Serialized Form

Package net.sf.taverna.raven

Class net.sf.taverna.raven.RavenException extends java.lang.Exception implements Serializable

serialVersionUID: 1L

Class net.sf.taverna.raven.SplashScreen extends javax.swing.JWindow implements Serializable

serialVersionUID: -3444472402764959095L

Serialized Fields

canClose

boolean canClose

timedOut

boolean timedOut

progress

javax.swing.JProgressBar progress

listener

net.sf.taverna.raven.SplashScreen.SplashListener listener

Package net.sf.taverna.raven.plugins.event

Class net.sf.taverna.raven.plugins.event.PluginEvent extends java.util.EventObject implements Serializable

serialVersionUID: 1L

Serialized Fields

plugin

Plugin plugin

action

int action

Class net.sf.taverna.raven.plugins.event.PluginManagerEvent extends java.util.EventObject implements Serializable

serialVersionUID: 1L

Serialized Fields

plugin

Plugin plugin

index

int index

Package net.sf.taverna.raven.plugins.ui

Class net.sf.taverna.raven.plugins.ui.AddPluginSiteFrame extends javax.swing.JDialog implements Serializable

Serialized Fields

jContentPane

javax.swing.JPanel jContentPane

okButton

javax.swing.JButton okButton

cancelButton

javax.swing.JButton cancelButton

urlText

javax.swing.JTextField urlText

nameText

javax.swing.JTextField nameText

name

java.lang.String name

url

java.lang.String url

Class net.sf.taverna.raven.plugins.ui.PluginListCellRenderer extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

pluginManager

PluginManager pluginManager

name

javax.swing.JLabel name

description

javax.swing.JLabel description

version

javax.swing.JLabel version

status

javax.swing.JLabel status

status2

javax.swing.JLabel status2

Class net.sf.taverna.raven.plugins.ui.PluginListModel extends javax.swing.AbstractListModel implements Serializable

Serialized Fields

pluginManager

PluginManager pluginManager

Class net.sf.taverna.raven.plugins.ui.PluginManagerFrame extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

jContentPane

javax.swing.JPanel jContentPane

updateButton

javax.swing.JButton updateButton

findPluginsButton

javax.swing.JButton findPluginsButton

pluginManager

PluginManager pluginManager

jScrollPane

javax.swing.JScrollPane jScrollPane

jList

javax.swing.JList jList

enableButton

javax.swing.JButton enableButton

uninstallButton

javax.swing.JButton uninstallButton

findUpdatesButton

javax.swing.JButton findUpdatesButton

closeButton

javax.swing.JButton closeButton

managerListener

PluginManagerListener managerListener

Class net.sf.taverna.raven.plugins.ui.PluginSiteFrame extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

pluginManager

PluginManager pluginManager

pluginSites

java.util.List<E> pluginSites

installationScheduled

java.util.List<E> installationScheduled

installButton

javax.swing.JButton installButton

cancelButton

javax.swing.JButton cancelButton

addSiteButton

javax.swing.JButton addSiteButton

listeners

java.util.Map<K,V> listeners

addSiteFrame

AddPluginSiteFrame addSiteFrame

scrollPane

javax.swing.JScrollPane scrollPane

Class net.sf.taverna.raven.plugins.ui.UpdatesAvailableIcon extends javax.swing.JLabel implements Serializable

Serialized Fields

updatePluginMouseAdaptor

net.sf.taverna.raven.plugins.ui.UpdatesAvailableIcon.UpdatePluginsMouseAdaptor updatePluginMouseAdaptor

CHECK_INTERVAL

int CHECK_INTERVAL

updateLock

java.lang.Object updateLock

Package net.sf.taverna.raven.profile.ui

Class net.sf.taverna.raven.profile.ui.ProfileVersionCellRenderer extends javax.swing.JPanel implements Serializable

Serialized Fields

name

javax.swing.JLabel name

version

javax.swing.JLabel version

description

javax.swing.JLabel description

currentVersion

java.lang.String currentVersion

Class net.sf.taverna.raven.profile.ui.ProfileVersionListFrame extends javax.swing.JDialog implements Serializable

Serialized Fields

contentPane

javax.swing.JPanel contentPane

scrollPane

javax.swing.JScrollPane scrollPane

list

javax.swing.JList list

switchButton

javax.swing.JButton switchButton

closeButton

javax.swing.JButton closeButton

currentVersion

java.lang.String currentVersion

Class net.sf.taverna.raven.profile.ui.ProfileVersionListModel extends javax.swing.AbstractListModel implements Serializable

Serialized Fields

versions

java.util.List<E> versions

Package net.sf.taverna.raven.repository

Class net.sf.taverna.raven.repository.ArtifactNotFoundException extends RavenException implements Serializable

serialVersionUID: 1L

Class net.sf.taverna.raven.repository.ArtifactStateException extends RavenException implements Serializable

serialVersionUID: 1L

Serialized Fields

state

ArtifactStatus state

validStates

ArtifactStatus[] validStates

Package net.sf.taverna.raven.spi

Class net.sf.taverna.raven.spi.InvalidProfileException extends RavenException implements Serializable

serialVersionUID: 1L

Package net.sf.taverna.t2.lang.ui

Class net.sf.taverna.t2.lang.ui.ShadedLabel extends javax.swing.JPanel implements Serializable

Serialized Fields

label

javax.swing.JLabel label

colour

java.awt.Color colour

toColour

java.awt.Color toColour

text

java.lang.String text

Class net.sf.taverna.t2.lang.ui.ValidatingUserInputDialog extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

inputTitle

java.lang.String inputTitle

okButton

javax.swing.JButton okButton

cancelButton

javax.swing.JButton cancelButton

inputText

javax.swing.JTextArea inputText

inputPanel

javax.swing.JPanel inputPanel

iconLabel

javax.swing.JLabel iconLabel

valid

boolean valid

result

boolean result

Package net.sf.taverna.t2.partition

Class net.sf.taverna.t2.partition.HashSetModel extends java.util.HashSet<ItemType> implements Serializable

serialVersionUID: 5763277571663880941L

Serialized Fields

changeListeners

java.util.List<E> changeListeners

Class net.sf.taverna.t2.partition.Partition$1 extends java.lang.Object implements Serializable

Class net.sf.taverna.t2.partition.RootPartition$1 extends java.lang.Object implements Serializable

Package net.sf.taverna.t2.partition.ui

Class net.sf.taverna.t2.partition.ui.PartitionAlgorithmListEditor extends javax.swing.JPanel implements Serializable

serialVersionUID: 8206805090698009524L

Serialized Fields

selectedIndex

int selectedIndex

paList

java.util.List<E> paList

cornerSep

int cornerSep

labelHorizontalPad

int labelHorizontalPad

labelBottomPad

int labelBottomPad

labelTopPad

int labelTopPad

selectedStrokeWidth

float selectedStrokeWidth

Class net.sf.taverna.t2.partition.ui.UITest extends javax.swing.JFrame implements Serializable

serialVersionUID: -734851883737477053L

Package net.sf.taverna.t2.util.beanable

Class net.sf.taverna.t2.util.beanable.RetrievalException extends java.lang.RuntimeException implements Serializable

Class net.sf.taverna.t2.util.beanable.StorageException extends java.lang.RuntimeException implements Serializable

Package net.sf.taverna.update.plugin.event

Class net.sf.taverna.update.plugin.event.PluginEvent extends java.util.EventObject implements Serializable

serialVersionUID: 1L

Serialized Fields

plugin

Plugin plugin

action

int action

Class net.sf.taverna.update.plugin.event.PluginManagerEvent extends java.util.EventObject implements Serializable

serialVersionUID: 1L

Serialized Fields

plugin

Plugin plugin

index

int index

Package net.sf.taverna.update.plugin.ui

Class net.sf.taverna.update.plugin.ui.AddPluginSiteFrame extends javax.swing.JDialog implements Serializable

Serialized Fields

jContentPane

javax.swing.JPanel jContentPane

okButton

javax.swing.JButton okButton

cancelButton

javax.swing.JButton cancelButton

urlText

javax.swing.JTextField urlText

nameText

javax.swing.JTextField nameText

name

java.lang.String name

url

java.lang.String url

Class net.sf.taverna.update.plugin.ui.PluginListCellRenderer extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

pluginManager

PluginManager pluginManager

name

javax.swing.JLabel name

description

javax.swing.JLabel description

version

javax.swing.JLabel version

status

javax.swing.JLabel status

status2

javax.swing.JLabel status2

Class net.sf.taverna.update.plugin.ui.PluginListModel extends javax.swing.AbstractListModel implements Serializable

Serialized Fields

pluginManager

PluginManager pluginManager

Class net.sf.taverna.update.plugin.ui.PluginManagerFrame extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

jContentPane

javax.swing.JPanel jContentPane

updateButton

javax.swing.JButton updateButton

findPluginsButton

javax.swing.JButton findPluginsButton

pluginManager

PluginManager pluginManager

jScrollPane

javax.swing.JScrollPane jScrollPane

jList

javax.swing.JList jList

enableButton

javax.swing.JButton enableButton

uninstallButton

javax.swing.JButton uninstallButton

findUpdatesButton

javax.swing.JButton findUpdatesButton

closeButton

javax.swing.JButton closeButton

managerListener

PluginManagerListener managerListener

Class net.sf.taverna.update.plugin.ui.PluginSiteFrame extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

pluginManager

PluginManager pluginManager

pluginSites

java.util.List<E> pluginSites

installationScheduled

java.util.List<E> installationScheduled

installButton

javax.swing.JButton installButton

cancelButton

javax.swing.JButton cancelButton

addSiteButton

javax.swing.JButton addSiteButton

listeners

java.util.Map<K,V> listeners

addSiteFrame

AddPluginSiteFrame addSiteFrame

scrollPane

javax.swing.JScrollPane scrollPane

Class net.sf.taverna.update.plugin.ui.UpdatesAvailableIcon extends javax.swing.JLabel implements Serializable

Serialized Fields

updateProfileMouseAdaptor

net.sf.taverna.update.plugin.ui.UpdatesAvailableIcon.UpdateProfileMouseAdaptor updateProfileMouseAdaptor

updatePluginMouseAdaptor

net.sf.taverna.update.plugin.ui.UpdatesAvailableIcon.UpdatePluginsMouseAdaptor updatePluginMouseAdaptor

CHECK_INTERVAL

int CHECK_INTERVAL

Package net.sf.taverna.update.profile.ui

Class net.sf.taverna.update.profile.ui.ProfileVersionCellRenderer extends javax.swing.JPanel implements Serializable

Serialized Fields

name

javax.swing.JLabel name

version

javax.swing.JLabel version

description

javax.swing.JLabel description

currentVersion

java.lang.String currentVersion

Class net.sf.taverna.update.profile.ui.ProfileVersionListFrame extends javax.swing.JDialog implements Serializable

Serialized Fields

contentPane

javax.swing.JPanel contentPane

scrollPane

javax.swing.JScrollPane scrollPane

list

javax.swing.JList list

switchButton

javax.swing.JButton switchButton

closeButton

javax.swing.JButton closeButton

currentVersion

java.lang.String currentVersion

Class net.sf.taverna.update.profile.ui.ProfileVersionListModel extends javax.swing.AbstractListModel implements Serializable

Serialized Fields

versions

java.util.List<E> versions

Package net.sf.taverna.x2008.xml.plugins.impl

Class net.sf.taverna.x2008.xml.plugins.impl.ApplicationImpl extends org.apache.xmlbeans.impl.values.XmlComplexContentImpl implements Serializable

Class net.sf.taverna.x2008.xml.plugins.impl.ArtifactImpl extends org.apache.xmlbeans.impl.values.XmlComplexContentImpl implements Serializable

Class net.sf.taverna.x2008.xml.plugins.impl.CompatibilityImpl extends org.apache.xmlbeans.impl.values.XmlComplexContentImpl implements Serializable

Class net.sf.taverna.x2008.xml.plugins.impl.DependencyImpl extends org.apache.xmlbeans.impl.values.XmlComplexContentImpl implements Serializable

Class net.sf.taverna.x2008.xml.plugins.impl.DescribedPluginImpl extends IdentifiedPluginImpl implements Serializable

Class net.sf.taverna.x2008.xml.plugins.impl.IdentifiedPluginImpl extends org.apache.xmlbeans.impl.values.XmlComplexContentImpl implements Serializable

Class net.sf.taverna.x2008.xml.plugins.impl.PluginDocumentImpl extends org.apache.xmlbeans.impl.values.XmlComplexContentImpl implements Serializable

Class net.sf.taverna.x2008.xml.plugins.impl.PluginsDocumentImpl extends org.apache.xmlbeans.impl.values.XmlComplexContentImpl implements Serializable

Class net.sf.taverna.x2008.xml.plugins.impl.PluginsImpl extends org.apache.xmlbeans.impl.values.XmlComplexContentImpl implements Serializable

Class net.sf.taverna.x2008.xml.plugins.impl.ProfileImpl extends org.apache.xmlbeans.impl.values.XmlComplexContentImpl implements Serializable

Class net.sf.taverna.x2008.xml.plugins.impl.RepositoriesImpl extends org.apache.xmlbeans.impl.values.XmlComplexContentImpl implements Serializable

Package net.sf.taverna.zaria

Class net.sf.taverna.zaria.ZBasePane extends ZPane implements Serializable

Serialized Fields

child

ZTreeNode child

repository

Repository repository

registries

java.util.Map<K,V> registries

knownSpiNames

java.lang.String[] knownSpiNames

toggleEditAction

javax.swing.Action toggleEditAction

blur

BlurredGlassPane blur

namedComponentDefinitions

java.util.Map<K,V> namedComponentDefinitions

namedComponents

java.util.Map<K,V> namedComponents

Class net.sf.taverna.zaria.ZBlankComponent extends ZPane implements Serializable

Serialized Fields

actions

java.util.List<E> actions

createSplitPaneAction

javax.swing.Action createSplitPaneAction

createTabbedPaneAction

javax.swing.Action createTabbedPaneAction

createRavenPaneAction

javax.swing.Action createRavenPaneAction

Class net.sf.taverna.zaria.ZPane extends javax.swing.JComponent implements Serializable

Serialized Fields

editable

boolean editable

toolBar

javax.swing.JToolBar toolBar

Class net.sf.taverna.zaria.ZPane.ReplaceWithBlankAction extends javax.swing.AbstractAction implements Serializable

Class net.sf.taverna.zaria.ZRavenComponent extends ZPane implements Serializable

Serialized Fields

spiName

java.lang.String spiName

artifact

Artifact artifact

className

java.lang.String className

hasScrollPane

boolean hasScrollPane

contentArea

javax.swing.JPanel contentArea

contents

javax.swing.JComponent contents

actions

java.util.List<E> actions

registry

SpiRegistry registry

sharedName

java.lang.String sharedName

toggleScroll

ZRavenComponent.ToggleScrollPaneAction toggleScroll

selectSPI

javax.swing.Action selectSPI

selectInstance

javax.swing.Action selectInstance

nameComponent

javax.swing.Action nameComponent

selectNamedInstance

javax.swing.Action selectNamedInstance

Class net.sf.taverna.zaria.ZRavenComponent.NameComponentAction extends javax.swing.AbstractAction implements Serializable

Class net.sf.taverna.zaria.ZRavenComponent.SelectInstanceAction extends javax.swing.AbstractAction implements Serializable

Class net.sf.taverna.zaria.ZRavenComponent.SelectNamedInstanceAction extends javax.swing.AbstractAction implements Serializable

Class net.sf.taverna.zaria.ZRavenComponent.SelectSPIAction extends javax.swing.AbstractAction implements Serializable

Class net.sf.taverna.zaria.ZRavenComponent.ToggleScrollPaneAction extends javax.swing.AbstractAction implements Serializable

Class net.sf.taverna.zaria.ZSplitPane extends ZPane implements Serializable

Serialized Fields

splitPane

javax.swing.JSplitPane splitPane

dividerLocation

double dividerLocation

actions

java.util.List<E> actions

Class net.sf.taverna.zaria.ZSplitPane.DividerLocationSplitPane extends javax.swing.JSplitPane implements Serializable

Serialized Fields

initialDividerSet

boolean initialDividerSet

Class net.sf.taverna.zaria.ZTabbedPane extends ZPane implements Serializable

Serialized Fields

tabs

javax.swing.JTabbedPane tabs

actions

java.util.List<E> actions

removeTabAction

javax.swing.Action removeTabAction

demoteTabAction

javax.swing.Action demoteTabAction

promoteTabAction

javax.swing.Action promoteTabAction

colourTabAction

javax.swing.Action colourTabAction

tabName

javax.swing.JTextField tabName

Package net.sf.taverna.zaria.progress

Class net.sf.taverna.zaria.progress.BlurredGlassPane extends javax.swing.JComponent implements Serializable

Serialized Fields

frame

javax.swing.JFrame frame

active

boolean active

blur

java.awt.image.BufferedImage blur

filter

BoxBlurFilter filter

listener

java.awt.event.ComponentListener listener

Class net.sf.taverna.zaria.progress.InfiniteProgressPanel extends javax.swing.JComponent implements Serializable

Serialized Fields

ticker

java.awt.geom.Area[] ticker

animation

java.lang.Thread animation

started

boolean started

alphaLevel

int alphaLevel

rampDelay

int rampDelay

shield

float shield

text

java.lang.String text

barsCount

int barsCount

fps

float fps

hints

java.awt.RenderingHints hints

Package net.sf.taverna.zaria.raven

Class net.sf.taverna.zaria.raven.ArtifactDownloadDialog extends javax.swing.JDialog implements Serializable

Package net.sourceforge.taverna.io

Class net.sourceforge.taverna.io.TransmitterException extends java.lang.Exception implements Serializable

Serialized Fields

detailMsg

java.lang.String detailMsg

Package net.sourceforge.taverna.publish

Class net.sourceforge.taverna.publish.PublicationException extends java.lang.Exception implements Serializable

Class net.sourceforge.taverna.publish.PublishDialog extends javax.swing.JDialog implements Serializable

Class net.sourceforge.taverna.publish.RepositoryForm extends org.jdesktop.swing.form.JForm implements Serializable

Package net.sourceforge.taverna.scuflworkers.bsf

Class net.sourceforge.taverna.scuflworkers.bsf.BSFConfigPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

processor

BSFProcessor processor

scriptText

org.syntax.jedit.JEditTextArea scriptText

inputTable

javax.swing.JTable inputTable

outputTable

javax.swing.JTable outputTable

addInputButton

javax.swing.JButton addInputButton

addInputField

javax.swing.JTextField addInputField

addOutputButton

javax.swing.JButton addOutputButton

addOutputField

javax.swing.JTextField addOutputField

scriptEngineSelect

javax.swing.JComboBox scriptEngineSelect

deletePortAction

javax.swing.Action deletePortAction

Class net.sourceforge.taverna.scuflworkers.bsf.BSFProcessor extends Processor implements Serializable

Serialized Fields

theScript

java.lang.String theScript

language

java.lang.String language

Class net.sourceforge.taverna.scuflworkers.bsf.BSFScavenger extends Scavenger implements Serializable

Package nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor

Class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APConfigPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: -1596783050410457435L

Serialized Fields

processor

APProcessor processor

taskDescriptionTextArea

javax.swing.JTextArea taskDescriptionTextArea

inputPortsTable

javax.swing.JTable inputPortsTable

addInputButton

javax.swing.JButton addInputButton

outputPortsTable

javax.swing.JTable outputPortsTable

addOutputButton

javax.swing.JButton addOutputButton

deletePortAction

javax.swing.Action deletePortAction

Class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APProcessor extends Processor implements Serializable

serialVersionUID: 8799117109992658036L

Serialized Fields

taskDescription

java.lang.String taskDescription

Class nl.utwente.ewi.hmi.taverna.scuflworkers.abstractprocessor.APScavenger extends Scavenger implements Serializable

serialVersionUID: -6186599168134511411L

Package nl.utwente.ewi.hmi.taverna.scuflworkers.rshell

Class nl.utwente.ewi.hmi.taverna.scuflworkers.rshell.RshellConfigPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: -1596783050410457435L

Serialized Fields

processor

RshellProcessor processor

connectionSettings

RshellConnectionSettings connectionSettings

currentDirectory

java.io.File currentDirectory

scriptTextArea

javax.swing.JTextArea scriptTextArea

inputPortsTable

javax.swing.JTable inputPortsTable

addInputButton

javax.swing.JButton addInputButton

outputPortsTable

javax.swing.JTable outputPortsTable

addOutputButton

javax.swing.JButton addOutputButton

hostField

javax.swing.JTextField hostField

portField

javax.swing.JTextField portField

usernameField

javax.swing.JTextField usernameField

passwordField

javax.swing.JPasswordField passwordField

keepSessionAliveField

javax.swing.JCheckBox keepSessionAliveField

deletePortAction

javax.swing.Action deletePortAction

Class nl.utwente.ewi.hmi.taverna.scuflworkers.rshell.RshellConnectionSettings extends java.lang.Object implements Serializable

serialVersionUID: -8311679711262064315L

Serialized Fields

host

java.lang.String host

port

int port

username

java.lang.String username

password

java.lang.String password

keepSessionAlive

boolean keepSessionAlive

Class nl.utwente.ewi.hmi.taverna.scuflworkers.rshell.RshellInputPort extends InputPort implements Serializable

serialVersionUID: 6454564758308556076L

Serialized Fields

symanticType

RshellPortTypes.SymanticTypes symanticType

Class nl.utwente.ewi.hmi.taverna.scuflworkers.rshell.RshellOutputPort extends OutputPort implements Serializable

serialVersionUID: -3714649331013542345L

Serialized Fields

symanticType

RshellPortTypes.SymanticTypes symanticType

Class nl.utwente.ewi.hmi.taverna.scuflworkers.rshell.RshellProcessor extends Processor implements Serializable

serialVersionUID: 1652784664361353135L

Serialized Fields

script

java.lang.String script

connectionSettings

RshellConnectionSettings connectionSettings

Class nl.utwente.ewi.hmi.taverna.scuflworkers.rshell.RshellScavenger extends Scavenger implements Serializable

serialVersionUID: 1258935955566995997L

Package org.apache.bsf

Class org.apache.bsf.BSFException extends java.lang.Exception implements Serializable

Serialized Fields

reason

int reason

targetThrowable

java.lang.Throwable targetThrowable

Package org.biomoby.client.taverna.plugin

Class org.biomoby.client.taverna.plugin.BiomobyObjectProcessor extends Processor implements Serializable

serialVersionUID: 3545795464290122041L

Serialized Fields

endpoint

java.net.URL endpoint

mobyEndpoint

java.lang.String mobyEndpoint

worker

org.biomoby.shared.Central worker

mobyObject

org.biomoby.shared.MobyDataType mobyObject

serviceName

java.lang.String serviceName

authorityName

java.lang.String authorityName

Class org.biomoby.client.taverna.plugin.BiomobyObjectScavenger extends Scavenger implements Serializable

serialVersionUID: 3545233648191289400L

Serialized Fields

defaultResourceURL

java.lang.String defaultResourceURL

Deprecated.

Class org.biomoby.client.taverna.plugin.BioMobyObjectTreeCustomRenderer extends javax.swing.tree.DefaultTreeCellRenderer implements Serializable

serialVersionUID: 1L

Serialized Fields

leafForeground

java.awt.Color leafForeground

rootColor

java.awt.Color rootColor

feedsIntoColor

java.awt.Color feedsIntoColor

producedColor

java.awt.Color producedColor

authorityColor

java.awt.Color authorityColor

serviceColor

java.awt.Color serviceColor

objectColor

java.awt.Color objectColor

Class org.biomoby.client.taverna.plugin.BiomobyProcessor extends Processor implements Serializable

serialVersionUID: 1L

Serialized Fields

endpoint

java.net.URL endpoint

mobyEndpoint

java.lang.String mobyEndpoint

worker

org.biomoby.shared.Central worker

mobyService

org.biomoby.shared.MobyService mobyService

serviceName

java.lang.String serviceName

authorityName

java.lang.String authorityName

containSecondary

boolean containSecondary

parameterTable

org.biomoby.service.dashboard.data.ParametersTable parameterTable

Class org.biomoby.client.taverna.plugin.BiomobyScavenger extends Scavenger implements Serializable

serialVersionUID: 3545233648191289400L

Serialized Fields

helper

BiomobyScavengerWorker helper

showAliveOnly

boolean showAliveOnly

Class org.biomoby.client.taverna.plugin.BiomobyScavengerActionDialog extends javax.swing.JPanel implements Serializable

serialVersionUID: -57047613557546674L

Class org.biomoby.client.taverna.plugin.BiomobyScavengerDialog extends javax.swing.JPanel implements Serializable

serialVersionUID: -57047613557546674L

Serialized Fields

registryEndpoint

javax.swing.JTextField registryEndpoint

registryURI

javax.swing.JTextField registryURI

Class org.biomoby.client.taverna.plugin.BioMobyServiceTreeCustomRenderer extends javax.swing.tree.DefaultTreeCellRenderer implements Serializable

serialVersionUID: 1L

Serialized Fields

leafForeground

java.awt.Color leafForeground

rootColor

java.awt.Color rootColor

feedsIntoColor

java.awt.Color feedsIntoColor

producedColor

java.awt.Color producedColor

authorityColor

java.awt.Color authorityColor

serviceColor

java.awt.Color serviceColor

objectColor

java.awt.Color objectColor

Class org.biomoby.client.taverna.plugin.MobyPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

textArea

javax.swing.JTextArea textArea

text

java.lang.String text

name

java.lang.String name

jLabel

javax.swing.JLabel jLabel

Class org.biomoby.client.taverna.plugin.MobyParseDatatypeProcessor extends Processor implements Serializable

serialVersionUID: 1L

Serialized Fields

datatypeName

java.lang.String datatypeName

registryEndpoint

java.lang.String registryEndpoint

workflowName

java.lang.String workflowName

articleNameUsedByService

java.lang.String articleNameUsedByService

central

org.biomoby.shared.Central central

datatype

org.biomoby.shared.MobyDataType datatype

Class org.biomoby.client.taverna.plugin.MobyParseDatatypeScavenger extends Scavenger implements Serializable

serialVersionUID: 1L

Class org.biomoby.client.taverna.plugin.SimpleActionFrame extends javax.swing.JPanel implements Serializable

serialVersionUID: -6611234116434482238L

Serialized Fields

action

AbstractProcessorAction action

name

java.lang.String name

Package org.embl.ebi.escience.baclava

Class org.embl.ebi.escience.baclava.DataThing extends java.lang.Object implements Serializable

Serialized Fields

theDataObject

java.lang.Object theDataObject

metadataMap

java.util.HashMap<K,V> metadataMap

myMarkup

SemanticMarkup myMarkup

lsid

java.util.HashMap<K,V> lsid

Class org.embl.ebi.escience.baclava.NoMetadataFoundException extends java.lang.RuntimeException implements Serializable

Package org.embl.ebi.escience.baclava.factory

Class org.embl.ebi.escience.baclava.factory.DataThingTreeNode extends javax.swing.tree.DefaultMutableTreeNode implements Serializable

Serialized Fields

dataThing

DataThing dataThing

nodeThing

DataThing nodeThing

Class org.embl.ebi.escience.baclava.factory.DataThingTreeNodeRenderer extends javax.swing.tree.DefaultTreeCellRenderer implements Serializable

Package org.embl.ebi.escience.baclava.iterator

Class org.embl.ebi.escience.baclava.iterator.BaclavaIteratorNode extends javax.swing.tree.DefaultMutableTreeNode implements Serializable

Serialized Fields

iterator

BaclavaIterator iterator

name

java.lang.String name

Class org.embl.ebi.escience.baclava.iterator.JoinIteratorNode extends javax.swing.tree.DefaultMutableTreeNode implements Serializable

Serialized Fields

iterator

JoinIterator iterator

Class org.embl.ebi.escience.baclava.iterator.LockStepIteratorNode extends javax.swing.tree.DefaultMutableTreeNode implements Serializable

Serialized Fields

iterator

LockStepIterator iterator

Package org.embl.ebi.escience.baclava.store

Class org.embl.ebi.escience.baclava.store.DuplicateLSIDException extends java.lang.Exception implements Serializable

Class org.embl.ebi.escience.baclava.store.NoSuchLSIDException extends java.lang.Exception implements Serializable

Package org.embl.ebi.escience.baclava.tools

Class org.embl.ebi.escience.baclava.tools.DataThingViewer extends javax.swing.JFrame implements Serializable

Serialized Fields

tabs

javax.swing.JTabbedPane tabs

toolbar

javax.swing.JToolBar toolbar

resultMap

java.util.Map<K,V> resultMap

fc

javax.swing.JFileChooser fc

Package org.embl.ebi.escience.scufl

Class org.embl.ebi.escience.scufl.AlternateProcessor extends java.lang.Object implements Serializable

Serialized Fields

alternate

Processor alternate

original

Processor original

inputMapping

java.util.Map<K,V> inputMapping

outputMapping

java.util.Map<K,V> outputMapping

Class org.embl.ebi.escience.scufl.ConcurrencyConstraint extends java.lang.Object implements Serializable

Serialized Fields

controller

Processor controller

target

Processor target

targetStateFrom

int targetStateFrom

targetStateTo

int targetStateTo

controllerStateGuard

int controllerStateGuard

name

java.lang.String name

model

ScuflModel model

Class org.embl.ebi.escience.scufl.ConcurrencyConstraintCreationException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.CrossNode extends javax.swing.tree.DefaultMutableTreeNode implements Serializable

Class org.embl.ebi.escience.scufl.DataConstraint extends java.lang.Object implements Serializable

Serialized Fields

model

ScuflModel model

sink

InputPort sink

source

OutputPort source

Class org.embl.ebi.escience.scufl.DataConstraintCreationException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.DotNode extends javax.swing.tree.DefaultMutableTreeNode implements Serializable

Class org.embl.ebi.escience.scufl.DuplicateConcurrencyConstraintNameException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.DuplicatePortNameException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.DuplicateProcessorNameException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.InputPort extends Port implements Serializable

Serialized Fields

mergeMode

int mergeMode

defaultValue

java.lang.String defaultValue

isOptional

boolean isOptional

cv

java.lang.String[] cv

Class org.embl.ebi.escience.scufl.InternalSinkPortHolder extends Processor implements Serializable

Class org.embl.ebi.escience.scufl.InternalSourcePortHolder extends Processor implements Serializable

Class org.embl.ebi.escience.scufl.LeafNode extends javax.swing.tree.DefaultMutableTreeNode implements Serializable

Class org.embl.ebi.escience.scufl.MalformedNameException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.OutputPort extends Port implements Serializable

Class org.embl.ebi.escience.scufl.Port extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

processor

Processor processor

syntacticType

java.lang.String syntacticType

metadata

SemanticMarkup metadata

Class org.embl.ebi.escience.scufl.PortCreationException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.PortSemanticMarkup extends SemanticMarkup implements Serializable

Class org.embl.ebi.escience.scufl.Processor extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

description

java.lang.String description

ports

java.util.ArrayList<E> ports

model

ScuflModel model

timeout

int timeout

retries

int retries

retryDelay

int retryDelay

backoff

double backoff

critical

boolean critical

If a processor is critical its execution failure will fail the workflow

alternates

java.util.List<E> alternates

parentProcessor

Processor parentProcessor

templates

java.util.List<E> templates

iterationStrategy

IterationStrategy iterationStrategy

breakpoint

boolean breakpoint

boring

boolean boring

workerThreads

int workerThreads

The number of threads that this processor will use when running on an implicit iteration run

logLevel

int logLevel

The log level for this processor

Class org.embl.ebi.escience.scufl.ProcessorCreationException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.ScuflException extends java.lang.Exception implements Serializable

Class org.embl.ebi.escience.scufl.ScuflModel extends java.lang.Object implements Serializable

Serialized Fields

processors

java.util.List<E> processors

The processors defined by this workflow, ArrayList of Processor subclasses.

sinks

InternalSinkPortHolder sinks

An internal processor implementation to hold the overall workflow outputs, appearing as InputPort objects and acting as sinks for data from the externally visible processors.

sources

InternalSourcePortHolder sources

An internal processor implementation to hold the overall workflow source links; these appear as OutputPort objects in this processor.

constraints

java.util.ArrayList<E> constraints

The concurrency constraints defined by this workflow, ArrayList of ConcurrencyConstraint objects.

description

WorkflowDescription description

A workflow description object containing fields such as a free text description, author list etc

dataconstraints

java.util.ArrayList<E> dataconstraints

The data flow constraints defined by this workflow, ArrayList of DataConstraint objects.

logLevel

int logLevel

The log level for the model overall

offline

boolean offline

Set to true if the workflow definition is being loaded in offline mode, i.e. no network activity

listeners

java.util.List<E> listeners

The active model listeners for this model. Always synchronize(listeners).

pendingEvents

java.util.List<E> pendingEvents

Events pending to be processed by the notify thread. Always synchronize(pendingEvents).

notifyThread

org.embl.ebi.escience.scufl.NotifyThread notifyThread

Thread that processes events and pass them on to the listeners. Started by ScuflModel.addListener(ScuflModelEventListener) and stopped by ScuflModel.removeListener(ScuflModelEventListener) and ScuflModel.removeListeners() if there are no more listeners.

notifyThread will be null if it is not running. Access to modify this variable must be synchronized on ScuflModel.listeners

isFiringEvents

boolean isFiringEvents

Whether the model should fire events to its listeners

Class org.embl.ebi.escience.scufl.ScuflModelEventPrinter extends java.lang.Object implements Serializable

Serialized Fields

writer

java.io.PrintStream writer

Class org.embl.ebi.escience.scufl.SemanticMarkup extends java.lang.Object implements Serializable

Serialized Fields

description

java.lang.String description

semanticType

java.lang.String semanticType

mimeTypeList

java.util.List<E> mimeTypeList

subject

java.lang.Object subject

Class org.embl.ebi.escience.scufl.SetOnlineException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.UnknownPortException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.UnknownProcessorException extends ScuflException implements Serializable

Package org.embl.ebi.escience.scufl.enactor

Class org.embl.ebi.escience.scufl.enactor.UnknownWorkflowInstanceException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scufl.enactor.WorkflowSubmissionException extends ScuflException implements Serializable

Package org.embl.ebi.escience.scufl.parser

Class org.embl.ebi.escience.scufl.parser.XScuflFormatException extends ScuflException implements Serializable

serialVersionUID: -7557424386012201728L

Package org.embl.ebi.escience.scufl.view

Class org.embl.ebi.escience.scufl.view.DotView extends java.lang.Object implements Serializable

Serialized Fields

model

ScuflModel model

cacheValid

boolean cacheValid

cachedRepresentation

java.lang.String cachedRepresentation

portDisplay

int portDisplay

displayTypes

boolean displayTypes

lralign

boolean lralign

showBoring

boolean showBoring

fillColours

java.lang.String[] fillColours

expandWorkflow

boolean expandWorkflow

Class org.embl.ebi.escience.scufl.view.TreeModelView extends javax.swing.tree.DefaultTreeModel implements Serializable

Serialized Fields

workflow

ScuflModel workflow

inputRootNode

javax.swing.tree.MutableTreeNode inputRootNode

outputRootNode

javax.swing.tree.MutableTreeNode outputRootNode

processorRootNode

javax.swing.tree.MutableTreeNode processorRootNode

datalinkRootNode

javax.swing.tree.MutableTreeNode datalinkRootNode

constraintRootNode

javax.swing.tree.MutableTreeNode constraintRootNode

Class org.embl.ebi.escience.scufl.view.TreeTableModelView extends TreeModelView implements Serializable

Class org.embl.ebi.escience.scufl.view.XScuflView extends java.lang.Object implements Serializable

Serialized Fields

model

ScuflModel model

cacheValid

boolean cacheValid

cachedRepresentation

java.lang.String cachedRepresentation

cachedDocument

org.jdom.Document cachedDocument

Package org.embl.ebi.escience.scuflui

Class org.embl.ebi.escience.scuflui.AdvancedModelExplorer extends javax.swing.JPanel implements Serializable

Serialized Fields

explorer

ScuflModelTreeTable explorer

tabs

javax.swing.JTabbedPane tabs

propertiesPanel

javax.swing.JPanel propertiesPanel

selectedObject

java.lang.Object selectedObject

model

ScuflModel model

workOffline

javax.swing.JCheckBox workOffline

fc

javax.swing.JFileChooser fc

listener

ScuflModelEventListener listener

Class org.embl.ebi.escience.scuflui.AdvancedModelExplorer.WorkflowMetadata extends javax.swing.JPanel implements Serializable

Serialized Fields

wd

WorkflowDescription wd

updated

boolean updated

documentFocusListener

org.embl.ebi.escience.scuflui.AdvancedModelExplorer.WorkflowMetadata.DocumentFocusListener documentFocusListener

Class org.embl.ebi.escience.scuflui.BlankScavengerTreePanel extends ScavengerTreePanel implements Serializable

serialVersionUID: 8333709449450772744L

Class org.embl.ebi.escience.scuflui.DotTextArea extends javax.swing.JTextArea implements Serializable

Serialized Fields

dot

DotView dot

model

ScuflModel model

updateStatus

int updateStatus

Class org.embl.ebi.escience.scuflui.EnactorEventMonitor extends javax.swing.JTextArea implements Serializable

Serialized Fields

dispatcher

WorkflowEventDispatcher dispatcher

listener

WorkflowEventListener listener

Class org.embl.ebi.escience.scuflui.EnactorInvocation extends javax.swing.JPanel implements Serializable

Serialized Fields

workflowStatusUpdateReady

boolean workflowStatusUpdateReady

theModel

ScuflModel theModel

statusTableModel

EnactorStatusTableModel statusTableModel

workflowEditor

WorkflowEditor workflowEditor

workflowInstance

WorkflowInstance workflowInstance

resultsText

javax.swing.JTextArea resultsText

provenanceText

javax.swing.JTextArea provenanceText

provenancePanel

javax.swing.JPanel provenancePanel

individualResults

javax.swing.JTabbedPane individualResults

resultsPanel

javax.swing.JPanel resultsPanel

tabs

javax.swing.JTabbedPane tabs

toolbar

javax.swing.JToolBar toolbar

flowLabel

javax.swing.JLabel flowLabel

closeButton

javax.swing.JButton closeButton

results

javax.swing.JPanel results

Class org.embl.ebi.escience.scuflui.EnactorStatusTableModel extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

scuflModel

ScuflModel scuflModel

rows

int rows

data

java.lang.Object[][] data

columnNames

java.lang.String[] columnNames

Class org.embl.ebi.escience.scuflui.InputsNotMatchingException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scuflui.IterationStrategyEditor extends javax.swing.JTree implements Serializable

Serialized Fields

pathSource

javax.swing.tree.TreePath pathSource

imgGhost

java.awt.image.BufferedImage imgGhost

ptOffset

java.awt.Point ptOffset

strategy

IterationStrategy strategy

Class org.embl.ebi.escience.scuflui.IterationStrategyEditorControl extends javax.swing.JPanel implements Serializable

Serialized Fields

strategy

IterationStrategy strategy

tree

IterationStrategyEditor tree

addCross

javax.swing.JButton addCross

addDot

javax.swing.JButton addDot

normalize

javax.swing.JButton normalize

remove

javax.swing.JButton remove

change

javax.swing.JButton change

selectedNode

javax.swing.tree.MutableTreeNode selectedNode

Class org.embl.ebi.escience.scuflui.ResultItemPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

renderers

RendererRegistry renderers

workflowInstance

WorkflowInstance workflowInstance

processorName

java.lang.String processorName

portName

java.lang.String portName

Class org.embl.ebi.escience.scuflui.ScavengerTreePanel extends javax.swing.JPanel implements Serializable

Serialized Fields

tree

DefaultScavengerTree tree

regex

javax.swing.JTextField regex

find

javax.swing.JButton find

progBar

javax.swing.JProgressBar progBar

watchLoads

javax.swing.JCheckBox watchLoads

isWatchingLoads

boolean isWatchingLoads

eventListener

ScuflModelEventListener eventListener

initialised

boolean initialised

scuflModel

ScuflModel scuflModel

Class org.embl.ebi.escience.scuflui.ScuflDiagramPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

displayPolicyStrings

java.lang.String[] displayPolicyStrings

saveTypes

java.lang.String[] saveTypes

saveExtensions

java.lang.String[] saveExtensions

saveTypeNames

java.lang.String[] saveTypeNames

alignment

java.lang.String[] alignment

diagram

ScuflSVGDiagram diagram

fc

javax.swing.JFileChooser fc

model

ScuflModel model

Class org.embl.ebi.escience.scuflui.ScuflModelTreeTableContrib extends ScuflModelTreeTable implements Serializable

Class org.embl.ebi.escience.scuflui.ScuflSemanticMarkupEditor extends javax.swing.JPanel implements Serializable

Serialized Fields

theMetadata

SemanticMarkup theMetadata

selectedOntologyNode

javax.swing.JTextField selectedOntologyNode

treeModel

javax.swing.tree.DefaultTreeModel treeModel

ontologyTree

javax.swing.JTree ontologyTree

descriptionText

javax.swing.JTextArea descriptionText

mimeTypeListModel

javax.swing.DefaultListModel mimeTypeListModel

mimeTypeList

javax.swing.JList mimeTypeList

Class org.embl.ebi.escience.scuflui.ScuflSVGDiagram extends javax.swing.JComponent implements Serializable

Serialized Fields

dotViewSettings

java.util.WeakHashMap<K,V> dotViewSettings

fitToWindow

boolean fitToWindow

model

ScuflModel model

dot

DotView dot

graphicValid

boolean graphicValid

svgCanvas

org.apache.batik.swing.JSVGCanvas svgCanvas

pane

org.apache.batik.swing.JSVGScrollPane pane

updateTimer

java.util.Timer updateTimer

updating

boolean updating

resizeListener

java.awt.event.ComponentListener resizeListener

Class org.embl.ebi.escience.scuflui.TemplateEditor extends javax.swing.JComponent implements Serializable

Serialized Fields

theProcessor

Processor theProcessor

existingTemplates

javax.swing.JPanel existingTemplates

defaultTemplates

javax.swing.JPanel defaultTemplates

Class org.embl.ebi.escience.scuflui.WorkflowInputMapBuilder extends javax.swing.JPanel implements Serializable

Serialized Fields

loadInputDocAction

java.awt.event.ActionListener loadInputDocAction

saveInputDocAction

java.awt.event.ActionListener saveInputDocAction

fileChooser

javax.swing.JFileChooser fileChooser

model

ScuflModel model

rootNode

org.embl.ebi.escience.scuflui.WorkflowInputMapBuilder.InputsRootNode rootNode

treeModel

javax.swing.tree.DefaultTreeModel treeModel

splitter

javax.swing.JSplitPane splitter

portTree

javax.swing.JTree portTree

loadInputsButton

javax.swing.JButton loadInputsButton

newInputButton

javax.swing.JButton newInputButton

newListButton

javax.swing.JButton newListButton

removeButton

javax.swing.JButton removeButton

newInputAction

java.awt.event.ActionListener newInputAction

newListAction

java.awt.event.ActionListener newListAction

removeAction

java.awt.event.ActionListener removeAction

loadFilesAction

java.awt.event.ActionListener loadFilesAction

initialized

boolean initialized

Class org.embl.ebi.escience.scuflui.WorkflowInputMapBuilder.PortDescription extends javax.swing.JPanel implements Serializable

Serialized Fields

port

Port port

Class org.embl.ebi.escience.scuflui.WorkflowInputPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

model

ScuflModel model

diagramAndInputs

WorkflowInputPanel.DiagramAndInputs diagramAndInputs

Class org.embl.ebi.escience.scuflui.WorkflowInputPanel.DescriptionAndDiagram extends javax.swing.JPanel implements Serializable

Serialized Fields

diagram

ScuflSVGDiagram diagram

Class org.embl.ebi.escience.scuflui.WorkflowInputPanel.DiagramAndInputs extends javax.swing.JSplitPane implements Serializable

Serialized Fields

descAndDiag

WorkflowInputPanel.DescriptionAndDiagram descAndDiag

inputs

WorkflowInputPanel.Inputs inputs

initialDividerSet

boolean initialDividerSet

Class org.embl.ebi.escience.scuflui.WorkflowInputPanel.Header extends javax.swing.JPanel implements Serializable

Serialized Fields

header

ShadedLabel header

Class org.embl.ebi.escience.scuflui.WorkflowInputPanel.Input extends javax.swing.JPanel implements Serializable

Serialized Fields

port

Port port

Class org.embl.ebi.escience.scuflui.WorkflowInputPanel.Inputs extends javax.swing.JPanel implements Serializable

Serialized Fields

builder

WorkflowInputMapBuilder builder

Class org.embl.ebi.escience.scuflui.WorkflowInputPanel.RunButtons extends javax.swing.JPanel implements Serializable

Serialized Fields

runAction

javax.swing.Action runAction

Class org.embl.ebi.escience.scuflui.WorkflowInstanceContainer extends javax.swing.JPanel implements Serializable

Serialized Fields

firstInstance

java.util.Calendar firstInstance

helpPanel

javax.swing.JPanel helpPanel

tabs

javax.swing.JTabbedPane tabs

invocations

java.util.Map<K,V> invocations

timeFormat

java.text.DateFormat timeFormat

dateFormat

java.text.DateFormat dateFormat

Class org.embl.ebi.escience.scuflui.WorkflowInstanceContainer.HelpPanel extends javax.swing.JPanel implements Serializable

Class org.embl.ebi.escience.scuflui.XScuflTextArea extends javax.swing.JTextArea implements Serializable

Serialized Fields

xscufl

XScuflView xscufl

model

ScuflModel model

updateStatus

int updateStatus

Class org.embl.ebi.escience.scuflui.XScuflTree extends javax.swing.JComponent implements Serializable

Serialized Fields

model

ScuflModel model

xscufl

XScuflView xscufl

updateStatus

int updateStatus

Package org.embl.ebi.escience.scuflui.actions

Class org.embl.ebi.escience.scuflui.actions.AddDataConstraintAction extends ScuflModelAction implements Serializable

Serialized Fields

source

Port source

target

Port target

Class org.embl.ebi.escience.scuflui.actions.AddInputAction extends ScuflModelAction implements Serializable

Class org.embl.ebi.escience.scuflui.actions.AddOutputAction extends ScuflModelAction implements Serializable

Class org.embl.ebi.escience.scuflui.actions.EditMetadataAction extends ModelObjectAction implements Serializable

Class org.embl.ebi.escience.scuflui.actions.ImportWorkflowFromFileAction extends OpenWorkflowFromFileAction implements Serializable

Class org.embl.ebi.escience.scuflui.actions.ImportWorkflowFromURLAction extends OpenWorkflowFromURLAction implements Serializable

Class org.embl.ebi.escience.scuflui.actions.ModelObjectAction extends ScuflModelAction implements Serializable

Serialized Fields

modelObject

java.lang.Object modelObject

Object the action is performed on

Class org.embl.ebi.escience.scuflui.actions.OfflineToggleModel extends javax.swing.JToggleButton.ToggleButtonModel implements Serializable

Serialized Fields

model

ScuflModel model

Class org.embl.ebi.escience.scuflui.actions.OpenWorkflowFromFileAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

fileChooser

javax.swing.JFileChooser fileChooser

parentComponent

java.awt.Component parentComponent

Class org.embl.ebi.escience.scuflui.actions.OpenWorkflowFromURLAction extends OpenWorkflowFromFileAction implements Serializable

Serialized Fields

parentComponent

java.awt.Component parentComponent

Class org.embl.ebi.escience.scuflui.actions.PasswordInput extends javax.swing.JDialog implements Serializable

Serialized Fields

password

java.lang.String password

username

java.lang.String username

url

java.net.URL url

tryCount

int tryCount

cancelButton

javax.swing.JButton cancelButton

jLabel1

javax.swing.JLabel jLabel1

jLabel2

javax.swing.JLabel jLabel2

messageLabel

javax.swing.JLabel messageLabel

okButton

javax.swing.JButton okButton

passwordTextField

javax.swing.JPasswordField passwordTextField

urlLabel

javax.swing.JLabel urlLabel

usernameTextField

javax.swing.JTextField usernameTextField

Class org.embl.ebi.escience.scuflui.actions.RemoveAction extends ModelObjectAction implements Serializable

Class org.embl.ebi.escience.scuflui.actions.RenameAction extends ModelObjectAction implements Serializable

Class org.embl.ebi.escience.scuflui.actions.ResetAction extends ScuflModelAction implements Serializable

Serialized Fields

parentComponent

java.awt.Component parentComponent

Class org.embl.ebi.escience.scuflui.actions.RunWorkflowAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

parentComponent

java.awt.Component parentComponent

Class org.embl.ebi.escience.scuflui.actions.SaveWorkflowAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

parentComponent

java.awt.Component parentComponent

Class org.embl.ebi.escience.scuflui.actions.ScuflModelAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

model

ScuflModel model

Class org.embl.ebi.escience.scuflui.actions.ScuflModelActionSPI extends ScuflModelAction implements Serializable

Class org.embl.ebi.escience.scuflui.actions.SetDefaultValueAction extends ModelObjectAction implements Serializable

Package org.embl.ebi.escience.scuflui.dnd

Class org.embl.ebi.escience.scuflui.dnd.FactorySpecFragment extends SpecFragment implements Serializable

Serialized Fields

name

java.lang.String name

Class org.embl.ebi.escience.scuflui.dnd.ProcessorSpecFragment extends SpecFragment implements Serializable

Serialized Fields

name

java.lang.String name

Class org.embl.ebi.escience.scuflui.dnd.SpecFragment extends java.lang.Object implements Serializable

Serialized Fields

specElement

org.jdom.Element specElement

Package org.embl.ebi.escience.scuflui.facets

Class org.embl.ebi.escience.scuflui.facets.FacetsTable extends javax.swing.JPanel implements Serializable

Serialized Fields

headings

java.util.List<E> headings

columns

java.util.List<E> columns

headingHeight

int headingHeight

rowHeights

int[] rowHeights

isInScrollPane

boolean isInScrollPane

columnHeaders

javax.swing.JComponent columnHeaders

table

javax.swing.JComponent table

nsync

FTableColumnModelListener nsync

columnModel

FTableColumnModel columnModel

dataThing

DataThing dataThing

finders

FacetFinderRegistry finders

renderers

RendererRegistry renderers

rows

int rows

Class org.embl.ebi.escience.scuflui.facets.FTableColumnModelEvent extends java.util.EventObject implements Serializable

Serialized Fields

fromIndex

int fromIndex

toIndex

int toIndex

cause

java.beans.PropertyChangeEvent cause

Class org.embl.ebi.escience.scuflui.facets.PropertySheet extends javax.swing.JPanel implements Serializable

Package org.embl.ebi.escience.scuflui.graph

Class org.embl.ebi.escience.scuflui.graph.WorkflowEdgeRenderer extends org.jgraph.graph.EdgeRenderer implements Serializable

Serialized Fields

tension

float tension

Class org.embl.ebi.escience.scuflui.graph.WorkflowEditor extends org.jgraph.JGraph implements Serializable

Serialized Fields

layoutManager

RowLayout layoutManager

Class org.embl.ebi.escience.scuflui.graph.WorkflowEditor.ShowBoringModel extends javax.swing.JToggleButton.ToggleButtonModel implements Serializable

Package org.embl.ebi.escience.scuflui.renderers

Class org.embl.ebi.escience.scuflui.renderers.RendererException extends ScuflException implements Serializable

Package org.embl.ebi.escience.scuflui.results

Class org.embl.ebi.escience.scuflui.results.ResultTable extends javax.swing.JTable implements Serializable

Serialized Fields

listeners

java.util.Collection<E> listeners

selectedResult

ResultThing selectedResult

selectedCell

ResultTableCell selectedCell

Class org.embl.ebi.escience.scuflui.results.ResultTablePanel extends javax.swing.JPanel implements Serializable

Serialized Fields

resultTable

ResultTable resultTable

split

javax.swing.JSplitPane split

Package org.embl.ebi.escience.scuflui.shared

Class org.embl.ebi.escience.scuflui.shared.ExtendedJTree extends javax.swing.JTree implements Serializable

Serialized Fields

pattern

java.lang.String pattern

Class org.embl.ebi.escience.scuflui.shared.NoContextMenuFoundException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scuflui.shared.NodeColouringRenderer extends javax.swing.tree.DefaultTreeCellRenderer implements Serializable

Serialized Fields

pattern

java.lang.String pattern

plain

boolean plain

Class org.embl.ebi.escience.scuflui.shared.ScuflModelExplorerRenderer extends NodeColouringRenderer implements Serializable

Serialized Fields

significantObject

java.lang.Object significantObject

Class org.embl.ebi.escience.scuflui.shared.ShadedLabel extends javax.swing.JPanel implements Serializable

Serialized Fields

label

javax.swing.JLabel label

colour

java.awt.Color colour

toColour

java.awt.Color toColour

Class org.embl.ebi.escience.scuflui.shared.XMLTree extends javax.swing.JTree implements Serializable

Serialized Fields

textSizeLimit

int textSizeLimit

fc

javax.swing.JFileChooser fc

rootElement

org.jdom.Element rootElement

Package org.embl.ebi.escience.scuflui.treeview

Class org.embl.ebi.escience.scuflui.treeview.ScuflModelExplorer extends javax.swing.JTree implements Serializable

Serialized Fields

model

ScuflModel model

treeModel

TreeModelView treeModel

Class org.embl.ebi.escience.scuflui.treeview.ScuflModelTreeTable extends JTreeTable implements Serializable

Serialized Fields

model

ScuflModel model

lastInterestingProcessor

Processor lastInterestingProcessor

treeModel

TreeTableModelView treeModel

pathToSelect

javax.swing.tree.TreePath pathToSelect

Class org.embl.ebi.escience.scuflui.treeview.ScuflModelTreeTable.ScuflModelTreeTableCellEditor extends javax.swing.DefaultCellEditor implements Serializable

Package org.embl.ebi.escience.scuflui.workbench

Class org.embl.ebi.escience.scuflui.workbench.AboutBox extends javax.swing.JDialog implements Serializable

Serialized Fields

jContentPane

javax.swing.JPanel jContentPane

detailsPane

javax.swing.JPanel detailsPane

splashscreen

javax.swing.JLabel splashscreen

BACKGROUND_COLOUR

java.awt.Color BACKGROUND_COLOUR

Class org.embl.ebi.escience.scuflui.workbench.DefaultScavengerTree extends ExtendedJTree implements Serializable

serialVersionUID: -5395001232451125620L

Serialized Fields

parentPanel

ScavengerTreePanel parentPanel

populating

boolean populating

scavengingInProgressCount

int scavengingInProgressCount

model

ScuflModel model

The model that this scavenger will create processor for

root

javax.swing.tree.DefaultMutableTreeNode root

The root node

treeModel

javax.swing.tree.DefaultTreeModel treeModel

The tree model

scavengerList

java.util.ArrayList<E> scavengerList

A list of the names of all the scavengers contained within this tree

count

int count

A private count to avoid name duplication on created nodes

Class org.embl.ebi.escience.scuflui.workbench.FileScavenger extends Scavenger implements Serializable

Class org.embl.ebi.escience.scuflui.workbench.NestedFileChooser extends javax.swing.JFileChooser implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

checkbox

java.awt.Checkbox checkbox

Class org.embl.ebi.escience.scuflui.workbench.Scavenger extends javax.swing.tree.DefaultMutableTreeNode implements Serializable

Class org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException extends ScuflException implements Serializable

Class org.embl.ebi.escience.scuflui.workbench.ScavengerTreeRenderer extends ScuflModelExplorerRenderer implements Serializable

Class org.embl.ebi.escience.scuflui.workbench.URLBasedScavenger extends Scavenger implements Serializable

Class org.embl.ebi.escience.scuflui.workbench.Workbench extends javax.swing.JFrame implements Serializable

Serialized Fields

aboutBox

AboutBox aboutBox

basePane

ZBasePane basePane

workflowModels

ScuflModelSet workflowModels

perspectives

WorkbenchPerspectives perspectives

repository

Repository repository

modelmap

ModelMap modelmap

menuBar

Workbench.WorkbenchMenuBar menuBar

workflowChanges

WorkflowChanges workflowChanges

Class org.embl.ebi.escience.scuflui.workbench.Workbench.ExitAction extends javax.swing.AbstractAction implements Serializable

Class org.embl.ebi.escience.scuflui.workbench.Workbench.WorkbenchMenuBar extends javax.swing.JMenuBar implements Serializable

Serialized Fields

file

javax.swing.JMenu file

tools

javax.swing.JMenu tools

advanced

javax.swing.JMenu advanced

workflows

javax.swing.JMenu workflows

help

javax.swing.JMenu help

refreshingWorkflowsmenu

boolean refreshingWorkflowsmenu

MAX_REFRESH

int MAX_REFRESH

Class org.embl.ebi.escience.scuflui.workbench.WorkbenchZBasePane extends ZBasePane implements Serializable

Package org.embl.ebi.escience.scuflworkers.apiconsumer

Class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerProcessor extends DependencyProcessor implements Serializable

Serialized Fields

definition

APIConsumerDefinition definition

Class org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerScavenger extends Scavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.beanshell

Class org.embl.ebi.escience.scuflworkers.beanshell.BeanshellConfigPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

processor

BeanshellProcessor processor

scriptText

org.syntax.jedit.JEditTextArea scriptText

inputTable

javax.swing.JTable inputTable

outputTable

javax.swing.JTable outputTable

addInputButton

javax.swing.JButton addInputButton

addInputField

javax.swing.JTextField addInputField

addOutputButton

javax.swing.JButton addOutputButton

addOutputField

javax.swing.JTextField addOutputField

deletePortAction

javax.swing.Action deletePortAction

Class org.embl.ebi.escience.scuflworkers.beanshell.BeanshellProcessor extends DependencyProcessor implements Serializable

Serialized Fields

theScript

java.lang.String theScript

Class org.embl.ebi.escience.scuflworkers.beanshell.BeanshellScavenger extends Scavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.biomart

Class org.embl.ebi.escience.scuflworkers.biomart.BiomartConfigPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

biomartProcessor

BiomartProcessor biomartProcessor

Class org.embl.ebi.escience.scuflworkers.biomart.BiomartProcessor extends Processor implements Serializable

Serialized Fields

query

org.biomart.martservice.MartQuery query

queryListener

org.biomart.martservice.query.QueryListener queryListener

Class org.embl.ebi.escience.scuflworkers.biomart.BiomartScavenger extends URLBasedScavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.biomoby

Class org.embl.ebi.escience.scuflworkers.biomoby.BiomobyProcessor extends Processor implements Serializable

Serialized Fields

endpoint

java.net.URL endpoint

mobyEndpoint

java.lang.String mobyEndpoint

worker

org.biomoby.shared.Central worker

mobyService

org.biomoby.shared.MobyService mobyService

serviceName

java.lang.String serviceName

authorityName

java.lang.String authorityName

Class org.embl.ebi.escience.scuflworkers.biomoby.BiomobyScavenger extends Scavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.dependency

Class org.embl.ebi.escience.scuflworkers.dependency.DependenciesPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

processor

DependencyProcessor processor

classLoaderOptions

DependenciesPanel.ClassloaderOptions classLoaderOptions

jarFilesPanel

DependenciesPanel.JarFiles jarFilesPanel

artifactsPanel

DependenciesPanel.Artifacts artifactsPanel

Class org.embl.ebi.escience.scuflworkers.dependency.DependenciesPanel.Artifacts extends javax.swing.JPanel implements Serializable

Class org.embl.ebi.escience.scuflworkers.dependency.DependenciesPanel.ClassloaderOptions extends javax.swing.JPanel implements Serializable

Serialized Fields

description

javax.swing.JLabel description

Class org.embl.ebi.escience.scuflworkers.dependency.DependenciesPanel.JarFiles extends javax.swing.JPanel implements Serializable

Serialized Fields

warning

javax.swing.JLabel warning

Class org.embl.ebi.escience.scuflworkers.dependency.DependencyProcessor extends Processor implements Serializable

Serialized Fields

classLoaderSharing

DependencyProcessor.ClassLoaderSharing classLoaderSharing

Current classloader sharing policy, by default DependencyProcessor.ClassLoaderSharing.iteration.

libDir

java.io.File libDir

Where to find local JAR files. By default this is the directory lib in .taverna

localDependencies

java.util.LinkedHashSet<E> localDependencies

Local dependencies, ie. filenames of JARs. The files should be present in DependencyProcessor.libDir, and the paths should be relative.

artifactDependencies

java.util.LinkedHashSet<E> artifactDependencies

Artifact dependencies. These artifacts should be available from the centrally known repositories or from one of the listed repositories in repositories.

repositories

java.util.LinkedHashSet<E> repositories

Repositories to use when searching for artifacts. In addition, the system repositories will be searched.

Package org.embl.ebi.escience.scuflworkers.inferno

Class org.embl.ebi.escience.scuflworkers.inferno.InfernoProcessor extends Processor implements Serializable

Serialized Fields

host

java.lang.String host

service

java.lang.String service

port

int port

Class org.embl.ebi.escience.scuflworkers.inferno.InfernoScavenger extends Scavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.java

Class org.embl.ebi.escience.scuflworkers.java.LocalServiceProcessor extends Processor implements Serializable

Serialized Fields

workerClassName

java.lang.String workerClassName

theImplementation

LocalWorker theImplementation

Class org.embl.ebi.escience.scuflworkers.java.LocalServiceScavenger extends Scavenger implements Serializable

serialVersionUID: -901978754221092069L

Class org.embl.ebi.escience.scuflworkers.java.XMLSplittableInputPort extends InputPort implements Serializable

Class org.embl.ebi.escience.scuflworkers.java.XMLSplittableOutputPort extends OutputPort implements Serializable

Package org.embl.ebi.escience.scuflworkers.notification

Class org.embl.ebi.escience.scuflworkers.notification.NotificationProcessor extends Processor implements Serializable

Class org.embl.ebi.escience.scuflworkers.notification.NotificationScavenger extends Scavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.rdfgenerator

Class org.embl.ebi.escience.scuflworkers.rdfgenerator.RDFGeneratorProcessor extends Processor implements Serializable

Class org.embl.ebi.escience.scuflworkers.rdfgenerator.RDFGeneratorScavenger extends Scavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.rserv

Class org.embl.ebi.escience.scuflworkers.rserv.RservConfigPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

processor

RservProcessor processor

scriptText

org.syntax.jedit.JEditTextArea scriptText

inputTable

javax.swing.JTable inputTable

outputTable

javax.swing.JTable outputTable

addInputButton

javax.swing.JButton addInputButton

addInputField

javax.swing.JTextField addInputField

addOutputButton

javax.swing.JButton addOutputButton

addOutputField

javax.swing.JTextField addOutputField

hostname

javax.swing.JTextField hostname

port

javax.swing.JTextField port

username

javax.swing.JTextField username

password

javax.swing.JPasswordField password

deletePortAction

javax.swing.Action deletePortAction

Class org.embl.ebi.escience.scuflworkers.rserv.RservInputPort extends InputPort implements Serializable

Serialized Fields

javaType

java.lang.String javaType

Class org.embl.ebi.escience.scuflworkers.rserv.RservProcessor extends Processor implements Serializable

Serialized Fields

script

java.lang.String script

hostname

java.lang.String hostname

port

int port

username

java.lang.String username

password

java.lang.String password

Class org.embl.ebi.escience.scuflworkers.rserv.RservScavenger extends Scavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.soaplab

Class org.embl.ebi.escience.scuflworkers.soaplab.MissingSoaplabException extends java.lang.Exception implements Serializable

Class org.embl.ebi.escience.scuflworkers.soaplab.PollingPropertiesEditor.PollingPropertiesPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

processor

SoaplabProcessor processor

col

java.awt.Color col

col2

java.awt.Color col2

interval

javax.swing.JTextField interval

intervalmax

javax.swing.JTextField intervalmax

backoff

javax.swing.JTextField backoff

Class org.embl.ebi.escience.scuflworkers.soaplab.SoaplabProcessor extends Processor implements Serializable

Serialized Fields

endpoint

java.net.URL endpoint

pollingInterval

int pollingInterval

pollingBackoff

double pollingBackoff

pollingIntervalMax

int pollingIntervalMax

triedNewForm

boolean triedNewForm

Class org.embl.ebi.escience.scuflworkers.soaplab.SoaplabScavenger extends Scavenger implements Serializable

Serialized Fields

base

java.lang.String base

The base URL of the Soaplab service

Package org.embl.ebi.escience.scuflworkers.stringconstant

Class org.embl.ebi.escience.scuflworkers.stringconstant.StringConstantProcessor extends Processor implements Serializable

Serialized Fields

theStringValue

java.lang.String theStringValue

Class org.embl.ebi.escience.scuflworkers.stringconstant.StringConstantScavenger extends Scavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.talisman

Class org.embl.ebi.escience.scuflworkers.talisman.TalismanProcessor extends Processor implements Serializable

Serialized Fields

tscriptURL

java.lang.String tscriptURL

tscriptURLObject

java.net.URL tscriptURLObject

inputs

java.util.Map<K,V> inputs

outputs

java.util.Map<K,V> outputs

triggerName

java.lang.String triggerName

talismanDefinitionURL

java.lang.String talismanDefinitionURL

Class org.embl.ebi.escience.scuflworkers.talisman.TalismanScavenger extends Scavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.web

Class org.embl.ebi.escience.scuflworkers.web.WebScavenger extends Scavenger implements Serializable

serialVersionUID: -4238626422988051418L

Serialized Fields

treeModel

javax.swing.tree.DefaultTreeModel treeModel

progressDisplayNode

javax.swing.tree.DefaultMutableTreeNode progressDisplayNode

Package org.embl.ebi.escience.scuflworkers.workflow

Class org.embl.ebi.escience.scuflworkers.workflow.AddNestedWorkflowAction extends ScuflModelActionSPI implements Serializable

Serialized Fields

createNew

org.embl.ebi.escience.scuflworkers.workflow.AddNestedWorkflowAction.CreateNewNestedWorkflowAction createNew

openFile

org.embl.ebi.escience.scuflworkers.workflow.AddNestedWorkflowAction.OpenNestedWorkflowFromFileAction openFile

openURL

AddNestedWorkflowAction.OpenNestedWorkflowFromURLAction openURL

Class org.embl.ebi.escience.scuflworkers.workflow.AddNestedWorkflowAction.OpenNestedWorkflowFromURLAction extends javax.swing.AbstractAction implements Serializable

Class org.embl.ebi.escience.scuflworkers.workflow.WorkflowProcessor extends Processor implements Serializable

Serialized Fields

theInternalModel

ScuflModel theInternalModel

definitionURL

java.lang.String definitionURL

eventListener

ScuflModelEventListener eventListener

Class org.embl.ebi.escience.scuflworkers.workflow.WorkflowScavenger extends URLBasedScavenger implements Serializable

Package org.embl.ebi.escience.scuflworkers.wsdl

Class org.embl.ebi.escience.scuflworkers.wsdl.WSDLBasedProcessor extends Processor implements Serializable

serialVersionUID: 6669263809722072508L

Serialized Fields

operationName

java.lang.String operationName

wsdlLocation

java.lang.String wsdlLocation

inNames

java.lang.String[] inNames

outNames

java.lang.String[] outNames

inTypes

java.lang.Class<T>[] inTypes

outTypes

java.lang.Class<T>[] outTypes

parser

net.sf.taverna.wsdl.parser.WSDLParser parser

service

org.apache.wsif.WSIFService service

Class org.embl.ebi.escience.scuflworkers.wsdl.WSDLBasedScavenger extends URLBasedScavenger implements Serializable

serialVersionUID: 5281708181579790512L

Serialized Fields

wsdlLocation

java.lang.String wsdlLocation

Package org.embl.ebi.escience.treetable

Class org.embl.ebi.escience.treetable.JTreeTable extends javax.swing.JTable implements Serializable

Serialized Fields

tree

JTreeTable.TreeTableCellRenderer tree

A subclass of JTree.

Class org.embl.ebi.escience.treetable.JTreeTable.TreeTableCellEditor extends javax.swing.DefaultCellEditor implements Serializable

Class org.embl.ebi.escience.treetable.JTreeTable.TreeTableCellRenderer extends javax.swing.JTree implements Serializable

Serialized Fields

visibleRow

int visibleRow

Last table/tree row asked to renderer.

highlightBorder

javax.swing.border.Border highlightBorder

Class org.embl.ebi.escience.treetable.JTreeTable.TreeTableTextField extends javax.swing.JTextField implements Serializable

Serialized Fields

offset

int offset

Class org.embl.ebi.escience.treetable.TreeTableModelAdapter extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

tree

javax.swing.JTree tree

treeTableModel

TreeTableModel treeTableModel

Package uk.ac.soton.itinnovation.taverna.enactor.broker

Class uk.ac.soton.itinnovation.taverna.enactor.broker.WorkflowSubmitException extends java.lang.Exception implements Serializable

Package uk.ac.soton.itinnovation.taverna.enactor.entities

Class uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException extends java.lang.Exception implements Serializable