base.data.Property

getInstance(String, String, String) - Static method in class ambit2.base.data.Property

getIterator(Target) - Method in interface ambit2.base.interfaces.IBatchProcessor

getIUPACReference() - Static method in class ambit2.base.data.LiteratureEntry

getKey() - Method in exception ambit2.base.exceptions.PropertyNotInTemplateException

getLabel() - Method in class ambit2.base.data.Property

getLabel() - Method in class ambit2.base.data.QLabel

getLastName() - Method in class ambit2.base.data.AmbitUser

getLoggedFromHost() - Method in class ambit2.base.data.AmbitUser

getMap() - Method in class ambit2.base.data.StructureRecord

getMax() - Method in class ambit2.base.data.PropertyStats

getMaxValue() - Method in class ambit2.base.data.Range

getMessage() - Method in exception ambit2.base.processors.ProcessorException

getMin() - Method in class ambit2.base.data.PropertyStats

getMinValue() - Method in class ambit2.base.data.Range

getName() - Method in class ambit2.base.data.AmbitUser

getName() - Method in class ambit2.base.data.LiteratureEntry

getName() - Method in class ambit2.base.data.Profile

getName() - Method in class ambit2.base.data.Property

getName() - Method in class ambit2.base.data.StringBean

getNameInstance() - Static method in class ambit2.base.data.Property

getNumberOfProperties() - Method in class ambit2.base.data.StructureRecord

getNumberOfProperties() - Method in interface ambit2.base.interfaces.IStructureRecord

getOptions() - Method in class ambit2.base.data.SelectionBean

getOrder() - Method in class ambit2.base.data.Property

getOutput() - Method in class ambit2.base.processors.AbstractReporter

getOutput() - Method in class ambit2.base.processors.batch.BatchReporter

getOutput() - Method in interface ambit2.base.processors.Reporter

getOutputFile() - Method in class ambit2.base.external.CommandShell

getParentTemplate() - Method in class ambit2.base.data.Dictionary

getPassword() - Method in class ambit2.base.data.AmbitUser

getPath(File) - Method in class ambit2.base.external.CommandShell

getProcessorChain() - Method in interface ambit2.base.interfaces.IBatchProcessor

getProcessorChain() - Method in class ambit2.base.processors.batch.BatchProcessor

getProcessors() - Method in class ambit2.base.processors.batch.BatchReporter

getProperties() - Static method in class ambit2.base.config.Preferences

getProperties(boolean) - Method in class ambit2.base.data.Profile

getProperties() - Method in class ambit2.base.data.StructureRecord

getProperties() - Method in interface ambit2.base.interfaces.IStructureRecord

getProperty(String) - Static method in class ambit2.base.config.Preferences

getProperty() - Method in class ambit2.base.data.PropertyTemplateStats

getProperty(Property) - Method in class ambit2.base.data.StructureRecord

getProperty(Property) - Method in interface ambit2.base.interfaces.IStructureRecord

getPropertyChangeSupport() - Static method in class ambit2.base.config.Preferences

getRecords(IBatchStatistics.RECORDS_STATS) - Method in interface ambit2.base.interfaces.IBatchStatistics

Returns number of records of a type

getRecords(IBatchStatistics.RECORDS_STATS) - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

getRecords() - Method in class ambit2.base.processors.StructureRecordsAppender

getReference() - Method in class ambit2.base.data.Property

getReference() - Method in class ambit2.base.data.StructureRecord

getReference() - Method in interface ambit2.base.interfaces.IStructureRecord

getRelationship() - Method in class ambit2.base.data.Dictionary

getResponseType() - Method in interface ambit2.base.interfaces.IInputOutputState

getResult(Target) - Method in interface ambit2.base.interfaces.IBatchProcessor

getResultCaption() - Method in interface ambit2.base.interfaces.IBatchStatistics

getResultCaption() - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

getRowCount() - Method in class ambit2.base.data.PropertiesTableModel

getSelected() - Method in class ambit2.base.data.SelectionBean

getSelection() - Method in interface ambit2.base.data.ISelectableRecords

getSize() - Method in class ambit2.base.data.ProfileListModel

getSmiles() - Method in class ambit2.base.data.StructureRecord

getSmiles() - Method in interface ambit2.base.interfaces.IChemical

getSuffix(String) - Static method in class ambit2.base.io.AmbitFileFilter

getSuffix(File) - Static method in class ambit2.base.io.AmbitFileFilter

getSuffix(String) - Static method in class ambit2.base.io.MolFileFilter

getSuffix(File) - Static method in class ambit2.base.io.MolFileFilter

getTemplate() - Method in class ambit2.base.data.Dictionary

getTemplate() - Method in class ambit2.base.data.PropertyTemplateStats

getTemplate() - Method in exception ambit2.base.exceptions.PropertyNotInTemplateException

getText() - Method in class ambit2.base.data.QLabel

getTimeElapsed(IBatchStatistics.RECORDS_STATS) - Method in interface ambit2.base.interfaces.IBatchStatistics

Return time elapsed for of records of a type

getTimeElapsed() - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

getTimeElapsed(IBatchStatistics.RECORDS_STATS) - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

getTitle() - Method in class ambit2.base.data.AmbitUser

getTitle() - Method in class ambit2.base.data.ClassHolder

getTitle() - Method in class ambit2.base.data.LiteratureEntry

getTitle() - Method in class ambit2.base.data.Property

getTitle() - Method in class ambit2.base.data.SelectionBean

getTitle() - Method in interface ambit2.base.processors.IAmbitResult

getType() - Method in class ambit2.base.data.AmbitUser

getUnits() - Method in class ambit2.base.data.Property

getURL() - Method in class ambit2.base.data.LiteratureEntry

getUrl() - Method in class ambit2.base.data.Property

getUser() - Method in class ambit2.base.data.QLabel

getValueAt(int, int) - Method in class ambit2.base.data.PropertiesTableModel

getVisibleIndex(int) - Method in class ambit2.base.data.ProfileListModel

getWritableContent() - Method in class ambit2.base.data.StructureRecord

getWritableContent() - Method in interface ambit2.base.interfaces.IStructureRecord

getWww() - Method in class ambit2.base.data.AmbitUser

guessLabel(String) - Static method in class ambit2.base.data.Property

public constructors for web services

H

hash - Variable in class ambit2.base.data.StructureRecord

hashCode() - Method in class ambit2.base.data.LiteratureEntry

hashCode() - Method in class ambit2.base.data.Property

hasID() - Method in class ambit2.base.data.LiteratureEntry

header(Output, ItemList) - Method in class ambit2.base.processors.batch.BatchReporter

HOST - Static variable in class ambit2.base.config.Preferences

I

IAmbitResult - Interface in ambit2.base.processors

Provides means of accumulating results from processing multiple compounds by ambit2.processors.IAmbitProcessor TODO verify whether we need all of the methods here.

IBatchProcessor<Target,ItemInput,Result> - Interface in ambit2.base.interfaces

IBatchStatistics - Interface in ambit2.base.interfaces

Statistics of an IBatchProcessor process

IBatchStatistics.RECORDS_STATS - Enum in ambit2.base.interfaces

IChemical - Interface in ambit2.base.interfaces

icon - Variable in class ambit2.base.data.ClassHolder

id - Variable in class ambit2.base.data.LiteratureEntry

id - Variable in class ambit2.base.data.Property

id - Variable in class ambit2.base.data.Template

idchemical - Variable in class ambit2.base.data.StructureRecord

idstructure - Variable in class ambit2.base.data.StructureRecord

IFilteredColumns - Interface in ambit2.base.data

IInputOutputState - Interface in ambit2.base.interfaces

Status of the input reader/ output writer.

image - Variable in class ambit2.base.data.ClassHolder

inchi - Variable in class ambit2.base.data.StructureRecord

increment(IBatchStatistics.RECORDS_STATS) - Method in interface ambit2.base.interfaces.IBatchStatistics

Increments number of records of a type

increment(IBatchStatistics.RECORDS_STATS) - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

incrementTimeElapsed(IBatchStatistics.RECORDS_STATS, long) - Method in interface ambit2.base.interfaces.IBatchStatistics

Increments time elapsed for of records of a type

incrementTimeElapsed(IBatchStatistics.RECORDS_STATS, long) - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

info(Object) - Method in class ambit2.base.log.AmbitLogger

initialize() - Method in class ambit2.base.external.CommandShell

inProgress - Variable in class ambit2.base.processors.batch.DefaultBatchStatistics

inputFile - Variable in class ambit2.base.external.CommandShell

intervalAdded(ListDataEvent) - Method in class ambit2.base.data.ProfileListModel

intervalRemoved(ListDataEvent) - Method in class ambit2.base.data.ProfileListModel

IProcessor<Target,Result> - Interface in ambit2.base.interfaces

IRandomAccessChemObjectReader - Interface in ambit2.base.interfaces

Extension of ListIterator

isAbortOnError() - Method in class ambit2.base.processors.ProcessorsChain

isCellEditable(int, int) - Method in class ambit2.base.data.PropertiesTableModel

isDebugEnabled() - Method in class ambit2.base.log.AmbitLogger

ISelectableRecords - Interface in ambit2.base.data

ISelectableRecords.SELECTION_MODE - Enum in ambit2.base.data

isEnabled() - Method in class ambit2.base.data.Property

isEnabled() - Method in class ambit2.base.external.CommandShell

isEnabled() - Method in interface ambit2.base.interfaces.IProcessor

isEnabled() - Method in class ambit2.base.processors.DefaultAmbitProcessor

isEnabled() - Method in class ambit2.base.processors.ProcessorsChain

ISortableColumns - Interface in ambit2.base.data

isTimeToPrint(long) - Method in interface ambit2.base.interfaces.IBatchStatistics

isTimeToPrint(long) - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

IStructureRecord - Interface in ambit2.base.interfaces

IStructureRecord.MOL_TYPE - Enum in ambit2.base.interfaces

iterator() - Method in class ambit2.base.data.Profile

L

label - Variable in class ambit2.base.data.Property

label - Variable in class ambit2.base.data.QLabel

last() - Method in interface ambit2.base.interfaces.IRandomAccessChemObjectReader

last_time_print_stats - Variable in class ambit2.base.processors.batch.DefaultBatchStatistics

lastName - Variable in class ambit2.base.data.AmbitUser

ListReporter<Item,Output> - Class in ambit2.base.processors.batch

ListReporter() - Constructor for class ambit2.base.processors.batch.ListReporter

LiteratureEntry - Class in ambit2.base.data

A Literature entry:
title, URL

LiteratureEntry(String, String) - Constructor for class ambit2.base.data.LiteratureEntry

We need separate instances for web services

load(InputStream) - Static method in class ambit2.base.data.ClassHolder

load(InputStream) - Method in class ambit2.base.data.Template

load(Reader) - Method in class ambit2.base.data.Template

loadProperties() - Static method in class ambit2.base.config.Preferences

loggedFromHost - Variable in class ambit2.base.data.AmbitUser

logger - Static variable in class ambit2.base.external.CommandShell

logger - Static variable in class ambit2.base.io.SimpleErrorHandler

logger - Static variable in class ambit2.base.processors.DefaultAmbitProcessor

M

MAXRECORDS - Static variable in class ambit2.base.config.Preferences

maxValue - Variable in class ambit2.base.data.Range

MENGINE_LINUX - Static variable in class ambit2.base.config.Preferences

MENGINE_WIN - Static variable in class ambit2.base.config.Preferences

MESSAGE - Static variable in exception ambit2.base.exceptions.PropertyNotInTemplateException

minValue - Variable in class ambit2.base.data.Range

MolFileFilter - Class in ambit2.base.io

MolFileFilter() - Constructor for class ambit2.base.io.MolFileFilter

MolFileFilter(String, String) - Constructor for class ambit2.base.io.MolFileFilter

MOPAC_DIR - Static variable in class ambit2.base.config.Preferences

MOPAC_EXE - Static variable in class ambit2.base.config.Preferences

MSG_EMPTYFILE - Static variable in exception ambit2.base.exceptions.AmbitIOException

MSG_ERRORONOPEN - Static variable in exception ambit2.base.exceptions.AmbitIOException

MSG_ERRORONSAVE - Static variable in exception ambit2.base.exceptions.AmbitIOException

MSG_NOTFOUND - Static variable in exception ambit2.base.exceptions.AmbitIOException

MSG_OPENSUCCESS - Static variable in exception ambit2.base.exceptions.AmbitIOException

MSG_SAVESUCCESS - Static variable in exception ambit2.base.exceptions.AmbitIOException

MSG_UNSUPPORTEDFORMAT - Static variable in exception ambit2.base.exceptions.AmbitIOException

MyIOUtilities - Class in ambit2.base.io

This class is to simplify OpenFile / SaveFile dialogs calls

MyIOUtilities() - Constructor for class ambit2.base.io.MyIOUtilities

mysqlPassword() - Method in class ambit2.base.data.AmbitUser

N

name - Variable in class ambit2.base.data.AmbitUser

name - Variable in class ambit2.base.data.Profile

name - Variable in class ambit2.base.data.Property

name - Variable in class ambit2.base.data.StringBean

NotFoundException - Exception in ambit2.base.exceptions

Thrown if there are no results from a query

NotFoundException() - Constructor for exception ambit2.base.exceptions.NotFoundException

NotFoundException(String) - Constructor for exception ambit2.base.exceptions.NotFoundException

O

onError(ItemInput, Object, Result, Exception) - Method in interface ambit2.base.interfaces.IBatchProcessor

onItemProcessed(ItemInput, Object, Result) - Method in interface ambit2.base.interfaces.IBatchProcessor

onItemRead(ItemInput, Result) - Method in interface ambit2.base.interfaces.IBatchProcessor

OPENBABEL_LINUX - Static variable in class ambit2.base.config.Preferences

OPENBABEL_WIN - Static variable in class ambit2.base.config.Preferences

openFile(Frame, String, String[], String[]) - Static method in class ambit2.base.io.MyIOUtilities

options - Variable in class ambit2.base.data.SelectionBean

order - Variable in class ambit2.base.data.Property

os_LINUX - Static variable in class ambit2.base.external.CommandShell

os_MAC - Static variable in class ambit2.base.external.CommandShell

os_WINDOWS - Static variable in class ambit2.base.external.CommandShell

os_WINDOWSVISTA - Static variable in class ambit2.base.external.CommandShell

output - Variable in class ambit2.base.processors.AbstractReporter

output - Variable in class ambit2.base.processors.batch.BatchReporter

outputFile - Variable in class ambit2.base.external.CommandShell

P

p_title - Static variable in class ambit2.base.data.LiteratureEntry

p_url - Static variable in class ambit2.base.data.LiteratureEntry

parentTemplate - Variable in class ambit2.base.data.Dictionary

parseOutput(String, INPUT) - Method in class ambit2.base.external.CommandShell

Does nothing, override with smth meaningfull

PASSWORD - Static variable in class ambit2.base.config.Preferences

password - Variable in class ambit2.base.data.AmbitUser

PORT - Static variable in class ambit2.base.config.Preferences

Preferences - Class in ambit2.base.config

Preferences() - Constructor for class ambit2.base.config.Preferences

Preferences.VINDEX - Enum in ambit2.base.config

Preferences.VTAGS - Enum in ambit2.base.config

prefix - Variable in class ambit2.base.external.CommandShell

prepareInput(String, INPUT) - Method in class ambit2.base.external.CommandShell

Returns empty string, override with smth meaningfull

process(INPUT) - Method in class ambit2.base.external.CommandShell

process(Target) - Method in interface ambit2.base.interfaces.IProcessor

process(String, SAXParseException) - Method in class ambit2.base.io.SimpleErrorHandler

process(INPUT) - Method in class ambit2.base.processors.batch.BatchProcessor

process(ItemList) - Method in class ambit2.base.processors.batch.BatchReporter

process(String) - Method in class ambit2.base.processors.CASProcessor

process(Target) - Method in class ambit2.base.processors.ProcessorsChain

process(IStructureRecord) - Method in class ambit2.base.processors.StructureRecordsAppender

processItem(Item, Output) - Method in class ambit2.base.processors.batch.BatchReporter

processor - Variable in class ambit2.base.processors.batch.BatchProcessor

processor - Variable in exception ambit2.base.processors.ProcessorException

ProcessorException - Exception in ambit2.base.processors

ProcessorException(IProcessor, String) - Constructor for exception ambit2.base.processors.ProcessorException

ProcessorException(IProcessor, Exception) - Constructor for exception ambit2.base.processors.ProcessorException

processors - Variable in class ambit2.base.processors.batch.BatchReporter

ProcessorsChain<Target,Result,P extends IProcessor> - Class in ambit2.base.processors

A list or IProcessor to be executed sequentially.

ProcessorsChain() - Constructor for class ambit2.base.processors.ProcessorsChain

Profile<P extends Property> - Class in ambit2.base.data

A set of properties, defining a (e.g.

Profile() - Constructor for class ambit2.base.data.Profile

profile_property_added - Static variable in class ambit2.base.data.Profile

profile_property_change - Static variable in class ambit2.base.data.Profile

profile_property_removed - Static variable in class ambit2.base.data.Profile

ProfileListModel - Class in ambit2.base.data

ProfileListModel(Profile<Property>) - Constructor for class ambit2.base.data.ProfileListModel

ProfileListModel(Profile<Property>, Boolean) - Constructor for class ambit2.base.data.ProfileListModel

ProfileListModel(Hashtable<String, Profile<Property>>, Boolean) - Constructor for class ambit2.base.data.ProfileListModel

ProfileListModel(TypedListModel<Property>) - Constructor for class ambit2.base.data.ProfileListModel

ProfileListModel(TypedListModel<Property>, Boolean) - Constructor for class ambit2.base.data.ProfileListModel

properties - Variable in class ambit2.base.data.StructureRecord

PropertiesTableModel - Class in ambit2.base.data

Table model for Profile

PropertiesTableModel(TypedListModel<Property>, boolean, int) - Constructor for class ambit2.base.data.PropertiesTableModel

Property - Class in ambit2.base.data

Property(String) - Constructor for class ambit2.base.data.Property

Property(String, LiteratureEntry) - Constructor for class ambit2.base.data.Property

property - Variable in class ambit2.base.data.PropertyTemplateStats

Property.IO_QUESTION - Enum in ambit2.base.data

PROPERTY_BATCHSTATS - Static variable in class ambit2.base.processors.batch.BatchProcessor

propertyChangeSupport - Static variable in class ambit2.base.config.Preferences

propertyChangeSupport - Variable in class ambit2.base.processors.DefaultAmbitProcessor

PropertyNotInTemplateException - Exception in ambit2.base.exceptions

PropertyNotInTemplateException() - Constructor for exception ambit2.base.exceptions.PropertyNotInTemplateException

PropertyNotInTemplateException(Object, Template) - Constructor for exception ambit2.base.exceptions.PropertyNotInTemplateException

PropertyNotInTemplateException(String) - Constructor for exception ambit2.base.exceptions.PropertyNotInTemplateException

PropertyNotInTemplateException(Throwable) - Constructor for exception ambit2.base.exceptions.PropertyNotInTemplateException

PropertyNotInTemplateException(String, Throwable, Object, Template) - Constructor for exception ambit2.base.exceptions.PropertyNotInTemplateException

PropertyStats<T extends java.lang.Comparable<T>> - Class in ambit2.base.data

PropertyStats() - Constructor for class ambit2.base.data.PropertyStats

PropertyTemplateStats - Class in ambit2.base.data

PropertyTemplateStats() - Constructor for class ambit2.base.data.PropertyTemplateStats

PropertyTemplateStats(Property, String, long) - Constructor for class ambit2.base.data.PropertyTemplateStats

props - Static variable in class ambit2.base.config.Preferences

Q

QLabel - Class in ambit2.base.data

Quality label Q(experts) = (100*a+100*b +1) / (100*d + 10*c+1) 10 experts max labels OK,ProbablyOK,Unknown,ProbablyERROR,ERROR 1)automatic verification -> assigns OK, ? , Not OK 2)Expert verification (up to 10 experts) - assigns (a)OK(expert), (b) Almost OK (expert), (c) Almost Not OK (expert), (d) Not OK (expert)

QLabel() - Constructor for class ambit2.base.data.QLabel

QLabel(QLabel.QUALITY) - Constructor for class ambit2.base.data.QLabel

QLabel.QUALITY - Enum in ambit2.base.data

R

range - Variable in class ambit2.base.data.PropertyStats

Range<T extends java.lang.Comparable<T>> - Class in ambit2.base.data

Range() - Constructor for class ambit2.base.data.Range

Range(T) - Constructor for class ambit2.base.data.Range

Range(T, T) - Constructor for class ambit2.base.data.Range

readRecord(int) - Method in interface ambit2.base.interfaces.IRandomAccessChemObjectReader

records - Variable in class ambit2.base.processors.batch.DefaultBatchStatistics

records - Variable in class ambit2.base.processors.StructureRecordsAppender

reference - Variable in class ambit2.base.data.Property

reference - Variable in class ambit2.base.data.StructureRecord

regStatus - Variable in class ambit2.base.data.AmbitUser

relationship - Variable in class ambit2.base.data.Dictionary

removeProperty(Property) - Method in class ambit2.base.data.StructureRecord

removeProperty(Property) - Method in interface ambit2.base.interfaces.IStructureRecord

removePropertyChangeListener(String, PropertyChangeListener) - Method in class ambit2.base.data.Profile

removePropertyChangeListener(String, PropertyChangeListener) - Method in class ambit2.base.processors.DefaultAmbitProcessor

removePropertyChangeListener(PropertyChangeListener) - Method in class ambit2.base.processors.DefaultAmbitProcessor

removePropertyChangeListener(PropertyChangeListener) - Method in class ambit2.base.processors.ProcessorsChain

removePropertyChangeListener(String, PropertyChangeListener) - Method in class ambit2.base.processors.ProcessorsChain

Reporter<Content,Output> - Interface in ambit2.base.processors

resultCaption - Variable in class ambit2.base.processors.batch.DefaultBatchStatistics

runAsync - Variable in class ambit2.base.external.CommandShell

runShell(INPUT) - Method in class ambit2.base.external.CommandShell

runShell(INPUT, String) - Method in class ambit2.base.external.CommandShell

S

save(OutputStream) - Method in class ambit2.base.data.Property

save(Writer) - Method in class ambit2.base.data.Property

save(OutputStream) - Method in class ambit2.base.data.Template

save(Writer) - Method in class ambit2.base.data.Template

saveProperties(String) - Static method in class ambit2.base.config.Preferences

SCHEME - Static variable in class ambit2.base.config.Preferences

selected - Variable in class ambit2.base.data.SelectionBean

selectFile(Component, String, String, String[], String[], boolean) - Static method in class ambit2.base.io.MyIOUtilities

selectFile(Component, String, String, String[], String[], boolean, JComponent) - Static method in class ambit2.base.io.MyIOUtilities

Invokes OpenFile or SaveFile dialog

selectFiles(Component, String, String, String[], String[], boolean, JComponent) - Static method in class ambit2.base.io.MyIOUtilities

SelectionBean<T> - Class in ambit2.base.data

SelectionBean(List<T>) - Constructor for class ambit2.base.data.SelectionBean

SelectionBean() - Constructor for class ambit2.base.data.SelectionBean

SelectionBean(T[]) - Constructor for class ambit2.base.data.SelectionBean

SelectionBean(T[], String) - Constructor for class ambit2.base.data.SelectionBean

setAbortOnError(boolean) - Method in class ambit2.base.processors.ProcessorsChain

setAdditionalFiles(String[]) - Method in class ambit2.base.external.Command

setAddress(String) - Method in class ambit2.base.data.AmbitUser

setAffiliation(String) - Method in class ambit2.base.data.AmbitUser

setAvg(T) - Method in class ambit2.base.data.PropertyStats

setChanged() - Method in class ambit2.base.data.Profile

setCity(String) - Method in class ambit2.base.data.AmbitUser

setClazz(String) - Method in class ambit2.base.data.ClassHolder

setClazz(Class) - Method in class ambit2.base.data.Property

setContent(String) - Method in class ambit2.base.data.StructureRecord

setContent(String) - Method in interface ambit2.base.interfaces.IStructureRecord

setCount(long) - Method in class ambit2.base.data.PropertyStats

setCountry(String) - Method in class ambit2.base.data.AmbitUser

setCurrentRecord(long) - Method in interface ambit2.base.interfaces.IInputOutputState

setDescription(String) - Method in class ambit2.base.data.ClassHolder

setEmail(String) - Method in class ambit2.base.data.AmbitUser

setEnabled(boolean) - Method in class ambit2.base.data.Property

setEnabled(boolean) - Method in class ambit2.base.external.CommandShell

setEnabled(boolean) - Method in interface ambit2.base.interfaces.IProcessor

Enables/disables the processor

setEnabled(boolean) - Method in class ambit2.base.processors.DefaultAmbitProcessor

setEnabled(boolean) - Method in class ambit2.base.processors.ProcessorsChain

setExe(String) - Method in class ambit2.base.external.Command

setExitCode(int) - Method in class ambit2.base.external.CommandShell

setExtension(String) - Method in class ambit2.base.io.MolFileFilter

setFields(TypedListModel<Property>) - Method in class ambit2.base.data.PropertiesTableModel

setFilter(int, Object) - Method in interface ambit2.base.data.IFilteredColumns

setFirstName(String) - Method in class ambit2.base.data.AmbitUser

setFormat(String) - Method in class ambit2.base.data.StructureRecord

setFormat(String) - Method in interface ambit2.base.interfaces.IStructureRecord

setFormula(String) - Method in class ambit2.base.data.StructureRecord

setFormula(String) - Method in interface ambit2.base.interfaces.IChemical

setFrequency(long) - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

setHash(long) - Method in class ambit2.base.data.StructureRecord

setHash(long) - Method in interface ambit2.base.interfaces.IChemical

setIcon(String) - Method in class ambit2.base.data.ClassHolder

setId(int) - Method in class ambit2.base.data.LiteratureEntry

setId(int) - Method in class ambit2.base.data.Property

setId(int) - Method in class ambit2.base.data.Template

setIdchemical(int) - Method in class ambit2.base.data.StructureRecord

setIdchemical(int) - Method in interface ambit2.base.interfaces.IChemical

setIdstructure(int) - Method in class ambit2.base.data.StructureRecord

setIdstructure(int) - Method in interface ambit2.base.interfaces.IStructureRecord

setImage(ImageIcon) - Method in class ambit2.base.data.ClassHolder

setInchi(String) - Method in class ambit2.base.data.StructureRecord

setInchi(String) - Method in interface ambit2.base.interfaces.IChemical

setInputFile(String) - Method in class ambit2.base.external.CommandShell

setKey(Object) - Method in exception ambit2.base.exceptions.PropertyNotInTemplateException

setLabel(String) - Method in class ambit2.base.data.Property

setLabel(QLabel.QUALITY) - Method in class ambit2.base.data.QLabel

setLastName(String) - Method in class ambit2.base.data.AmbitUser

setMax(T) - Method in class ambit2.base.data.PropertyStats

setMaxValue(T) - Method in class ambit2.base.data.Range

setMin(T) - Method in class ambit2.base.data.PropertyStats

setMinValue(T) - Method in class ambit2.base.data.Range

setName(String) - Method in class ambit2.base.data.AmbitUser

setName(String) - Method in class ambit2.base.data.Profile

setName(String) - Method in class ambit2.base.data.StringBean

setOptions(List<T>) - Method in class ambit2.base.data.SelectionBean

setOrder(int) - Method in class ambit2.base.data.Property

setOutput(Output) - Method in class ambit2.base.processors.AbstractReporter

setOutput(Output) - Method in class ambit2.base.processors.batch.BatchReporter

setOutput(Output) - Method in interface ambit2.base.processors.Reporter

setOutputFile(String) - Method in class ambit2.base.external.CommandShell

setParentTemplate(String) - Method in class ambit2.base.data.Dictionary

setPassword(String) - Method in class ambit2.base.data.AmbitUser

setProcessorChain(ProcessorsChain<ItemInput, Result, IProcessor>) - Method in interface ambit2.base.interfaces.IBatchProcessor

setProcessorChain(ProcessorsChain<Target, IBatchStatistics, IProcessor>) - Method in class ambit2.base.processors.batch.BatchProcessor

setProcessors(ProcessorsChain<Item, IBatchStatistics, IProcessor>) - Method in class ambit2.base.processors.batch.BatchReporter

setProperty(String, String) - Static method in class ambit2.base.config.Preferences

setProperty(Property) - Method in class ambit2.base.data.PropertyTemplateStats

setProperty(Property, Object) - Method in class ambit2.base.data.StructureRecord

setProperty(Property, Object) - Method in interface ambit2.base.interfaces.IStructureRecord

setPropertyChangeSupport(PropertyChangeSupport) - Static method in class ambit2.base.config.Preferences

setRecords(IBatchStatistics.RECORDS_STATS, long) - Method in interface ambit2.base.interfaces.IBatchStatistics

Sets number of records of a type

setRecords(IBatchStatistics.RECORDS_STATS, long) - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

setRecords(List<IStructureRecord>) - Method in class ambit2.base.processors.StructureRecordsAppender

setReference(LiteratureEntry) - Method in class ambit2.base.data.Property

setReference(LiteratureEntry) - Method in class ambit2.base.data.StructureRecord

setReference(LiteratureEntry) - Method in interface ambit2.base.interfaces.IStructureRecord

setRelationship(String) - Method in class ambit2.base.data.Dictionary

setResponseType(String) - Method in interface ambit2.base.interfaces.IInputOutputState

setResultCaption(String) - Method in interface ambit2.base.interfaces.IBatchStatistics

setResultCaption(String) - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

setSelected(int) - Method in class ambit2.base.data.SelectionBean

setSelected(T) - Method in class ambit2.base.data.SelectionBean

setSelection(ISelectableRecords.SELECTION_MODE) - Method in interface ambit2.base.data.ISelectableRecords

setSmiles(String) - Method in class ambit2.base.data.StructureRecord

setSmiles(String) - Method in interface ambit2.base.interfaces.IChemical

setStackLength(int) - Method in class ambit2.base.log.AmbitLogger

Sets the number of StackTraceElements to be printed in DEBUG mode when calling debug(Throwable).

setTemplate(String) - Method in class ambit2.base.data.Dictionary

setTemplate(String) - Method in class ambit2.base.data.PropertyTemplateStats

setTemplate(Template) - Method in exception ambit2.base.exceptions.PropertyNotInTemplateException

setText(String) - Method in class ambit2.base.data.QLabel

setTimeElapsed(IBatchStatistics.RECORDS_STATS, long) - Method in interface ambit2.base.interfaces.IBatchStatistics

Sets time elapsed for of records of a type

setTimeElapsed(IBatchStatistics.RECORDS_STATS, long) - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

setTitle(String) - Method in class ambit2.base.data.AmbitUser

setTitle(String) - Method in class ambit2.base.data.ClassHolder

setTitle(String) - Method in class ambit2.base.data.SelectionBean

setTitle(String) - Method in interface ambit2.base.processors.IAmbitResult

setType(AmbitUser.USER_TYPE) - Method in class ambit2.base.data.AmbitUser

setUnits(String) - Method in class ambit2.base.data.Property

setUser(AmbitUser) - Method in class ambit2.base.data.QLabel

setValueAt(Object, int, int) - Method in class ambit2.base.data.PropertiesTableModel

setVisible(Boolean) - Method in class ambit2.base.data.ProfileListModel

setWww(String) - Method in class ambit2.base.data.AmbitUser

shell - Variable in exception ambit2.base.external.ShellException

ShellException - Exception in ambit2.base.external

ShellException(CommandShell) - Constructor for exception ambit2.base.external.ShellException

ShellException(CommandShell, String) - Constructor for exception ambit2.base.external.ShellException

ShellException(CommandShell, String, Throwable) - Constructor for exception ambit2.base.external.ShellException

ShellException(CommandShell, Throwable) - Constructor for exception ambit2.base.external.ShellException

SHOW_AROMATICITY - Static variable in class ambit2.base.config.Preferences

SimpleErrorHandler - Class in ambit2.base.io

SimpleErrorHandler(String) - Constructor for class ambit2.base.io.SimpleErrorHandler

size() - Method in class ambit2.base.data.Profile

size() - Method in interface ambit2.base.interfaces.IRandomAccessChemObjectReader

SMI2SDF_LINUX - Static variable in class ambit2.base.config.Preferences

SMI2SDF_WIN - Static variable in class ambit2.base.config.Preferences

smiles - Variable in class ambit2.base.data.StructureRecord

SMILES_FIELD - Static variable in class ambit2.base.config.Preferences

SMILES_GEN - Static variable in class ambit2.base.config.Preferences

SMILESPARSER - Static variable in class ambit2.base.config.Preferences

sort(int, boolean) - Method in interface ambit2.base.data.ISortableColumns

START_MYSQL - Static variable in class ambit2.base.config.Preferences

STOP_AT_UNKNOWNATOMTYPES - Static variable in class ambit2.base.config.Preferences

StringBean - Class in ambit2.base.data

StringBean(String) - Constructor for class ambit2.base.data.StringBean

StructureRecord - Class in ambit2.base.data

StructureRecord() - Constructor for class ambit2.base.data.StructureRecord

StructureRecord(int, int, String, String) - Constructor for class ambit2.base.data.StructureRecord

StructureRecordsAppender - Class in ambit2.base.processors

StructureRecordsAppender() - Constructor for class ambit2.base.processors.StructureRecordsAppender

supported_extensions - Static variable in class ambit2.base.io.MolFileFilter

supported_exts_description - Static variable in class ambit2.base.io.MolFileFilter

T

template - Variable in class ambit2.base.data.Dictionary

template - Variable in class ambit2.base.data.PropertyTemplateStats

Template - Class in ambit2.base.data

Templates are just a (meaningful) set of properties

Template() - Constructor for class ambit2.base.data.Template

Template(String) - Constructor for class ambit2.base.data.Template

text - Variable in class ambit2.base.data.QLabel

time_elapsed - Variable in class ambit2.base.processors.batch.DefaultBatchStatistics

title - Variable in class ambit2.base.data.AmbitUser

title - Variable in class ambit2.base.data.ClassHolder

title - Variable in class ambit2.base.data.LiteratureEntry

title - Variable in class ambit2.base.data.SelectionBean

title - Variable in class ambit2.base.io.SimpleErrorHandler

toString() - Method in class ambit2.base.data.AmbitUser

toString() - Method in class ambit2.base.data.ClassHolder

toString() - Method in class ambit2.base.data.Dictionary

toString() - Method in class ambit2.base.data.LiteratureEntry

toString() - Method in class ambit2.base.data.Property

toString() - Method in class ambit2.base.data.PropertyStats

toString() - Method in class ambit2.base.data.PropertyTemplateStats

toString() - Method in class ambit2.base.data.QLabel

toString() - Method in class ambit2.base.data.Range

toString() - Method in class ambit2.base.data.SelectionBean

toString() - Method in class ambit2.base.data.StringBean

toString() - Method in class ambit2.base.data.StructureRecord

toString() - Method in class ambit2.base.data.Template

toString() - Method in class ambit2.base.external.Command

toString() - Method in class ambit2.base.processors.batch.DefaultBatchStatistics

toString() - Method in class ambit2.base.processors.DefaultAmbitProcessor

toString() - Method in class ambit2.base.processors.ProcessorsChain

toxForest_ext - Static variable in class ambit2.base.io.MolFileFilter

toxForest_ext_descr - Static variable in class ambit2.base.io.MolFileFilter

toxTree_ext - Static variable in class ambit2.base.io.MolFileFilter

toxTree_ext_descr - Static variable in class ambit2.base.io.MolFileFilter

toxTree_ext_descr_save - Static variable in class ambit2.base.io.MolFileFilter

toxTree_ext_save - Static variable in class ambit2.base.io.MolFileFilter

transform(Process, INPUT) - Method in class ambit2.base.external.CommandShell

transform(INPUT) - Method in class ambit2.base.external.CommandShell

transform_input(INPUT) - Method in class ambit2.base.external.CommandShell

type - Variable in class ambit2.base.data.AmbitUser

TypedListModel<P> - Interface in ambit2.base.data

U

units - Variable in class ambit2.base.data.Property

update(Object) - Method in interface ambit2.base.processors.IAmbitResult

updateConnectionData(String, String, String) - Method in class ambit2.base.data.AmbitUser

URL - Variable in class ambit2.base.data.LiteratureEntry

USER - Static variable in class ambit2.base.config.Preferences

user - Variable in class ambit2.base.data.QLabel

V

valueOf(String) - Static method in enum ambit2.base.config.Preferences.VINDEX

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.base.config.Preferences.VTAGS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.base.data.AmbitUser.USER_TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.base.data.ISelectableRecords.SELECTION_MODE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.base.data.Property.IO_QUESTION

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.base.data.QLabel.QUALITY

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.base.interfaces.IBatchStatistics.RECORDS_STATS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ambit2.base.interfaces.IStructureRecord.MOL_TYPE

Returns the enum constant of this type with the specified name.

values() - Static method in enum ambit2.base.config.Preferences.VINDEX

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.base.config.Preferences.VTAGS

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.base.data.AmbitUser.USER_TYPE

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.base.data.ISelectableRecords.SELECTION_MODE

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Method in class ambit2.base.data.Profile

values() - Static method in enum ambit2.base.data.Property.IO_QUESTION

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.base.data.QLabel.QUALITY

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.base.interfaces.IBatchStatistics.RECORDS_STATS

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum ambit2.base.interfaces.IStructureRecord.MOL_TYPE

Returns an array containing the constants of this enum type, in the order they're declared.

visibility - Variable in class ambit2.base.data.ProfileListModel

visibility - Variable in class ambit2.base.data.PropertiesTableModel

visibleFields - Variable in class ambit2.base.data.PropertiesTableModel

visibleIndex - Variable in class ambit2.base.data.ProfileListModel

W

warn(Object) - Method in class ambit2.base.log.AmbitLogger

Shows WARN output for the Object.

warning(SAXParseException) - Method in class ambit2.base.io.SimpleErrorHandler

write(Writer) - Method in interface ambit2.base.processors.IAmbitResult

Writes the object

www - Variable in class ambit2.base.data.AmbitUser

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