jalview

o*Todo List

o*Deprecated List

o+Class List

|o*jalview::analysis::AAFrequency

|o*org::biojava::dasobert::eventmodel::AbstractDasEvent

|o*org::biojava::dasobert::feature::AbstractFeatureTrack

|o*org::biojava::dasobert::feature::AbstractSegment

|o*uk::ac::ebi::www::picr::AccessionMappingService::AccessionMapperBindingStub

|o*uk::ac::ebi::www::picr::AccessionMappingService::AccessionMapperInterface

|o*uk::ac::ebi::www::picr::AccessionMappingService::AccessionMapperService

|o*uk::ac::ebi::www::picr::AccessionMappingService::AccessionMapperServiceLocator

|o*jalview::schemabinding::version2::AlcodMap

|o*jalview::schemabinding::version2::descriptors::AlcodMapDescriptor

|o*jalview::schemabinding::version2::Alcodon

|o*jalview::schemabinding::version2::descriptors::AlcodonDescriptor

|o*jalview::schemabinding::version2::AlcodonFrame

|o*jalview::schemabinding::version2::descriptors::AlcodonFrameDescriptor

|o*jalview::datamodel::AlignedCodonFrame

|o*jalview::io::AlignFile

|o*jalview::gui::AlignFrame

|o*jalview::appletgui::AlignFrame

|o*jalview::ws::rest::params::Alignment

|o*vamsas::objects::simple::Alignment

|o*jalview::datamodel::Alignment

|o*jalview::binding::Alignment

|o*vamsas::objects::simple::Alignment_Helper

|o*jalview::datamodel::AlignmentAnnotation

|o*jalview::datamodel::AlignmentI

|o*jalview::datamodel::AlignmentOrder

|o*jalview::appletgui::AlignmentPanel

|o*jalview::gui::AlignmentPanel

|o*jalview::ws::rest::AlignmentProcessor

|o*jalview::io::AlignmentProperties

|o*jalview::io::packed::JalviewDataset::AlignmentSet

|o*jalview::analysis::AlignmentSorter

|o*jalview::datamodel::AlignmentView

|o*jalview::api::AlignmentViewPanel

|o*jalview::structure::AlignmentViewPanelListener

|o*jalview::analysis::AlignSeq

|o*jalview::gui::AlignViewport

|o*jalview::appletgui::AlignViewport

|o*com::stevesoft::pat::AmpersandRule

|o*jalview::io::AMSAFile

|o*jalview::gui::WebserviceInfo::AnimatedPanel

|o*jalview::binding::Annotation

|o*jalview::schemabinding::version2::Annotation

|o*jalview::datamodel::Annotation

|o*jalview::gui::AnnotationColourChooser

|o*jalview::appletgui::AnnotationColourChooser

|o*jalview::schemes::AnnotationColourGradient

|o*jalview::schemabinding::version2::AnnotationColours

|o*jalview::schemabinding::version2::descriptors::AnnotationColoursDescriptor

|o*jalview::schemabinding::version2::descriptors::AnnotationDescriptor

|o*jalview::binding::AnnotationElement

|o*jalview::schemabinding::version2::AnnotationElement

|o*jalview::schemabinding::version2::descriptors::AnnotationElementDescriptor

|o*jalview::gui::AnnotationExporter

|o*jalview::ws::rest::params::AnnotationFile

|o*jalview::io::AnnotationFile

|o*jalview::gui::AnnotationLabels

|o*jalview::appletgui::AnnotationLabels

|o*jalview::gui::AnnotationPanel

|o*jalview::appletgui::AnnotationPanel

|o*com::stevesoft::pat::Any

|o*jalview::appletgui::APopupMenu

|o*jalview::gui::AppJmol

|o*jalview::gui::AppJmolBinding

|o*jalview::io::AppletFormatAdapter

|o*jalview::appletgui::AppletJmol

|o*jalview::appletgui::AppletJmolBinding

|o*MCview::AppletPDBCanvas

|o*MCview::AppletPDBViewer

|o*jalview::bin::ArgsParser

|o*jalview::ws::params::ArgumentI

|o*jalview::util::TableSorter::Arrow

|o*jalview::ws::seqfetcher::ASequenceFetcher

|o*jalview::gui::AssociatePdbFileWithSeq

|o*MCview::Atom

|o*jalview::ws::jws2::AWS2Thread

|o*jalview::ws::AWsJob

|o*jalview::ws::AWSThread

|o*jalview::util::AWTConsole

|o*com::stevesoft::pat::BackG

|o*com::stevesoft::pat::BackMatch

|o*com::stevesoft::pat::BackRefRule

|o*com::stevesoft::pat::Backup

|o*com::stevesoft::pat::BadRangeArgs

|o*jalview::datamodel::xdb::embl::BasePosition

|o*com::stevesoft::pat::BasicStringBufferLike

|o*jalview::datamodel::BinaryNode

|o*jalview::datamodel::BinarySequence

|o*com::stevesoft::pat::Bits

|o*jalview::io::WSWUBlastClient::BlastThread

|o*jalview::io::BLCFile

|o*jalview::gui::BlogReader

|o*jalview::schemes::Blosum62ColourScheme

|o*MCview::Bond

|o*jalview::ws::params::simple::BooleanOption

|o*com::stevesoft::pat::Boundary

|o*com::stevesoft::pat::Bracket

|o*com::stevesoft::pat::Branch

|o*jalview::util::BrowserLauncher

|o*jalview::schemes::BuriedColourScheme

|o*jalview::bin::Cache

|o*com::stevesoft::pat::CaseMgr

|o*jalview::commands::ChangeCaseCommand

|o*com::stevesoft::pat::ChangeRule

|o*jalview::gui::ChannelsRenderer

|o*com::stevesoft::pat::wrap::CharArrayBufferWrap

|o*com::stevesoft::pat::wrap::CharArrayWrap

|o*jalview::datamodel::CigarArray

|o*jalview::datamodel::CigarBase

|o*jalview::datamodel::CigarCigar

|o*jalview::datamodel::CigarSimple

|o*jalview::io::ClansFile

|o*jalview::io::ClustalFile

|o*jalview::schemes::ClustalxColourScheme

|o*jalview::analysis::Cluster

|o*com::stevesoft::pat::CodeRule

|o*com::stevesoft::pat::CodeVal

|o*jalview::gui::ColorEditor

|o*jalview::gui::FeatureSettings::ColorRenderer

|o*jalview::binding::Colour

|o*jalview::schemabinding::version2::Colour

|o*jalview::schemabinding::version2::descriptors::ColourDescriptor

|o*jalview::schemes::ColourSchemeI

|o*jalview::schemes::ColourSchemeProperty

|o*jalview::datamodel::ColumnSelection

|o*jalview::commands::CommandI

|o*jalview::util::Comparison

|o*jalview::schemes::Consensus

|o*jalview::schemes::ConsensusColour

|o*jalview::gui::AlignViewport::ConsensusThread

|o*jalview::appletgui::AlignViewport::ConsensusThread

|o*jalview::analysis::Conservation

|o*jalview::appletgui::AlignViewport::ConservationThread

|o*jalview::gui::ConservationThread

|o*jalview::gui::Console

|o*jalview::gui::ConsoleDocument

|o*jalview::gui::ConsoleTextPane

|o*jalview::analysis::CrossRef

|o*uk::ac::ebi::picr::model::CrossReference

|o*uk::ac::ebi::picr::model::CrossReference_Helper

|o*com::stevesoft::pat::Ctrl

|o*com::stevesoft::pat::Custom

|o*com::stevesoft::pat::CustomEndpoint

|o*jalview::gui::CutAndPasteTransfer

|o*jalview::appletgui::CutAndPasteTransfer

|o*org::biojava::dasobert::dasregistry::Das1Source

|o*org::biojava::dasobert::das2::Das2Capability

|o*org::biojava::dasobert::das2::Das2CapabilityImpl

|o*org::biojava::dasobert::das2::Das2Source

|o*org::biojava::dasobert::das2::io::DAS2SourceHandler

|o*org::biojava::dasobert::das2::Das2SourceImpl

|o*org::biojava::dasobert::dasregistry::Das2Validator

|o*org::biojava::dasobert::das::DAS_Feature_Handler

|o*org::biojava::dasobert::das::DAS_FeatureRetrieve

|o*org::biojava::dasobert::das::DAS_Sequence_Handler

|o*org::biojava::dasobert::dasregistry::DasCoordinateSystem

|o*org::biojava::dasobert::dasregistry::DasCoordSysComparator

|o*jalview::ws::DasSequenceFeatureFetcher

|o*jalview::ws::dbsources::DasSequenceSource

|o*jalview::ws::dbsources::das::DasSequenceSourceListener

|o*org::biojava::dasobert::dasregistry::DasSource

|o*jalview::gui::DasSourceBrowser

|o*org::biojava::dasobert::dasregistry::DasSourceComparator

|o*org::biojava::dasobert::das2::DasSourceConverter

|o*org::biojava::dasobert::das2::io::DasSourceReader

|o*org::biojava::dasobert::das2::io::DasSourceReaderImpl

|o*jalview::gui::DasSourceBrowser::DASTableModel

|o*uk::ac::ebi::www::Data

|o*jalview::io::packed::DataProvider

|o*jalview::io::vamsas::Datasetsequence

|o*jalview::io::vamsas::DatastoreItem

|o*jalview::io::vamsas::DatastoreRegistry

|o*jalview::io::vamsas::Dbref

|o*jalview::schemabinding::version2::DBRef

|o*jalview::util::DBRefUtils::DbRefComp

|o*jalview::schemabinding::version2::descriptors::DBRefDescriptor

|o*jalview::datamodel::DBRefEntry

|o*jalview::ws::DBRefFetcher

|o*jalview::io::DBRefFile

|o*jalview::datamodel::DBRefSource

|o*jalview::util::DBRefUtils

|o*jalview::ws::seqfetcher::DbSourceProxy

|o*jalview::ws::seqfetcher::DbSourceProxyImpl

|o*jalview::gui::Desktop

|o*jalview::util::TableSorter::Directive

|o*com::stevesoft::pat::DirFileRegex

|o*jalview::ws::jws1::Discoverer

|o*jalview::analysis::Dna

|o*com::stevesoft::pat::DotMulti

|o*jalview::ws::ebi::EBIFetchClient

|o*jalview::ws::dbsources::EbiFileRetrievedProxy

|o*jalview::commands::EditCommand::Edit

|o*jalview::commands::EditCommand

|o*jalview::gui::EditNameDialog

|o*jalview::appletgui::EditNameDialog

|o*jalview::ws::dbsources::EmblCdsSouce

|o*jalview::datamodel::xdb::embl::EmblEntry

|o*jalview::datamodel::xdb::embl::EmblError

|o*jalview::datamodel::xdb::embl::EmblFeature

|o*jalview::datamodel::xdb::embl::EmblFeatureLocations

|o*jalview::datamodel::xdb::embl::EmblFeatureLocElement

|o*jalview::datamodel::xdb::embl::EmblFile

|o*jalview::datamodel::xdb::embl::EmblSequence

|o*jalview::ws::dbsources::EmblSource

|o*jalview::ws::dbsources::EmblXmlSource

|o*jalview::appletgui::EmbmenuFrame

|o*com::stevesoft::pat::End

|o*jalview::ws::EnfinEnvision2OneWay

|o*jalview::gui::EnterListener

|o*org::jibble::epsgraphics::EpsDocument

|o*org::jibble::epsgraphics::EpsException

|o*org::jibble::epsgraphics::EpsGraphics2D

|o*jalview::gui::EPSOptions

|o*jalview::gui::ScriptWindow::ExecuteCommandThread

|o*jalview::appletgui::ExtJmol

|o*jalview::io::FastaFile

|o*com::stevesoft::pat::FastBracket

|o*com::stevesoft::pat::FastChar

|o*com::stevesoft::pat::FastMulti

|o*jalview::binding::Feature

|o*jalview::schemabinding::version2::Feature

|o*jalview::gui::FeatureColourChooser

|o*jalview::appletgui::FeatureColourChooser

|o*jalview::appletgui::FeatureRenderer::FeatureColourPanel

|o*org::biojava::dasobert::feature::FeatureComparator

|o*jalview::schemabinding::version2::descriptors::FeatureDescriptor

|o*org::biojava::dasobert::eventmodel::FeatureEvent

|o*jalview::bin::FeatureFetcher

|o*jalview::gui::FeatureIcon

|o*org::biojava::dasobert::eventmodel::FeatureListener

|o*org::biojava::dasobert::feature::FeatureMapComparator

|o*jalview::datamodel::FeatureProperties

|o*jalview::api::FeatureRenderer

|o*jalview::gui::FeatureRenderer

|o*jalview::appletgui::FeatureRenderer

|o*jalview::gui::FeatureRenderer::FeatureRendererSettings

|o*jalview::binding::Features

|o*jalview::schemabinding::version2::Features

|o*jalview::schemabinding::version2::descriptors::FeaturesDescriptor

|o*jalview::gui::FeatureSettings

|o*jalview::appletgui::FeatureSettings

|o*jalview::binding::FeatureSettings

|o*jalview::schemabinding::version2::FeatureSettings

|o*jalview::schemabinding::version2::descriptors::FeatureSettingsDescriptor

|o*jalview::io::FeaturesFile

|o*jalview::gui::FeatureSettings::FeatureTableModel

|o*org::biojava::dasobert::das::FeatureThread

|o*org::biojava::dasobert::feature::FeatureTrack

|o*org::biojava::dasobert::feature::FeatureTrackConverter

|o*org::biojava::dasobert::feature::FeatureTrackImpl

|o*jalview::ws::DasSequenceFeatureFetcher::FetchDBRefs

|o*jalview::io::FileLoader

|o*jalview::io::FileParse

|o*com::stevesoft::pat::FileRegex

|o*jalview::analysis::Finder

|o*jalview::gui::Finder

|o*jalview::appletgui::Finder

|o*jalview::gui::FontChooser

|o*jalview::appletgui::FontChooser

|o*jalview::util::Format

|o*jalview::io::FormatAdapter

|o*jalview::jbgui::GAlignFrame

|o*jalview::jbgui::GAlignmentPanel

|o*jalview::jbgui::GCutAndPasteTransfer

|o*jalview::jbgui::GDasSourceBrowser

|o*jalview::jbgui::GDesktop

|o*jalview::ws::dbsources::GeneDbSource

|o*jalview::jbgui::GFinder

|o*jalview::jbgui::GFontChooser

|o*jalview::jbgui::GPairwiseAlignPanel

|o*jalview::jbgui::GPCAPanel

|o*jalview::jbgui::GPreferences

|o*jalview::schemes::GraduatedColor

|o*jalview::datamodel::GraphLine

|o*jalview::jbgui::GRestInputParamEditDialog

|o*jalview::jbgui::GRestServiceEditorPane

|o*com::stevesoft::pat::Group

|o*jalview::schemabinding::version2::Group

|o*jalview::schemabinding::version2::descriptors::GroupDescriptor

|o*jalview::analysis::Grouping

|o*jalview::util::GroupUrlLink

|o*jalview::jbgui::GSequenceLink

|o*jalview::jbgui::GSliderPanel

|o*jalview::jbgui::GStructureViewer

|o*jalview::jbgui::GTreePanel

|o*jalview::jbgui::GUserDefinedColours

|o*jalview::jbgui::GWebserviceInfo

|o*jalview::jbgui::GWsPreferences

|o*jalview::schemes::HelixColourScheme

|o*jalview::schemabinding::version2::HiddenColumns

|o*jalview::schemabinding::version2::descriptors::HiddenColumnsDescriptor

|o*jalview::datamodel::HiddenSequences

|o*org::biojava::dasobert::feature::HistogramFeature

|o*org::biojava::dasobert::feature::HistogramSegment

|o*jalview::io::HTMLOutput

|o*jalview::ws::io::mime::HttpContentHandler

|o*jalview::ws::rest::HttpResultSet

|o*jalview::schemes::HydrophobicColourScheme

|o*jalview::gui::IdCanvas

|o*jalview::appletgui::IdCanvas

|o*jalview::io::IdentifyFile

|o*jalview::gui::IdPanel

|o*jalview::appletgui::IdPanel

|o*jalview::gui::IdwidthAdjuster

|o*jalview::appletgui::IdwidthAdjuster

|o*jalview::util::ImageMaker

|o*jalview::io::WSWUBlastClient::ImageTwirler

|o*vamsas::IMsaWS

|o*uk::ac::ebi::www::InputParams

|o*jalview::ws::rest::InputType

|o*jalview::ws::params::simple::IntegerParameter

|o*jalview::ws::params::InvalidArgumentException

|o*jalview::gui::IProgressIndicator

|o*jalview::gui::IProgressIndicatorHandler

|o*ext::vamsas::IRegistry

|o*ext::vamsas::IRegistryService

|o*ext::vamsas::IRegistryServiceLocator

|o*jalview::gui::ItemsRenderer

|o*jalview::ws::jws2::dm::JabaOption

|o*jalview::ws::jws2::dm::JabaParameter

|o*jalview::ws::jws2::JabaParamStore

|o*jalview::ws::jws2::JabaPreset

|o*jalview::ws::jws2::dm::JabaValueConstrain

|o*jalview::ws::jws2::dm::JabaWsParamSet

|o*jalview::ws::jws2::JabaWsServerQuery

|o*jalview::bin::Jalview

|o*jalview::gui::Jalview2XML

|o*jalview::gui::Jalview2XML_V1

|o*jalview::gui::JalviewAppender

|o*jalview::gui::JalviewChangeSupport

|o*jalview::io::packed::JalviewDataset

|o*jalview::gui::JalviewDialog

|o*jalview::io::JalviewFileChooser

|o*jalview::io::JalviewFileFilter

|o*jalview::io::JalviewFileView

|o*jalview::ext::jmol::JalviewJmolBinding

|o*jalview::bin::JalviewLite

|o*jalview::javascript::JalviewLiteJsApi

|o*jalview::bin::JalviewLiteURLRetrieve

|o*jalview::ws::io::mime::JalviewMimeContentHandler

|o*jalview::binding::JalviewModel

|o*jalview::schemabinding::version2::JalviewModel

|o*jalview::schemabinding::version2::descriptors::JalviewModelDescriptor

|o*jalview::binding::JalviewModelSequence

|o*jalview::schemabinding::version2::JalviewModelSequence

|o*jalview::schemabinding::version2::descriptors::JalviewModelSequenceDescriptor

|o*jalview::binding::JalviewUserColours

|o*jalview::schemabinding::version2::JalviewUserColours

|o*jalview::schemabinding::version2::descriptors::JalviewUserColoursDescriptor

|o*jalview::util::jarInputStreamProvider

|o*jalview::schemabinding::version2::JGroup

|o*jalview::binding::JGroup

|o*jalview::schemabinding::version2::descriptors::JGroupDescriptor

|o*jalview::ext::jmol::JmolCommands

|o*jalview::io::JnetAnnotationMaker

|o*jalview::ws::rest::params::JobConstant

|o*jalview::ws::JobStateSummary

|o*ext::vamsas::Jpred

|o*jalview::ws::jws1::JPredClient

|o*jalview::io::JPredFile

|o*jalview::ws::jws1::JPredThread::JPredJob

|o*vamsas::objects::simple::JpredResult

|o*vamsas::objects::simple::JpredResult_Helper

|o*ext::vamsas::JpredService

|o*ext::vamsas::JpredServiceLocator

|o*ext::vamsas::JpredSoapBindingStub

|o*jalview::ws::jws1::JPredThread

|o*jalview::javascript::JsCallBack

|o*jalview::schemabinding::version2::JSeq

|o*jalview::binding::JSeq

|o*jalview::schemabinding::version2::descriptors::JSeqDescriptor

|o*jalview::javascript::JSFunctionExec

|o*jalview::javascript::JsSelectionSender

|o*jalview::gui::Jalview2XML::JvAnnotRow

|o*jalview::appletgui::JVDialog

|o*jalview::gui::JvSwingUtils

|o*jalview::ws::jws1::JWS1Thread

|o*jalview::ws::jws2::Jws2Client

|o*jalview::ws::jws2::Jws2Discoverer

|o*jalview::ws::jws2::Jws2Discoverer::Jws2Instance

|o*jalview::ws::jws2::JWs2Job

|o*jalview::gui::BlogReader::LaunchJvBrowserOnItem

|o*com::stevesoft::pat::LeftRule

|o*jalview::bin::JalviewLite::LoadingThread

|o*jalview::bin::JalviewLite::LoadJmolThread

|o*jalview::io::vamsas::LocalDocSyncObject

|o*com::stevesoft::pat::lookAhead

|o*jalview::util::MapList

|o*jalview::schemabinding::version2::MapListFrom

|o*jalview::schemabinding::version2::descriptors::MapListFromDescriptor

|o*jalview::schemabinding::version2::MapListTo

|o*jalview::schemabinding::version2::descriptors::MapListToDescriptor

|o*jalview::schemabinding::version2::MapListType

|o*jalview::schemabinding::version2::descriptors::MapListTypeDescriptor

|o*jalview::schemabinding::version2::Mapping

|o*jalview::datamodel::Mapping

|o*jalview::schemabinding::version2::MappingChoice

|o*jalview::schemabinding::version2::descriptors::MappingChoiceDescriptor

|o*jalview::schemabinding::version2::descriptors::MappingDescriptor

|o*jalview::datamodel::SearchResults::Match

|o*jalview::math::Matrix

|o*jalview::io::MatrixFile

|o*MCview::MCMatrix

|o*jalview::ws::io::mime::MimeTypes

|o*jalview::io::ModellerDescription

|o*jalview::util::TableSorter::MouseHandler

|o*jalview::javascript::MouseOverListener

|o*jalview::javascript::MouseOverStructureListener

|o*vamsas::objects::simple::MsaResult

|o*vamsas::objects::simple::MsaResult_Helper

|o*jalview::ws::jws2::MsaWSClient

|o*jalview::ws::jws1::MsaWSClient

|o*jalview::ws::jws1::MsaWSThread::MsaWSJob

|o*jalview::ws::jws2::MsaWSThread::MsaWSJob

|o*jalview::ws::jws2::MsaWSThread

|o*jalview::ws::jws1::MsaWSThread

|o*vamsas::objects::simple::Msfalignment

|o*vamsas::objects::simple::Msfalignment_Helper

|o*jalview::io::MSFfile

|o*com::stevesoft::pat::Multi

|o*com::stevesoft::pat::Multi_stage2

|o*com::stevesoft::pat::MultiMin

|o*ext::vamsas::MuscleWS

|o*ext::vamsas::MuscleWSService

|o*ext::vamsas::MuscleWSServiceLocator

|o*ext::vamsas::MuscleWSSoapBindingStub

|o*jalview::appletgui::FeatureSettings::MyCheckbox

|o*jalview::gui::Desktop::MyDesktopManager

|o*jalview::gui::Desktop::MyDesktopPane

|o*jalview::io::NewickFile

|o*jalview::analysis::NJTree

|o*jalview::datamodel::NodeTransformI

|o*com::stevesoft::pat::NonDirFileRegex

|o*com::stevesoft::pat::NoPattern

|o*com::stevesoft::pat::NotImplementedError

|o*jalview::ws::rest::NoValidInputDataException

|o*jalview::schemes::NucleotideColourScheme

|o*com::stevesoft::pat::NullPattern

|o*com::stevesoft::pat::NullRule

|o*com::stevesoft::pat::NUnicodeAlpha

|o*com::stevesoft::pat::NUnicodeCurrency

|o*com::stevesoft::pat::NUnicodeDigit

|o*com::stevesoft::pat::NUnicodeMath

|o*com::stevesoft::pat::NUnicodePunct

|o*com::stevesoft::pat::NUnicodeW

|o*com::stevesoft::pat::NUnicodeWhite

|o*vamsas::objects::simple::Object

|o*vamsas::objects::simple::Object_Helper

|o*org::biojava::dasobert::eventmodel::ObjectListener

|o*com::stevesoft::pat::oneChar

|o*jalview::gui::OOMWarning

|o*jalview::ws::params::simple::Option

|o*jalview::gui::OptsAndParamsPage::OptionBox

|o*jalview::ws::params::OptionI

|o*jalview::gui::OptsAndParamsPage

|o*jalview::gui::OptsParametersContainerI

|o*com::stevesoft::pat::Or

|o*jalview::commands::OrderCommand

|o*com::stevesoft::pat::OrMark

|o*jalview::schemabinding::version2::OtherData

|o*jalview::schemabinding::version2::descriptors::OtherDataDescriptor

|o*jalview::gui::OverviewPanel

|o*jalview::appletgui::OverviewPanel

|o*jalview::appletgui::PaintRefresher

|o*jalview::gui::PaintRefresher

|o*jalview::gui::PairwiseAlignPanel

|o*jalview::appletgui::PairwiseAlignPanel

|o*jalview::gui::OptsAndParamsPage::ParamBox

|o*jalview::ws::params::ParamDatastoreI

|o*jalview::ws::params::simple::Parameter

|o*jalview::ws::params::ParameterI

|o*jalview::ws::jws2::ParameterUtils

|o*jalview::ws::params::ParamManager

|o*jalview::util::ParseHtmlBodyAndLinks

|o*jalview::io::packed::ParsePackedSet

|o*com::stevesoft::pat::parsePerl

|o*jalview::analysis::ParseProperties

|o*com::stevesoft::pat::PartialBuffer

|o*com::stevesoft::pat::patInf

|o*com::stevesoft::pat::patInt

|o*com::stevesoft::pat::Pattern

|o*com::stevesoft::pat::PatternSub

|o*jalview::analysis::PCA

|o*jalview::appletgui::PCAPanel

|o*jalview::gui::PCAPanel

|o*jalview::gui::PCAPanel::PCAPrinter

|o*jalview::ws::dbsources::Pdb

|o*MCview::PDBCanvas

|o*MCview::PDBChain

|o*jalview::schemabinding::version2::Pdbentry

|o*jalview::datamodel::PDBEntry

|o*jalview::binding::Pdbentry

|o*jalview::schemabinding::version2::descriptors::PdbentryDescriptor

|o*jalview::schemabinding::version2::PdbentryItem

|o*jalview::binding::PdbentryItem

|o*jalview::schemabinding::version2::descriptors::PdbentryItemDescriptor

|o*MCview::PDBfile

|o*jalview::schemabinding::version2::Pdbids

|o*jalview::binding::Pdbids

|o*jalview::schemabinding::version2::descriptors::PdbidsDescriptor

|o*MCview::PDBViewer

|o*jalview::ws::dbsources::Pfam

|o*jalview::io::PfamFile

|o*jalview::ws::dbsources::PfamFull

|o*jalview::ws::dbsources::PfamSeed

|o*jalview::schemes::PIDColourScheme

|o*jalview::io::PileUpfile

|o*jalview::io::PIRFile

|o*jalview::util::Platform

|o*com::stevesoft::pat::PopRule

|o*jalview::gui::PopupMenu

|o*jalview::gui::Preferences

|o*jalview::gui::PrintThread

|o*jalview::gui::PromptUserConfig

|o*com::stevesoft::pat::Prop

|o*jalview::binding::Property

|o*jalview::schemabinding::version2::Property

|o*jalview::schemabinding::version2::descriptors::PropertyDescriptor

|o*jalview::datamodel::Provenance

|o*jalview::datamodel::ProvenanceEntry

|o*com::stevesoft::pat::Pthings

|o*com::stevesoft::pat::PushRule

|o*jalview::datamodel::xdb::embl::Qualifier

|o*jalview::util::QuickSort

|o*com::stevesoft::pat::wrap::RandomAccessFileWrap

|o*com::stevesoft::pat::Range

|o*jalview::io::vamsas::Rangetype

|o*com::stevesoft::pat::RBuffer

|o*jalview::io::JalviewFileChooser::RecentlyOpened

|o*jalview::appletgui::RedundancyPanel

|o*jalview::gui::RedundancyPanel

|o*com::stevesoft::pat::Regex

|o*com::stevesoft::pat::RegexReader

|o*com::stevesoft::pat::RegexTokenizer

|o*com::stevesoft::pat::RegexWriter

|o*com::stevesoft::pat::RegHolder

|o*ext::vamsas::RegistryServiceSoapBindingStub

|o*com::stevesoft::pat::RegOpt

|o*com::stevesoft::pat::RegRes

|o*com::stevesoft::pat::RegSyntax

|o*com::stevesoft::pat::RegSyntaxError

|o*jalview::commands::RemoveGapColCommand

|o*jalview::commands::RemoveGapsCommand

|o*jalview::appletgui::AppletJmol::RenderPanel

|o*jalview::gui::AppJmol::RenderPanel

|o*com::stevesoft::pat::Replacer

|o*com::stevesoft::pat::ReplaceRule

|o*jalview::io::ModellerDescription::resCode

|o*MCview::Residue

|o*jalview::schemes::ResidueColourScheme

|o*jalview::schemes::ResidueProperties

|o*jalview::ws::rest::RestClient

|o*jalview::gui::RestInputParamEditDialog

|o*jalview::ws::rest::RestJob

|o*jalview::ws::rest::RestJobThread

|o*jalview::ws::rest::RestServiceDescription

|o*jalview::gui::RestServiceEditorPane

|o*vamsas::objects::simple::Result

|o*vamsas::objects::simple::Result_Helper

|o*com::stevesoft::pat::RightRule

|o*jalview::gui::RotatableCanvas

|o*jalview::appletgui::RotatableCanvas

|o*jalview::math::RotatableMatrix

|o*jalview::util::TableSorter::Row

|o*com::stevesoft::pat::Rthings

|o*com::stevesoft::pat::RuleHolder

|o*jalview::appletgui::ScalePanel

|o*jalview::gui::ScalePanel

|o*jalview::datamodel::AlignmentView::ScGroup

|o*jalview::schemes::ScoreColourScheme

|o*jalview::schemes::ScoreMatrix

|o*jalview::gui::ScriptWindow

|o*jalview::appletgui::IdPanel::ScrollThread

|o*jalview::gui::IdPanel::ScrollThread

|o*jalview::appletgui::SeqPanel::ScrollThread

|o*jalview::gui::SeqPanel::ScrollThread

|o*jalview::datamodel::SearchResults

|o*vamsas::objects::simple::Secstructpred

|o*vamsas::objects::simple::Secstructpred_Helper

|o*org::biojava::dasobert::feature::Segment

|o*org::biojava::dasobert::feature::SegmentComparator

|o*org::biojava::dasobert::feature::SegmentImpl

|o*jalview::structure::SelectionListener

|o*jalview::structure::SelectionSource

|o*jalview::gui::SeqCanvas

|o*jalview::appletgui::SeqCanvas

|o*jalview::datamodel::SeqCigar

|o*jalview::ws::rest::params::SeqGroupIndexVector

|o*jalview::analysis::SequenceIdMatcher::SeqIdName

|o*jalview::ws::rest::params::SeqIdVector

|o*jalview::gui::SeqPanel

|o*jalview::appletgui::SeqPanel

|o*ext::vamsas::SeqSearchI

|o*vamsas::objects::simple::SeqSearchResult

|o*vamsas::objects::simple::SeqSearchResult_Helper

|o*ext::vamsas::SeqSearchServiceLocator

|o*ext::vamsas::SeqSearchServiceService

|o*ext::vamsas::SeqSearchServiceSoapBindingStub

|o*jalview::ws::jws1::SeqSearchWSClient

|o*jalview::ws::jws1::SeqSearchWSThread::SeqSearchWSJob

|o*jalview::ws::jws1::SeqSearchWSThread

|o*jalview::analysis::SeqsetUtils

|o*jalview::schemabinding::version2::Sequence

|o*jalview::datamodel::Sequence

|o*jalview::binding::Sequence

|o*vamsas::objects::simple::Sequence

|o*vamsas::objects::simple::Sequence_Helper

|o*jalview::schemabinding::version2::descriptors::SequenceDescriptor

|o*org::biojava::dasobert::eventmodel::SequenceEvent

|o*jalview::datamodel::SequenceFeature

|o*jalview::io::vamsas::Sequencefeature

|o*jalview::ws::SequenceFetcher

|o*jalview::gui::SequenceFetcher

|o*jalview::datamodel::SequenceGroup

|o*jalview::datamodel::SequenceI

|o*jalview::analysis::SequenceIdMatcher

|o*org::biojava::dasobert::eventmodel::SequenceListener

|o*jalview::structure::SequenceListener

|o*jalview::io::vamsas::Sequencemapping

|o*jalview::datamodel::SequenceNode

|o*jalview::datamodel::SequencePoint

|o*jalview::appletgui::SequenceRenderer

|o*jalview::gui::SequenceRenderer

|o*jalview::api::SequenceRenderer

|o*jalview::binding::SequenceSet

|o*jalview::schemabinding::version2::SequenceSet

|o*vamsas::objects::simple::SequenceSet

|o*vamsas::objects::simple::SequenceSet_Helper

|o*jalview::schemabinding::version2::descriptors::SequenceSetDescriptor

|o*jalview::schemabinding::version2::SequenceSetProperties

|o*jalview::schemabinding::version2::descriptors::SequenceSetPropertiesDescriptor

|o*jalview::api::SequenceStructureBinding

|o*org::biojava::dasobert::das::SequenceThread

|o*jalview::binding::SequenceType

|o*jalview::schemabinding::version2::SequenceType

|o*jalview::schemabinding::version2::descriptors::SequenceTypeDescriptor

|o*jalview::ws::rest::params::SeqVector

|o*ext::vamsas::ServiceHandle

|o*ext::vamsas::ServiceHandles

|o*jalview::binding::Setting

|o*jalview::schemabinding::version2::Setting

|o*jalview::schemabinding::version2::descriptors::SettingDescriptor

|o*jalview::util::ShiftList

|o*jalview::io::SimpleBlastFile

|o*jalview::io::packed::SimpleDataProvider

|o*com::stevesoft::pat::Skip

|o*com::stevesoft::pat::Skip2

|o*com::stevesoft::pat::SkipBMH

|o*com::stevesoft::pat::Skipped

|o*jalview::appletgui::SliderPanel

|o*jalview::gui::SliderPanel

|o*jalview::commands::SlideSequencesCommand

|o*jalview::util::TableSorter::SortableHeaderRenderer

|o*com::stevesoft::pat::SpecialRule

|o*jalview::gui::SplashScreen

|o*com::stevesoft::pat::Start

|o*jalview::io::StockholmFile

|o*jalview::schemes::StrandColourScheme

|o*com::stevesoft::pat::StringBufferLike

|o*com::stevesoft::pat::wrap::StringBufferWrap

|o*jalview::ws::params::simple::StringChoiceParameter

|o*com::stevesoft::pat::StringLike

|o*com::stevesoft::pat::StringRule

|o*com::stevesoft::pat::wrap::StringWrap

|o*com::stevesoft::pat::StrPos

|o*jalview::structure::StructureListener

|o*jalview::structure::StructureMapping

|o*jalview::structure::StructureMappingcommandSet

|o*jalview::structure::StructureSelectionManager

|o*jalview::api::StructureSelectionManagerProvider

|o*jalview::schemabinding::version2::StructureState

|o*jalview::schemabinding::version2::descriptors::StructureStateDescriptor

|o*com::stevesoft::pat::SubMark

|o*jalview::util::TableSorter::TableModelHandler

|o*jalview::util::TableSorter

|o*jalview::schemes::TaylorColourScheme

|o*jalview::gui::TextColourChooser

|o*jalview::schemabinding::version2::ThresholdLine

|o*jalview::schemabinding::version2::descriptors::ThresholdLineDescriptor

|o*jalview::appletgui::Tooltip

|o*com::stevesoft::pat::Transformer

|o*jalview::appletgui::TransparencySetter

|o*com::stevesoft::pat::TransPat

|o*com::stevesoft::pat::TransRepRule

|o*jalview::io::vamsas::Tree

|o*jalview::ws::rest::params::Tree

|o*jalview::schemabinding::version2::Tree

|o*jalview::binding::Tree

|o*jalview::appletgui::TreeCanvas

|o*jalview::gui::TreeCanvas

|o*jalview::schemabinding::version2::descriptors::TreeDescriptor

|o*jalview::gui::TreePanel::TreeLoader

|o*jalview::appletgui::TreePanel::TreeLoader

|o*jalview::gui::TreePanel

|o*jalview::appletgui::TreePanel

|o*jalview::commands::TrimRegionCommand

|o*jalview::schemes::TurnColourScheme

|o*jalview::ws::rest::RestServiceDescription::UIinfo

|o*com::stevesoft::pat::UnicodeAlpha

|o*com::stevesoft::pat::UnicodeCurrency

|o*com::stevesoft::pat::UnicodeDigit

|o*com::stevesoft::pat::UnicodeLower

|o*com::stevesoft::pat::UnicodeMath

|o*com::stevesoft::pat::UnicodePunct

|o*com::stevesoft::pat::UnicodeUpper

|o*com::stevesoft::pat::UnicodeW

|o*com::stevesoft::pat::UnicodeWhite

|o*jalview::ws::dbsources::Uniprot

|o*jalview::datamodel::UniprotEntry

|o*jalview::datamodel::UniprotFile

|o*jalview::datamodel::UniprotProteinName

|o*jalview::datamodel::UniprotSequence

|o*com::stevesoft::pat::UniValidator

|o*jalview::ws::dbsources::UnprotName

|o*uk::ac::ebi::picr::model::UPEntry

|o*uk::ac::ebi::picr::model::UPEntry_Helper

|o*jalview::util::UrlLink

|o*jalview::util::GroupUrlLink::UrlStringTooLongException

|o*jalview::binding::UserColours

|o*jalview::schemabinding::version2::UserColours

|o*jalview::schemes::UserColourScheme

|o*jalview::binding::UserColourScheme

|o*jalview::schemabinding::version2::UserColourScheme

|o*jalview::schemabinding::version2::descriptors::UserColourSchemeDescriptor

|o*jalview::schemabinding::version2::descriptors::UserColoursDescriptor

|o*jalview::appletgui::UserDefinedColours

|o*jalview::gui::UserDefinedColours

|o*jalview::gui::UserQuestionnaireCheck

|o*com::stevesoft::pat::Validator

|o*jalview::ws::params::ValueConstrainI

|o*jalview::binding::VAMSAS

|o*jalview::schemabinding::version2::VAMSAS

|o*jalview::io::VamsasAppDatastore

|o*jalview::gui::VamsasApplication

|o*jalview::schemabinding::version2::descriptors::VAMSASDescriptor

|o*jalview::structure::VamsasListener

|o*jalview::schemabinding::version2::VamsasModel

|o*jalview::binding::VamsasModel

|o*jalview::schemabinding::version2::descriptors::VamsasModelDescriptor

|o*jalview::structure::VamsasSource

|o*jalview::io::AnnotationFile::ViewDef

|o*jalview::schemabinding::version2::Viewport

|o*jalview::binding::Viewport

|o*jalview::schemabinding::version2::descriptors::ViewportDescriptor

|o*jalview::gui::ViewSelectionMenu

|o*jalview::gui::ViewSelectionMenu::ViewSetProvider

|o*com::stevesoft::pat::WantMoreTextReplaceRule

|o*jalview::gui::WebserviceInfo

|o*jalview::schemabinding::version2::WebServiceParameterSet

|o*jalview::schemabinding::version2::descriptors::WebServiceParameterSetDescriptor

|o*com::stevesoft::pat::wrap::WriterWrap

|o*jalview::ws::jws1::WS1Client

|o*jalview::ws::WSClient

|o*jalview::ws::WSClientI

|o*uk::ac::ebi::www::WSFile

|o*jalview::ws::jws1::WSJob

|o*vamsas::objects::simple::WsJobId

|o*vamsas::objects::simple::WsJobId_Helper

|o*jalview::gui::WsJobParameters

|o*jalview::ws::WSMenuEntryProviderI

|o*jalview::ws::params::WsParamSetI

|o*jalview::gui::WsParamSetManager

|o*jalview::gui::WsPreferences

|o*uk::ac::ebi::www::WSWUBlast

|o*jalview::io::WSWUBlastClient

|o*uk::ac::ebi::www::WSWUBlastService

|o*uk::ac::ebi::www::WSWUBlastServiceLocator

|o*uk::ac::ebi::www::WSWUBlastSoapBindingStub

|o*jalview::schemes::ZappoColourScheme

|\*MCview::Zsort

o+Class Hierarchy

|o*jalview::analysis::AAFrequency

|o+org::biojava::dasobert::eventmodel::AbstractDasEvent

|o+uk::ac::ebi::www::picr::AccessionMappingService::AccessionMapperInterface

|o+uk::ac::ebi::www::picr::AccessionMappingService::AccessionMapperService

|o*jalview::schemabinding::version2::AlcodMap

|o*jalview::schemabinding::version2::descriptors::AlcodMapDescriptor

|o*jalview::schemabinding::version2::Alcodon

|o*jalview::schemabinding::version2::descriptors::AlcodonDescriptor

|o*jalview::schemabinding::version2::AlcodonFrame

|o*jalview::schemabinding::version2::descriptors::AlcodonFrameDescriptor

|o*jalview::datamodel::AlignedCodonFrame

|o*jalview::binding::Alignment

|o*vamsas::objects::simple::Alignment_Helper

|o*jalview::datamodel::AlignmentAnnotation

|o+jalview::datamodel::AlignmentI

|o*jalview::datamodel::AlignmentOrder

|o+jalview::ws::rest::AlignmentProcessor

|o*jalview::io::AlignmentProperties

|o*jalview::io::packed::JalviewDataset::AlignmentSet

|o*jalview::analysis::AlignmentSorter

|o*jalview::datamodel::AlignmentView

|o+jalview::api::AlignmentViewPanel

|o*jalview::structure::AlignmentViewPanelListener

|o*jalview::analysis::AlignSeq

|o*jalview::gui::WebserviceInfo::AnimatedPanel

|o*jalview::binding::Annotation

|o*jalview::schemabinding::version2::Annotation

|o*jalview::datamodel::Annotation

|o*jalview::gui::AnnotationColourChooser

|o*jalview::appletgui::AnnotationColourChooser

|o*jalview::schemabinding::version2::AnnotationColours

|o*jalview::schemabinding::version2::descriptors::AnnotationColoursDescriptor

|o*jalview::schemabinding::version2::descriptors::AnnotationDescriptor

|o*jalview::binding::AnnotationElement

|o*jalview::schemabinding::version2::AnnotationElement

|o*jalview::schemabinding::version2::descriptors::AnnotationElementDescriptor

|o*jalview::gui::AnnotationExporter

|o*jalview::io::AnnotationFile

|o*jalview::gui::AnnotationLabels

|o*jalview::appletgui::AnnotationLabels

|o*jalview::gui::AnnotationPanel

|o*jalview::appletgui::AnnotationPanel

|o*jalview::appletgui::APopupMenu

|o+jalview::io::AppletFormatAdapter

|o*MCview::AppletPDBCanvas

|o*MCview::AppletPDBViewer

|o*jalview::bin::ArgsParser

|o+jalview::ws::params::ArgumentI

|o*jalview::util::TableSorter::Arrow

|o+jalview::ws::seqfetcher::ASequenceFetcher

|o*jalview::gui::AssociatePdbFileWithSeq

|o*MCview::Atom

|o+jalview::ws::AWsJob

|o+jalview::ws::AWSThread

|o*jalview::util::AWTConsole

|o*jalview::datamodel::xdb::embl::BasePosition

|o+com::stevesoft::pat::BasicStringBufferLike

|o+jalview::datamodel::BinaryNode

|o*com::stevesoft::pat::Bits

|o*jalview::io::WSWUBlastClient::BlastThread

|o*jalview::gui::BlogReader

|o*MCview::Bond

|o*jalview::util::BrowserLauncher

|o*jalview::bin::Cache

|o*com::stevesoft::pat::CaseMgr

|o*jalview::gui::ChannelsRenderer

|o+jalview::datamodel::CigarBase

|o*jalview::analysis::Cluster

|o*com::stevesoft::pat::CodeVal

|o*jalview::gui::ColorEditor

|o*jalview::gui::FeatureSettings::ColorRenderer

|o*jalview::binding::Colour

|o*jalview::schemabinding::version2::Colour

|o*jalview::schemabinding::version2::descriptors::ColourDescriptor

|o+jalview::schemes::ColourSchemeI

|o*jalview::schemes::ColourSchemeProperty

|o*jalview::datamodel::ColumnSelection

|o+jalview::commands::CommandI

|o*jalview::util::Comparison

|o*jalview::schemes::Consensus

|o*jalview::schemes::ConsensusColour

|o*jalview::gui::AlignViewport::ConsensusThread

|o*jalview::appletgui::AlignViewport::ConsensusThread

|o*jalview::analysis::Conservation

|o*jalview::appletgui::AlignViewport::ConservationThread

|o*jalview::gui::ConservationThread

|o*jalview::gui::Console

|o*jalview::gui::ConsoleDocument

|o*jalview::gui::ConsoleTextPane

|o*jalview::analysis::CrossRef

|o*uk::ac::ebi::picr::model::CrossReference

|o*uk::ac::ebi::picr::model::CrossReference_Helper

|o*com::stevesoft::pat::Ctrl

|o*jalview::gui::CutAndPasteTransfer

|o*jalview::appletgui::CutAndPasteTransfer

|o+org::biojava::dasobert::das2::Das2Capability

|o+org::biojava::dasobert::das2::Das2Source

|o*org::biojava::dasobert::das2::io::DAS2SourceHandler

|o*org::biojava::dasobert::dasregistry::Das2Validator

|o*org::biojava::dasobert::das::DAS_Feature_Handler

|o*org::biojava::dasobert::das::DAS_FeatureRetrieve

|o*org::biojava::dasobert::das::DAS_Sequence_Handler

|o*org::biojava::dasobert::dasregistry::DasCoordinateSystem

|o*org::biojava::dasobert::dasregistry::DasCoordSysComparator

|o*jalview::ws::DasSequenceFeatureFetcher

|o+org::biojava::dasobert::dasregistry::DasSource

|o*jalview::gui::DasSourceBrowser

|o*org::biojava::dasobert::dasregistry::DasSourceComparator

|o*org::biojava::dasobert::das2::DasSourceConverter

|o+org::biojava::dasobert::das2::io::DasSourceReader

|o*jalview::gui::DasSourceBrowser::DASTableModel

|o*uk::ac::ebi::www::Data

|o+jalview::io::packed::DataProvider

|o+jalview::io::vamsas::DatastoreItem

|o*jalview::io::vamsas::DatastoreRegistry

|o*jalview::schemabinding::version2::DBRef

|o*jalview::util::DBRefUtils::DbRefComp

|o*jalview::schemabinding::version2::descriptors::DBRefDescriptor

|o*jalview::datamodel::DBRefEntry

|o*jalview::ws::DBRefFetcher

|o*jalview::datamodel::DBRefSource

|o*jalview::util::DBRefUtils

|o+jalview::ws::seqfetcher::DbSourceProxy

|o*jalview::util::TableSorter::Directive

|o*jalview::ws::jws1::Discoverer

|o*jalview::analysis::Dna

|o*jalview::ws::ebi::EBIFetchClient

|o*jalview::commands::EditCommand::Edit

|o*jalview::gui::EditNameDialog

|o*jalview::datamodel::xdb::embl::EmblEntry

|o*jalview::datamodel::xdb::embl::EmblError

|o*jalview::datamodel::xdb::embl::EmblFeature

|o*jalview::datamodel::xdb::embl::EmblFeatureLocations

|o*jalview::datamodel::xdb::embl::EmblFeatureLocElement

|o*jalview::datamodel::xdb::embl::EmblFile

|o*jalview::datamodel::xdb::embl::EmblSequence

|o+jalview::appletgui::EmbmenuFrame

|o+jalview::gui::EnterListener

|o*org::jibble::epsgraphics::EpsDocument

|o*org::jibble::epsgraphics::EpsException

|o*org::jibble::epsgraphics::EpsGraphics2D

|o*jalview::gui::EPSOptions

|o*jalview::gui::ScriptWindow::ExecuteCommandThread

|o+jalview::binding::Feature

|o+jalview::schemabinding::version2::Feature

|o*jalview::appletgui::FeatureColourChooser

|o*jalview::appletgui::FeatureRenderer::FeatureColourPanel

|o*org::biojava::dasobert::feature::FeatureComparator

|o+jalview::schemabinding::version2::descriptors::FeatureDescriptor

|o*jalview::bin::FeatureFetcher

|o*jalview::gui::FeatureIcon

|o*org::biojava::dasobert::eventmodel::FeatureListener

|o*org::biojava::dasobert::feature::FeatureMapComparator

|o*jalview::datamodel::FeatureProperties

|o+jalview::api::FeatureRenderer

|o*jalview::gui::FeatureRenderer::FeatureRendererSettings

|o*jalview::gui::FeatureSettings

|o*jalview::appletgui::FeatureSettings

|o*jalview::binding::FeatureSettings

|o*jalview::schemabinding::version2::FeatureSettings

|o*jalview::schemabinding::version2::descriptors::FeatureSettingsDescriptor

|o*jalview::gui::FeatureSettings::FeatureTableModel

|o*org::biojava::dasobert::das::FeatureThread

|o+org::biojava::dasobert::feature::FeatureTrack

|o*org::biojava::dasobert::feature::FeatureTrackConverter

|o*jalview::ws::DasSequenceFeatureFetcher::FetchDBRefs

|o*jalview::io::FileLoader

|o+jalview::io::FileParse

|o*jalview::analysis::Finder

|o*jalview::gui::Finder

|o*jalview::appletgui::Finder

|o*jalview::gui::FontChooser

|o*jalview::appletgui::FontChooser

|o*jalview::util::Format

|o+jalview::jbgui::GAlignFrame

|o*jalview::jbgui::GAlignmentPanel

|o*jalview::jbgui::GCutAndPasteTransfer

|o*jalview::jbgui::GDasSourceBrowser

|o+jalview::jbgui::GDesktop

|o*jalview::jbgui::GFinder

|o*jalview::jbgui::GFontChooser

|o*jalview::jbgui::GPairwiseAlignPanel

|o*jalview::jbgui::GPCAPanel

|o*jalview::jbgui::GPreferences

|o*jalview::schemes::GraduatedColor

|o*jalview::datamodel::GraphLine

|o+jalview::jbgui::GRestInputParamEditDialog

|o+jalview::jbgui::GRestServiceEditorPane

|o*jalview::schemabinding::version2::Group

|o*jalview::schemabinding::version2::descriptors::GroupDescriptor

|o*jalview::analysis::Grouping

|o*jalview::util::GroupUrlLink

|o*jalview::jbgui::GSequenceLink

|o*jalview::jbgui::GSliderPanel

|o+jalview::jbgui::GStructureViewer

|o*jalview::jbgui::GTreePanel

|o*jalview::jbgui::GUserDefinedColours

|o*jalview::jbgui::GWebserviceInfo

|o+jalview::jbgui::GWsPreferences

|o*jalview::schemabinding::version2::HiddenColumns

|o*jalview::schemabinding::version2::descriptors::HiddenColumnsDescriptor

|o*jalview::datamodel::HiddenSequences

|o*jalview::io::HTMLOutput

|o*jalview::ws::io::mime::HttpContentHandler

|o*jalview::gui::IdCanvas

|o*jalview::appletgui::IdCanvas

|o*jalview::io::IdentifyFile

|o*jalview::gui::IdPanel

|o*jalview::appletgui::IdPanel

|o*jalview::gui::IdwidthAdjuster

|o*jalview::appletgui::IdwidthAdjuster

|o*jalview::util::ImageMaker

|o*jalview::io::WSWUBlastClient::ImageTwirler

|o*vamsas::IMsaWS

|o*uk::ac::ebi::www::InputParams

|o+jalview::ws::rest::InputType

|o*jalview::ws::params::InvalidArgumentException

|o+jalview::gui::IProgressIndicator

|o*jalview::gui::IProgressIndicatorHandler

|o+ext::vamsas::IRegistry

|o+ext::vamsas::IRegistryService

|o*jalview::gui::ItemsRenderer

|o*jalview::ws::jws2::JabaWsServerQuery

|o*jalview::bin::Jalview

|o*jalview::gui::Jalview2XML

|o*jalview::gui::Jalview2XML_V1

|o*jalview::gui::JalviewAppender

|o*jalview::gui::JalviewChangeSupport

|o*jalview::io::packed::JalviewDataset

|o+jalview::gui::JalviewDialog

|o*jalview::io::JalviewFileChooser

|o*jalview::io::JalviewFileFilter

|o*jalview::io::JalviewFileView

|o+jalview::javascript::JalviewLiteJsApi

|o*jalview::bin::JalviewLiteURLRetrieve

|o*jalview::ws::io::mime::JalviewMimeContentHandler

|o*jalview::binding::JalviewModel

|o*jalview::schemabinding::version2::JalviewModel

|o*jalview::schemabinding::version2::descriptors::JalviewModelDescriptor

|o*jalview::binding::JalviewModelSequence

|o*jalview::schemabinding::version2::JalviewModelSequence

|o*jalview::schemabinding::version2::descriptors::JalviewModelSequenceDescriptor

|o+jalview::binding::JalviewUserColours

|o+jalview::schemabinding::version2::JalviewUserColours

|o+jalview::schemabinding::version2::descriptors::JalviewUserColoursDescriptor

|o*jalview::util::jarInputStreamProvider

|o*jalview::schemabinding::version2::JGroup

|o*jalview::binding::JGroup

|o*jalview::schemabinding::version2::descriptors::JGroupDescriptor

|o*jalview::ext::jmol::JmolCommands

|o*jalview::io::JnetAnnotationMaker

|o*jalview::ws::JobStateSummary

|o+ext::vamsas::Jpred

|o*vamsas::objects::simple::JpredResult_Helper

|o+ext::vamsas::JpredService

|o+jalview::javascript::JsCallBack

|o*jalview::schemabinding::version2::JSeq

|o*jalview::binding::JSeq

|o*jalview::schemabinding::version2::descriptors::JSeqDescriptor

|o+jalview::javascript::JSFunctionExec

|o*jalview::gui::Jalview2XML::JvAnnotRow

|o+jalview::appletgui::JVDialog

|o*jalview::gui::JvSwingUtils

|o*jalview::ws::jws2::Jws2Discoverer::Jws2Instance

|o*jalview::gui::BlogReader::LaunchJvBrowserOnItem

|o*jalview::bin::JalviewLite::LoadingThread

|o*jalview::bin::JalviewLite::LoadJmolThread

|o*jalview::util::MapList

|o*jalview::schemabinding::version2::MapListFrom

|o*jalview::schemabinding::version2::descriptors::MapListFromDescriptor

|o*jalview::schemabinding::version2::MapListTo

|o*jalview::schemabinding::version2::descriptors::MapListToDescriptor

|o+jalview::schemabinding::version2::MapListType

|o+jalview::schemabinding::version2::descriptors::MapListTypeDescriptor

|o*jalview::datamodel::Mapping

|o*jalview::schemabinding::version2::MappingChoice

|o*jalview::schemabinding::version2::descriptors::MappingChoiceDescriptor

|o*jalview::datamodel::SearchResults::Match

|o*jalview::math::Matrix

|o*MCview::MCMatrix

|o*jalview::ws::io::mime::MimeTypes

|o*jalview::io::ModellerDescription

|o*jalview::util::TableSorter::MouseHandler

|o*vamsas::objects::simple::MsaResult_Helper

|o*vamsas::objects::simple::Msfalignment

|o*vamsas::objects::simple::Msfalignment_Helper

|o+ext::vamsas::MuscleWS

|o+ext::vamsas::MuscleWSService

|o*jalview::appletgui::FeatureSettings::MyCheckbox

|o*jalview::gui::Desktop::MyDesktopManager

|o*jalview::gui::Desktop::MyDesktopPane

|o*jalview::analysis::NJTree

|o*jalview::datamodel::NodeTransformI

|o*com::stevesoft::pat::NotImplementedError

|o*jalview::ws::rest::NoValidInputDataException

|o+vamsas::objects::simple::Object

|o*vamsas::objects::simple::Object_Helper

|o+org::biojava::dasobert::eventmodel::ObjectListener

|o*jalview::gui::OOMWarning

|o*jalview::gui::OptsAndParamsPage::OptionBox

|o*jalview::gui::OptsAndParamsPage

|o+jalview::gui::OptsParametersContainerI

|o*jalview::schemabinding::version2::OtherData

|o*jalview::schemabinding::version2::descriptors::OtherDataDescriptor

|o*jalview::gui::OverviewPanel

|o*jalview::appletgui::OverviewPanel

|o*jalview::appletgui::PaintRefresher

|o*jalview::gui::PaintRefresher

|o*jalview::gui::PairwiseAlignPanel

|o*jalview::appletgui::PairwiseAlignPanel

|o*jalview::gui::OptsAndParamsPage::ParamBox

|o+jalview::ws::params::ParamDatastoreI

|o*jalview::ws::jws2::ParameterUtils

|o+jalview::ws::params::ParamManager

|o*jalview::util::ParseHtmlBodyAndLinks

|o*jalview::io::packed::ParsePackedSet

|o*com::stevesoft::pat::parsePerl

|o*jalview::analysis::ParseProperties

|o+com::stevesoft::pat::patInt

|o+com::stevesoft::pat::Pattern

|o*jalview::analysis::PCA

|o*jalview::gui::PCAPanel

|o*jalview::gui::PCAPanel::PCAPrinter

|o*MCview::PDBCanvas

|o*MCview::PDBChain

|o+jalview::schemabinding::version2::Pdbentry

|o*jalview::datamodel::PDBEntry

|o+jalview::binding::Pdbentry

|o+jalview::schemabinding::version2::descriptors::PdbentryDescriptor

|o*jalview::schemabinding::version2::PdbentryItem

|o*jalview::binding::PdbentryItem

|o*jalview::schemabinding::version2::descriptors::PdbentryItemDescriptor

|o*MCview::PDBViewer

|o*jalview::util::Platform

|o*jalview::gui::PopupMenu

|o*jalview::gui::Preferences

|o*jalview::gui::PrintThread

|o*jalview::gui::PromptUserConfig

|o*com::stevesoft::pat::Prop

|o*jalview::binding::Property

|o*jalview::schemabinding::version2::Property

|o*jalview::schemabinding::version2::descriptors::PropertyDescriptor

|o*jalview::datamodel::Provenance

|o*jalview::datamodel::ProvenanceEntry

|o*com::stevesoft::pat::Pthings

|o*jalview::datamodel::xdb::embl::Qualifier

|o*jalview::util::QuickSort

|o*com::stevesoft::pat::RBuffer

|o*jalview::io::JalviewFileChooser::RecentlyOpened

|o*jalview::gui::RedundancyPanel

|o*com::stevesoft::pat::RegexReader

|o*com::stevesoft::pat::RegexTokenizer

|o*com::stevesoft::pat::RegexWriter

|o*com::stevesoft::pat::RegHolder

|o*com::stevesoft::pat::RegOpt

|o+com::stevesoft::pat::RegRes

|o+com::stevesoft::pat::RegSyntax

|o*com::stevesoft::pat::RegSyntaxError

|o*jalview::appletgui::AppletJmol::RenderPanel

|o*jalview::gui::AppJmol::RenderPanel

|o*com::stevesoft::pat::Replacer

|o+com::stevesoft::pat::ReplaceRule

|o*jalview::io::ModellerDescription::resCode

|o*MCview::Residue

|o*jalview::schemes::ResidueProperties

|o*jalview::ws::rest::RestServiceDescription

|o+vamsas::objects::simple::Result

|o*vamsas::objects::simple::Result_Helper

|o*jalview::gui::RotatableCanvas

|o*jalview::appletgui::RotatableCanvas

|o*jalview::math::RotatableMatrix

|o*jalview::util::TableSorter::Row

|o*com::stevesoft::pat::Rthings

|o*jalview::appletgui::ScalePanel

|o*jalview::gui::ScalePanel

|o*jalview::datamodel::AlignmentView::ScGroup

|o*jalview::schemes::ScoreMatrix

|o*jalview::appletgui::IdPanel::ScrollThread

|o*jalview::gui::IdPanel::ScrollThread

|o*jalview::appletgui::SeqPanel::ScrollThread

|o*jalview::gui::SeqPanel::ScrollThread

|o*jalview::datamodel::SearchResults

|o*vamsas::objects::simple::Secstructpred

|o*vamsas::objects::simple::Secstructpred_Helper

|o+org::biojava::dasobert::feature::Segment

|o*org::biojava::dasobert::feature::SegmentComparator

|o+jalview::structure::SelectionListener

|o+jalview::structure::SelectionSource

|o*jalview::gui::SeqCanvas

|o*jalview::appletgui::SeqCanvas

|o*jalview::analysis::SequenceIdMatcher::SeqIdName

|o+ext::vamsas::SeqSearchI

|o*vamsas::objects::simple::SeqSearchResult_Helper

|o+ext::vamsas::SeqSearchServiceService

|o*jalview::analysis::SeqsetUtils

|o*vamsas::objects::simple::Sequence

|o*vamsas::objects::simple::Sequence_Helper

|o*jalview::datamodel::SequenceFeature

|o*jalview::gui::SequenceFetcher

|o*jalview::datamodel::SequenceGroup

|o+jalview::datamodel::SequenceI

|o*jalview::analysis::SequenceIdMatcher

|o+jalview::structure::SequenceListener

|o*jalview::datamodel::SequencePoint

|o+jalview::api::SequenceRenderer

|o*jalview::binding::SequenceSet

|o*jalview::schemabinding::version2::SequenceSet

|o*vamsas::objects::simple::SequenceSet

|o*vamsas::objects::simple::SequenceSet_Helper

|o*jalview::schemabinding::version2::descriptors::SequenceSetDescriptor

|o*jalview::schemabinding::version2::SequenceSetProperties

|o*jalview::schemabinding::version2::descriptors::SequenceSetPropertiesDescriptor

|o+jalview::api::SequenceStructureBinding

|o*org::biojava::dasobert::das::SequenceThread

|o+jalview::binding::SequenceType

|o+jalview::schemabinding::version2::SequenceType

|o+jalview::schemabinding::version2::descriptors::SequenceTypeDescriptor

|o*ext::vamsas::ServiceHandle

|o*ext::vamsas::ServiceHandles

|o*jalview::binding::Setting

|o*jalview::schemabinding::version2::Setting

|o*jalview::schemabinding::version2::descriptors::SettingDescriptor

|o*jalview::util::ShiftList

|o+com::stevesoft::pat::Skip

|o+jalview::appletgui::SliderPanel

|o*jalview::gui::SliderPanel

|o*jalview::util::TableSorter::SortableHeaderRenderer

|o*jalview::gui::SplashScreen

|o+com::stevesoft::pat::StringLike

|o*com::stevesoft::pat::StrPos

|o+jalview::structure::StructureListener

|o*jalview::structure::StructureMapping

|o*jalview::structure::StructureMappingcommandSet

|o*jalview::structure::StructureSelectionManager

|o+jalview::api::StructureSelectionManagerProvider

|o*jalview::schemabinding::version2::StructureState

|o*jalview::schemabinding::version2::descriptors::StructureStateDescriptor

|o*jalview::util::TableSorter::TableModelHandler

|o*jalview::util::TableSorter

|o*jalview::gui::TextColourChooser

|o*jalview::schemabinding::version2::ThresholdLine

|o*jalview::schemabinding::version2::descriptors::ThresholdLineDescriptor

|o*jalview::appletgui::Tooltip

|o*com::stevesoft::pat::Transformer

|o*jalview::appletgui::TransparencySetter

|o*jalview::schemabinding::version2::Tree

|o*jalview::binding::Tree

|o*jalview::appletgui::TreeCanvas

|o*jalview::gui::TreeCanvas

|o*jalview::schemabinding::version2::descriptors::TreeDescriptor

|o*jalview::gui::TreePanel::TreeLoader

|o*jalview::appletgui::TreePanel::TreeLoader

|o*jalview::gui::TreePanel

|o*jalview::ws::rest::RestServiceDescription::UIinfo

|o*jalview::datamodel::UniprotEntry

|o*jalview::datamodel::UniprotFile

|o*jalview::datamodel::UniprotProteinName

|o*jalview::datamodel::UniprotSequence

|o*uk::ac::ebi::picr::model::UPEntry

|o*uk::ac::ebi::picr::model::UPEntry_Helper

|o*jalview::util::UrlLink

|o*jalview::util::GroupUrlLink::UrlStringTooLongException

|o*jalview::binding::UserColours

|o*jalview::schemabinding::version2::UserColours

|o*jalview::schemabinding::version2::descriptors::UserColoursDescriptor

|o*jalview::appletgui::UserDefinedColours

|o*jalview::gui::UserDefinedColours

|o*jalview::gui::UserQuestionnaireCheck

|o+com::stevesoft::pat::Validator

|o+jalview::ws::params::ValueConstrainI

|o+jalview::binding::VAMSAS

|o+jalview::schemabinding::version2::VAMSAS

|o*jalview::io::VamsasAppDatastore

|o+jalview::schemabinding::version2::descriptors::VAMSASDescriptor

|o+jalview::structure::VamsasListener

|o+jalview::structure::VamsasSource

|o*jalview::io::AnnotationFile::ViewDef

|o*jalview::schemabinding::version2::Viewport

|o*jalview::binding::Viewport

|o*jalview::schemabinding::version2::descriptors::ViewportDescriptor

|o*jalview::gui::ViewSelectionMenu

|o+jalview::gui::ViewSelectionMenu::ViewSetProvider

|o*jalview::gui::WebserviceInfo

|o*jalview::schemabinding::version2::WebServiceParameterSet

|o*jalview::schemabinding::version2::descriptors::WebServiceParameterSetDescriptor

|o+jalview::ws::WSClient

|o+jalview::ws::WSClientI

|o*uk::ac::ebi::www::WSFile

|o*vamsas::objects::simple::WsJobId

|o*vamsas::objects::simple::WsJobId_Helper

|o+jalview::ws::WSMenuEntryProviderI

|o+jalview::ws::params::WsParamSetI

|o+uk::ac::ebi::www::WSWUBlast

|o*jalview::io::WSWUBlastClient

|o+uk::ac::ebi::www::WSWUBlastService

|\*MCview::Zsort

o*Class Members

o*Graphical Class Hierarchy

o+Namespace List

o+File List

|o*jalview/src/com/stevesoft/pat/AmpersandRule.java

|o*jalview/src/com/stevesoft/pat/Any.java

|o*jalview/src/com/stevesoft/pat/BackG.java

|o*jalview/src/com/stevesoft/pat/BackMatch.java

|o*jalview/src/com/stevesoft/pat/BackRefRule.java

|o*jalview/src/com/stevesoft/pat/Backup.java

|o*jalview/src/com/stevesoft/pat/BasicStringBufferLike.java

|o*jalview/src/com/stevesoft/pat/Bits.java

|o*jalview/src/com/stevesoft/pat/Boundary.java

|o*jalview/src/com/stevesoft/pat/Bracket.java

|o*jalview/src/com/stevesoft/pat/CaseMgr.java

|o*jalview/src/com/stevesoft/pat/ChangeRule.java

|o*jalview/src/com/stevesoft/pat/CodeRule.java

|o*jalview/src/com/stevesoft/pat/Ctrl.java

|o*jalview/src/com/stevesoft/pat/Custom.java

|o*jalview/src/com/stevesoft/pat/CustomEndpoint.java

|o*jalview/src/com/stevesoft/pat/DirFileRegex.java

|o*jalview/src/com/stevesoft/pat/DotMulti.java

|o*jalview/src/com/stevesoft/pat/End.java

|o*jalview/src/com/stevesoft/pat/FastBracket.java

|o*jalview/src/com/stevesoft/pat/FastMulti.java

|o*jalview/src/com/stevesoft/pat/FileRegex.java

|o*jalview/src/com/stevesoft/pat/Group.java

|o*jalview/src/com/stevesoft/pat/LeftRule.java

|o*jalview/src/com/stevesoft/pat/lookAhead.java

|o*jalview/src/com/stevesoft/pat/Multi.java

|o*jalview/src/com/stevesoft/pat/Multi_stage2.java

|o*jalview/src/com/stevesoft/pat/MultiMin.java

|o*jalview/src/com/stevesoft/pat/NonDirFileRegex.java

|o*jalview/src/com/stevesoft/pat/NoPattern.java

|o*jalview/src/com/stevesoft/pat/NotImplementedError.java

|o*jalview/src/com/stevesoft/pat/NullPattern.java

|o*jalview/src/com/stevesoft/pat/NullRule.java

|o*jalview/src/com/stevesoft/pat/oneChar.java

|o*jalview/src/com/stevesoft/pat/Or.java

|o*jalview/src/com/stevesoft/pat/OrMark.java

|o*jalview/src/com/stevesoft/pat/parsePerl.java

|o*jalview/src/com/stevesoft/pat/PartialBuffer.java

|o*jalview/src/com/stevesoft/pat/patInf.java

|o*jalview/src/com/stevesoft/pat/patInt.java

|o*jalview/src/com/stevesoft/pat/Pattern.java

|o*jalview/src/com/stevesoft/pat/PatternSub.java

|o*jalview/src/com/stevesoft/pat/PopRule.java

|o*jalview/src/com/stevesoft/pat/Prop.java

|o*jalview/src/com/stevesoft/pat/Pthings.java

|o*jalview/src/com/stevesoft/pat/PushRule.java

|o*jalview/src/com/stevesoft/pat/Range.java

|o*jalview/src/com/stevesoft/pat/RBuffer.java

|o*jalview/src/com/stevesoft/pat/Regex.java

|o*jalview/src/com/stevesoft/pat/RegexReader.java

|o*jalview/src/com/stevesoft/pat/RegexTokenizer.java

|o*jalview/src/com/stevesoft/pat/RegexWriter.java

|o*jalview/src/com/stevesoft/pat/RegOpt.java

|o*jalview/src/com/stevesoft/pat/RegRes.java

|o*jalview/src/com/stevesoft/pat/RegSyntax.java

|o*jalview/src/com/stevesoft/pat/RegSyntaxError.java

|o*jalview/src/com/stevesoft/pat/Replacer.java

|o*jalview/src/com/stevesoft/pat/ReplaceRule.java

|o*jalview/src/com/stevesoft/pat/RightRule.java

|o*jalview/src/com/stevesoft/pat/Rthings.java

|o*jalview/src/com/stevesoft/pat/RuleHolder.java

|o*jalview/src/com/stevesoft/pat/Skip.java

|o*jalview/src/com/stevesoft/pat/Skip2.java

|o*jalview/src/com/stevesoft/pat/SkipBMH.java

|o*jalview/src/com/stevesoft/pat/Skipped.java

|o*jalview/src/com/stevesoft/pat/SpecialRule.java

|o*jalview/src/com/stevesoft/pat/Start.java

|o*jalview/src/com/stevesoft/pat/StringBufferLike.java

|o*jalview/src/com/stevesoft/pat/StringLike.java

|o*jalview/src/com/stevesoft/pat/StringRule.java

|o*jalview/src/com/stevesoft/pat/StrPos.java

|o*jalview/src/com/stevesoft/pat/SubMark.java

|o*jalview/src/com/stevesoft/pat/Transformer.java

|o*jalview/src/com/stevesoft/pat/TransPat.java

|o*jalview/src/com/stevesoft/pat/UniValidator.java

|o*jalview/src/com/stevesoft/pat/Validator.java

|o*jalview/src/com/stevesoft/pat/WantMoreTextReplaceRule.java

|o*jalview/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java

|o*jalview/src/com/stevesoft/pat/wrap/CharArrayWrap.java

|o*jalview/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java

|o*jalview/src/com/stevesoft/pat/wrap/StringBufferWrap.java

|o*jalview/src/com/stevesoft/pat/wrap/StringWrap.java

|o*jalview/src/com/stevesoft/pat/wrap/WriterWrap.java

|o*jalview/src/ext/vamsas/IRegistry.java

|o*jalview/src/ext/vamsas/IRegistryService.java

|o*jalview/src/ext/vamsas/IRegistryServiceLocator.java

|o*jalview/src/ext/vamsas/Jpred.java

|o*jalview/src/ext/vamsas/JpredService.java

|o*jalview/src/ext/vamsas/JpredServiceLocator.java

|o*jalview/src/ext/vamsas/JpredSoapBindingStub.java

|o*jalview/src/ext/vamsas/MuscleWS.java

|o*jalview/src/ext/vamsas/MuscleWSService.java

|o*jalview/src/ext/vamsas/MuscleWSServiceLocator.java

|o*jalview/src/ext/vamsas/MuscleWSSoapBindingStub.java

|o*jalview/src/ext/vamsas/RegistryServiceSoapBindingStub.java

|o*jalview/src/ext/vamsas/SeqSearchI.java

|o*jalview/src/ext/vamsas/SeqSearchServiceLocator.java

|o*jalview/src/ext/vamsas/SeqSearchServiceService.java

|o*jalview/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java

|o*jalview/src/ext/vamsas/ServiceHandle.java

|o*jalview/src/ext/vamsas/ServiceHandles.java

|o*jalview/src/jalview/analysis/AAFrequency.java

|o*jalview/src/jalview/analysis/AlignmentSorter.java

|o*jalview/src/jalview/analysis/AlignSeq.java

|o*jalview/src/jalview/analysis/Conservation.java

|o*jalview/src/jalview/analysis/CrossRef.java

|o*jalview/src/jalview/analysis/Dna.java

|o*jalview/src/jalview/analysis/Finder.java

|o*jalview/src/jalview/analysis/Grouping.java

|o*jalview/src/jalview/analysis/NJTree.java

|o*jalview/src/jalview/analysis/ParseProperties.java

|o*jalview/src/jalview/analysis/PCA.java

|o*jalview/src/jalview/analysis/SeqsetUtils.java

|o*jalview/src/jalview/analysis/SequenceIdMatcher.java

|o*jalview/src/jalview/api/AlignmentViewPanel.java

|o*jalview/src/jalview/api/FeatureRenderer.java

|o*jalview/src/jalview/api/SequenceRenderer.java

|o*jalview/src/jalview/api/SequenceStructureBinding.java

|o*jalview/src/jalview/api/StructureSelectionManagerProvider.java

|o*jalview/src/jalview/appletgui/AlignFrame.java

|o*jalview/src/jalview/appletgui/AlignmentPanel.java

|o*jalview/src/jalview/appletgui/AlignViewport.java

|o*jalview/src/jalview/appletgui/AnnotationColourChooser.java

|o*jalview/src/jalview/appletgui/AnnotationLabels.java

|o*jalview/src/jalview/appletgui/AnnotationPanel.java

|o*jalview/src/jalview/appletgui/APopupMenu.java

|o*jalview/src/jalview/appletgui/AppletJmol.java

|o*jalview/src/jalview/appletgui/AppletJmolBinding.java

|o*jalview/src/jalview/appletgui/CutAndPasteTransfer.java

|o*jalview/src/jalview/appletgui/EditNameDialog.java

|o*jalview/src/jalview/appletgui/EmbmenuFrame.java

|o*jalview/src/jalview/appletgui/ExtJmol.java

|o*jalview/src/jalview/appletgui/FeatureColourChooser.java

|o*jalview/src/jalview/appletgui/FeatureRenderer.java

|o*jalview/src/jalview/appletgui/FeatureSettings.java

|o*jalview/src/jalview/appletgui/Finder.java

|o*jalview/src/jalview/appletgui/FontChooser.java

|o*jalview/src/jalview/appletgui/IdCanvas.java

|o*jalview/src/jalview/appletgui/IdPanel.java

|o*jalview/src/jalview/appletgui/IdwidthAdjuster.java

|o*jalview/src/jalview/appletgui/JVDialog.java

|o*jalview/src/jalview/appletgui/OverviewPanel.java

|o*jalview/src/jalview/appletgui/PaintRefresher.java

|o*jalview/src/jalview/appletgui/PairwiseAlignPanel.java

|o*jalview/src/jalview/appletgui/PCAPanel.java

|o*jalview/src/jalview/appletgui/RedundancyPanel.java

|o*jalview/src/jalview/appletgui/RotatableCanvas.java

|o*jalview/src/jalview/appletgui/ScalePanel.java

|o*jalview/src/jalview/appletgui/SeqCanvas.java

|o*jalview/src/jalview/appletgui/SeqPanel.java

|o*jalview/src/jalview/appletgui/SequenceRenderer.java

|o*jalview/src/jalview/appletgui/SliderPanel.java

|o*jalview/src/jalview/appletgui/Tooltip.java

|o*jalview/src/jalview/appletgui/TreeCanvas.java

|o*jalview/src/jalview/appletgui/TreePanel.java

|o*jalview/src/jalview/appletgui/UserDefinedColours.java

|o*jalview/src/jalview/bin/Cache.java

|o*jalview/src/jalview/bin/Jalview.java

|o*jalview/src/jalview/bin/JalviewLite.java

|o*jalview/src/jalview/bin/JalviewLiteURLRetrieve.java

|o*jalview/src/jalview/binding/Alignment.java

|o*jalview/src/jalview/binding/Annotation.java

|o*jalview/src/jalview/binding/AnnotationElement.java

|o*jalview/src/jalview/binding/Colour.java

|o*jalview/src/jalview/binding/Feature.java

|o*jalview/src/jalview/binding/Features.java

|o*jalview/src/jalview/binding/FeatureSettings.java

|o*jalview/src/jalview/binding/JalviewModel.java

|o*jalview/src/jalview/binding/JalviewModelSequence.java

|o*jalview/src/jalview/binding/JalviewUserColours.java

|o*jalview/src/jalview/binding/JGroup.java

|o*jalview/src/jalview/binding/JSeq.java

|o*jalview/src/jalview/binding/Pdbentry.java

|o*jalview/src/jalview/binding/PdbentryItem.java

|o*jalview/src/jalview/binding/Pdbids.java

|o*jalview/src/jalview/binding/Property.java

|o*jalview/src/jalview/binding/Sequence.java

|o*jalview/src/jalview/binding/SequenceSet.java

|o*jalview/src/jalview/binding/SequenceType.java

|o*jalview/src/jalview/binding/Setting.java

|o*jalview/src/jalview/binding/Tree.java

|o*jalview/src/jalview/binding/UserColours.java

|o*jalview/src/jalview/binding/UserColourScheme.java

|o*jalview/src/jalview/binding/VAMSAS.java

|o*jalview/src/jalview/binding/VamsasModel.java

|o*jalview/src/jalview/binding/Viewport.java

|o*jalview/src/jalview/commands/ChangeCaseCommand.java

|o*jalview/src/jalview/commands/CommandI.java

|o*jalview/src/jalview/commands/EditCommand.java

|o*jalview/src/jalview/commands/OrderCommand.java

|o*jalview/src/jalview/commands/RemoveGapColCommand.java

|o*jalview/src/jalview/commands/RemoveGapsCommand.java

|o*jalview/src/jalview/commands/SlideSequencesCommand.java

|o*jalview/src/jalview/commands/TrimRegionCommand.java

|o*jalview/src/jalview/datamodel/AlignedCodonFrame.java

|o*jalview/src/jalview/datamodel/Alignment.java

|o*jalview/src/jalview/datamodel/AlignmentAnnotation.java

|o*jalview/src/jalview/datamodel/AlignmentI.java

|o*jalview/src/jalview/datamodel/AlignmentOrder.java

|o*jalview/src/jalview/datamodel/AlignmentView.java

|o*jalview/src/jalview/datamodel/Annotation.java

|o*jalview/src/jalview/datamodel/BinaryNode.java

|o*jalview/src/jalview/datamodel/BinarySequence.java

|o*jalview/src/jalview/datamodel/CigarArray.java

|o*jalview/src/jalview/datamodel/CigarBase.java

|o*jalview/src/jalview/datamodel/CigarCigar.java

|o*jalview/src/jalview/datamodel/CigarSimple.java

|o*jalview/src/jalview/datamodel/ColumnSelection.java

|o*jalview/src/jalview/datamodel/DBRefEntry.java

|o*jalview/src/jalview/datamodel/DBRefSource.java

|o*jalview/src/jalview/datamodel/FeatureProperties.java

|o*jalview/src/jalview/datamodel/GraphLine.java

|o*jalview/src/jalview/datamodel/HiddenSequences.java

|o*jalview/src/jalview/datamodel/Mapping.java

|o*jalview/src/jalview/datamodel/NodeTransformI.java

|o*jalview/src/jalview/datamodel/PDBEntry.java

|o*jalview/src/jalview/datamodel/Provenance.java

|o*jalview/src/jalview/datamodel/ProvenanceEntry.java

|o*jalview/src/jalview/datamodel/SearchResults.java

|o*jalview/src/jalview/datamodel/SeqCigar.java

|o*jalview/src/jalview/datamodel/Sequence.java

|o*jalview/src/jalview/datamodel/SequenceFeature.java

|o*jalview/src/jalview/datamodel/SequenceGroup.java

|o*jalview/src/jalview/datamodel/SequenceI.java

|o*jalview/src/jalview/datamodel/SequenceNode.java

|o*jalview/src/jalview/datamodel/SequencePoint.java

|o*jalview/src/jalview/datamodel/UniprotEntry.java

|o*jalview/src/jalview/datamodel/UniprotFile.java

|o*jalview/src/jalview/datamodel/UniprotProteinName.java

|o*jalview/src/jalview/datamodel/UniprotSequence.java

|o*jalview/src/jalview/datamodel/xdb/embl/BasePosition.java

|o*jalview/src/jalview/datamodel/xdb/embl/EmblEntry.java

|o*jalview/src/jalview/datamodel/xdb/embl/EmblError.java

|o*jalview/src/jalview/datamodel/xdb/embl/EmblFeature.java

|o*jalview/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java

|o*jalview/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java

|o*jalview/src/jalview/datamodel/xdb/embl/EmblFile.java

|o*jalview/src/jalview/datamodel/xdb/embl/EmblSequence.java

|o*jalview/src/jalview/datamodel/xdb/embl/Qualifier.java

|o*jalview/src/jalview/ext/jmol/JalviewJmolBinding.java

|o*jalview/src/jalview/ext/jmol/JmolCommands.java

|o*jalview/src/jalview/gui/AlignFrame.java

|o*jalview/src/jalview/gui/AlignmentPanel.java

|o*jalview/src/jalview/gui/AlignViewport.java

|o*jalview/src/jalview/gui/AnnotationColourChooser.java

|o*jalview/src/jalview/gui/AnnotationExporter.java

|o*jalview/src/jalview/gui/AnnotationLabels.java

|o*jalview/src/jalview/gui/AnnotationPanel.java

|o*jalview/src/jalview/gui/AppJmol.java

|o*jalview/src/jalview/gui/AppJmolBinding.java

|o*jalview/src/jalview/gui/AssociatePdbFileWithSeq.java

|o*jalview/src/jalview/gui/BlogReader.java

|o*jalview/src/jalview/gui/ConservationThread.java

|o*jalview/src/jalview/gui/Console.java

|o*jalview/src/jalview/gui/CutAndPasteTransfer.java

|o*jalview/src/jalview/gui/DasSourceBrowser.java

|o*jalview/src/jalview/gui/Desktop.java

|o*jalview/src/jalview/gui/EditNameDialog.java

|o*jalview/src/jalview/gui/EPSOptions.java

|o*jalview/src/jalview/gui/FeatureColourChooser.java

|o*jalview/src/jalview/gui/FeatureRenderer.java

|o*jalview/src/jalview/gui/FeatureSettings.java

|o*jalview/src/jalview/gui/Finder.java

|o*jalview/src/jalview/gui/FontChooser.java

|o*jalview/src/jalview/gui/IdCanvas.java

|o*jalview/src/jalview/gui/IdPanel.java

|o*jalview/src/jalview/gui/IdwidthAdjuster.java

|o*jalview/src/jalview/gui/IProgressIndicator.java

|o*jalview/src/jalview/gui/IProgressIndicatorHandler.java

|o*jalview/src/jalview/gui/Jalview2XML.java

|o*jalview/src/jalview/gui/Jalview2XML_V1.java

|o*jalview/src/jalview/gui/JalviewAppender.java

|o*jalview/src/jalview/gui/JalviewChangeSupport.java

|o*jalview/src/jalview/gui/JalviewDialog.java

|o*jalview/src/jalview/gui/JvSwingUtils.java

|o*jalview/src/jalview/gui/OOMWarning.java

|o*jalview/src/jalview/gui/OptsAndParamsPage.java

|o*jalview/src/jalview/gui/OptsParametersContainerI.java

|o*jalview/src/jalview/gui/OverviewPanel.java

|o*jalview/src/jalview/gui/PaintRefresher.java

|o*jalview/src/jalview/gui/PairwiseAlignPanel.java

|o*jalview/src/jalview/gui/PCAPanel.java

|o*jalview/src/jalview/gui/PopupMenu.java

|o*jalview/src/jalview/gui/Preferences.java

|o*jalview/src/jalview/gui/PromptUserConfig.java

|o*jalview/src/jalview/gui/RedundancyPanel.java

|o*jalview/src/jalview/gui/RestInputParamEditDialog.java

|o*jalview/src/jalview/gui/RestServiceEditorPane.java

|o*jalview/src/jalview/gui/RotatableCanvas.java

|o*jalview/src/jalview/gui/ScalePanel.java

|o*jalview/src/jalview/gui/ScriptWindow.java

|o*jalview/src/jalview/gui/SeqCanvas.java

|o*jalview/src/jalview/gui/SeqPanel.java

|o*jalview/src/jalview/gui/SequenceFetcher.java

|o*jalview/src/jalview/gui/SequenceRenderer.java

|o*jalview/src/jalview/gui/SliderPanel.java

|o*jalview/src/jalview/gui/SplashScreen.java

|o*jalview/src/jalview/gui/TextColourChooser.java

|o*jalview/src/jalview/gui/TreeCanvas.java

|o*jalview/src/jalview/gui/TreePanel.java

|o*jalview/src/jalview/gui/UserDefinedColours.java

|o*jalview/src/jalview/gui/UserQuestionnaireCheck.java

|o*jalview/src/jalview/gui/VamsasApplication.java

|o*jalview/src/jalview/gui/ViewSelectionMenu.java

|o*jalview/src/jalview/gui/WebserviceInfo.java

|o*jalview/src/jalview/gui/WsJobParameters.java

|o*jalview/src/jalview/gui/WsParamSetManager.java

|o*jalview/src/jalview/gui/WsPreferences.java

|o*jalview/src/jalview/io/AlignFile.java

|o*jalview/src/jalview/io/AlignmentProperties.java

|o*jalview/src/jalview/io/AMSAFile.java

|o*jalview/src/jalview/io/AnnotationFile.java

|o*jalview/src/jalview/io/AppletFormatAdapter.java

|o*jalview/src/jalview/io/BLCFile.java

|o*jalview/src/jalview/io/ClansFile.java

|o*jalview/src/jalview/io/ClustalFile.java

|o*jalview/src/jalview/io/DBRefFile.java

|o*jalview/src/jalview/io/FastaFile.java

|o*jalview/src/jalview/io/FeaturesFile.java

|o*jalview/src/jalview/io/FileLoader.java

|o*jalview/src/jalview/io/FileParse.java

|o*jalview/src/jalview/io/FormatAdapter.java

|o*jalview/src/jalview/io/HTMLOutput.java

|o*jalview/src/jalview/io/IdentifyFile.java

|o*jalview/src/jalview/io/JalviewFileChooser.java

|o*jalview/src/jalview/io/JalviewFileFilter.java

|o*jalview/src/jalview/io/JalviewFileView.java

|o*jalview/src/jalview/io/JnetAnnotationMaker.java

|o*jalview/src/jalview/io/JPredFile.java

|o*jalview/src/jalview/io/MatrixFile.java

|o*jalview/src/jalview/io/ModellerDescription.java

|o*jalview/src/jalview/io/MSFfile.java

|o*jalview/src/jalview/io/NewickFile.java

|o*jalview/src/jalview/io/PfamFile.java

|o*jalview/src/jalview/io/PileUpfile.java

|o*jalview/src/jalview/io/PIRFile.java

|o*jalview/src/jalview/io/SimpleBlastFile.java

|o*jalview/src/jalview/io/StockholmFile.java

|o*jalview/src/jalview/io/VamsasAppDatastore.java

|o*jalview/src/jalview/io/WSWUBlastClient.java

|o*jalview/src/jalview/io/packed/DataProvider.java

|o*jalview/src/jalview/io/packed/JalviewDataset.java

|o*jalview/src/jalview/io/packed/ParsePackedSet.java

|o*jalview/src/jalview/io/packed/SimpleDataProvider.java

|o*jalview/src/jalview/io/vamsas/Datasetsequence.java

|o*jalview/src/jalview/io/vamsas/DatastoreItem.java

|o*jalview/src/jalview/io/vamsas/DatastoreRegistry.java

|o*jalview/src/jalview/io/vamsas/Dbref.java

|o*jalview/src/jalview/io/vamsas/LocalDocSyncObject.java

|o*jalview/src/jalview/io/vamsas/Rangetype.java

|o*jalview/src/jalview/io/vamsas/Sequencefeature.java

|o*jalview/src/jalview/io/vamsas/Sequencemapping.java

|o*jalview/src/jalview/io/vamsas/Tree.java

|o*jalview/src/jalview/javascript/JalviewLiteJsApi.java

|o*jalview/src/jalview/javascript/JsCallBack.java

|o*jalview/src/jalview/javascript/JSFunctionExec.java

|o*jalview/src/jalview/javascript/JsSelectionSender.java

|o*jalview/src/jalview/javascript/MouseOverListener.java

|o*jalview/src/jalview/javascript/MouseOverStructureListener.java

|o*jalview/src/jalview/jbgui/GAlignFrame.java

|o*jalview/src/jalview/jbgui/GAlignmentPanel.java

|o*jalview/src/jalview/jbgui/GCutAndPasteTransfer.java

|o*jalview/src/jalview/jbgui/GDasSourceBrowser.java

|o*jalview/src/jalview/jbgui/GDesktop.java

|o*jalview/src/jalview/jbgui/GFinder.java

|o*jalview/src/jalview/jbgui/GFontChooser.java

|o*jalview/src/jalview/jbgui/GPairwiseAlignPanel.java

|o*jalview/src/jalview/jbgui/GPCAPanel.java

|o*jalview/src/jalview/jbgui/GPreferences.java

|o*jalview/src/jalview/jbgui/GRestInputParamEditDialog.java

|o*jalview/src/jalview/jbgui/GRestServiceEditorPane.java

|o*jalview/src/jalview/jbgui/GSequenceLink.java

|o*jalview/src/jalview/jbgui/GSliderPanel.java

|o*jalview/src/jalview/jbgui/GStructureViewer.java

|o*jalview/src/jalview/jbgui/GTreePanel.java

|o*jalview/src/jalview/jbgui/GUserDefinedColours.java

|o*jalview/src/jalview/jbgui/GWebserviceInfo.java

|o*jalview/src/jalview/jbgui/GWsPreferences.java

|o*jalview/src/jalview/math/Matrix.java

|o*jalview/src/jalview/math/RotatableMatrix.java

|o*jalview/src/jalview/schemabinding/version2/AlcodMap.java

|o*jalview/src/jalview/schemabinding/version2/Alcodon.java

|o*jalview/src/jalview/schemabinding/version2/AlcodonFrame.java

|o*jalview/src/jalview/schemabinding/version2/Annotation.java

|o*jalview/src/jalview/schemabinding/version2/AnnotationColours.java

|o*jalview/src/jalview/schemabinding/version2/AnnotationElement.java

|o*jalview/src/jalview/schemabinding/version2/Colour.java

|o*jalview/src/jalview/schemabinding/version2/DBRef.java

|o*jalview/src/jalview/schemabinding/version2/Feature.java

|o*jalview/src/jalview/schemabinding/version2/Features.java

|o*jalview/src/jalview/schemabinding/version2/FeatureSettings.java

|o*jalview/src/jalview/schemabinding/version2/Group.java

|o*jalview/src/jalview/schemabinding/version2/HiddenColumns.java

|o*jalview/src/jalview/schemabinding/version2/JalviewModel.java

|o*jalview/src/jalview/schemabinding/version2/JalviewModelSequence.java

|o*jalview/src/jalview/schemabinding/version2/JalviewUserColours.java

|o*jalview/src/jalview/schemabinding/version2/JGroup.java

|o*jalview/src/jalview/schemabinding/version2/JSeq.java

|o*jalview/src/jalview/schemabinding/version2/MapListFrom.java

|o*jalview/src/jalview/schemabinding/version2/MapListTo.java

|o*jalview/src/jalview/schemabinding/version2/MapListType.java

|o*jalview/src/jalview/schemabinding/version2/Mapping.java

|o*jalview/src/jalview/schemabinding/version2/MappingChoice.java

|o*jalview/src/jalview/schemabinding/version2/OtherData.java

|o*jalview/src/jalview/schemabinding/version2/Pdbentry.java

|o*jalview/src/jalview/schemabinding/version2/PdbentryItem.java

|o*jalview/src/jalview/schemabinding/version2/Pdbids.java

|o*jalview/src/jalview/schemabinding/version2/Property.java

|o*jalview/src/jalview/schemabinding/version2/Sequence.java

|o*jalview/src/jalview/schemabinding/version2/SequenceSet.java

|o*jalview/src/jalview/schemabinding/version2/SequenceSetProperties.java

|o*jalview/src/jalview/schemabinding/version2/SequenceType.java

|o*jalview/src/jalview/schemabinding/version2/Setting.java

|o*jalview/src/jalview/schemabinding/version2/StructureState.java

|o*jalview/src/jalview/schemabinding/version2/ThresholdLine.java

|o*jalview/src/jalview/schemabinding/version2/Tree.java

|o*jalview/src/jalview/schemabinding/version2/UserColours.java

|o*jalview/src/jalview/schemabinding/version2/UserColourScheme.java

|o*jalview/src/jalview/schemabinding/version2/VAMSAS.java

|o*jalview/src/jalview/schemabinding/version2/VamsasModel.java

|o*jalview/src/jalview/schemabinding/version2/Viewport.java

|o*jalview/src/jalview/schemabinding/version2/WebServiceParameterSet.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java

|o*jalview/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java

|o*jalview/src/jalview/schemes/AnnotationColourGradient.java

|o*jalview/src/jalview/schemes/Blosum62ColourScheme.java

|o*jalview/src/jalview/schemes/BuriedColourScheme.java

|o*jalview/src/jalview/schemes/ClustalxColourScheme.java

|o*jalview/src/jalview/schemes/ColourSchemeI.java

|o*jalview/src/jalview/schemes/ColourSchemeProperty.java

|o*jalview/src/jalview/schemes/Consensus.java

|o*jalview/src/jalview/schemes/GraduatedColor.java

|o*jalview/src/jalview/schemes/HelixColourScheme.java

|o*jalview/src/jalview/schemes/HydrophobicColourScheme.java

|o*jalview/src/jalview/schemes/NucleotideColourScheme.java

|o*jalview/src/jalview/schemes/PIDColourScheme.java

|o*jalview/src/jalview/schemes/ResidueColourScheme.java

|o*jalview/src/jalview/schemes/ResidueProperties.java

|o*jalview/src/jalview/schemes/ScoreColourScheme.java

|o*jalview/src/jalview/schemes/ScoreMatrix.java

|o*jalview/src/jalview/schemes/StrandColourScheme.java

|o*jalview/src/jalview/schemes/TaylorColourScheme.java

|o*jalview/src/jalview/schemes/TurnColourScheme.java

|o*jalview/src/jalview/schemes/UserColourScheme.java

|o*jalview/src/jalview/schemes/ZappoColourScheme.java

|o*jalview/src/jalview/structure/AlignmentViewPanelListener.java

|o*jalview/src/jalview/structure/SelectionListener.java

|o*jalview/src/jalview/structure/SelectionSource.java

|o*jalview/src/jalview/structure/SequenceListener.java

|o*jalview/src/jalview/structure/StructureListener.java

|o*jalview/src/jalview/structure/StructureMapping.java

|o*jalview/src/jalview/structure/StructureMappingcommandSet.java

|o*jalview/src/jalview/structure/StructureSelectionManager.java

|o*jalview/src/jalview/structure/VamsasListener.java

|o*jalview/src/jalview/structure/VamsasSource.java

|o*jalview/src/jalview/util/AWTConsole.java

|o*jalview/src/jalview/util/BrowserLauncher.java

|o*jalview/src/jalview/util/Comparison.java

|o*jalview/src/jalview/util/DBRefUtils.java

|o*jalview/src/jalview/util/Format.java

|o*jalview/src/jalview/util/GroupUrlLink.java

|o*jalview/src/jalview/util/ImageMaker.java

|o*jalview/src/jalview/util/jarInputStreamProvider.java

|o*jalview/src/jalview/util/MapList.java

|o*jalview/src/jalview/util/ParseHtmlBodyAndLinks.java

|o*jalview/src/jalview/util/Platform.java

|o*jalview/src/jalview/util/QuickSort.java

|o*jalview/src/jalview/util/ShiftList.java

|o*jalview/src/jalview/util/TableSorter.java

|o*jalview/src/jalview/util/UrlLink.java

|o*jalview/src/jalview/ws/AWsJob.java

|o*jalview/src/jalview/ws/AWSThread.java

|o*jalview/src/jalview/ws/DasSequenceFeatureFetcher.java

|o*jalview/src/jalview/ws/DBRefFetcher.java

|o*jalview/src/jalview/ws/EnfinEnvision2OneWay.java

|o*jalview/src/jalview/ws/JobStateSummary.java

|o*jalview/src/jalview/ws/SequenceFetcher.java

|o*jalview/src/jalview/ws/WSClient.java

|o*jalview/src/jalview/ws/WSClientI.java

|o*jalview/src/jalview/ws/WSMenuEntryProviderI.java

|o*jalview/src/jalview/ws/dbsources/DasSequenceSource.java

|o*jalview/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java

|o*jalview/src/jalview/ws/dbsources/EmblCdsSouce.java

|o*jalview/src/jalview/ws/dbsources/EmblSource.java

|o*jalview/src/jalview/ws/dbsources/EmblXmlSource.java

|o*jalview/src/jalview/ws/dbsources/GeneDbSource.java

|o*jalview/src/jalview/ws/dbsources/Pdb.java

|o*jalview/src/jalview/ws/dbsources/Pfam.java

|o*jalview/src/jalview/ws/dbsources/PfamFull.java

|o*jalview/src/jalview/ws/dbsources/PfamSeed.java

|o*jalview/src/jalview/ws/dbsources/Uniprot.java

|o*jalview/src/jalview/ws/dbsources/UnprotName.java

|o*jalview/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java

|o*jalview/src/jalview/ws/ebi/EBIFetchClient.java

|o*jalview/src/jalview/ws/io/mime/HttpContentHandler.java

|o*jalview/src/jalview/ws/io/mime/JalviewMimeContentHandler.java

|o*jalview/src/jalview/ws/io/mime/MimeTypes.java

|o*jalview/src/jalview/ws/jws1/Discoverer.java

|o*jalview/src/jalview/ws/jws1/JPredClient.java

|o*jalview/src/jalview/ws/jws1/JPredThread.java

|o*jalview/src/jalview/ws/jws1/JWS1Thread.java

|o*jalview/src/jalview/ws/jws1/MsaWSClient.java

|o*jalview/src/jalview/ws/jws1/MsaWSThread.java

|o*jalview/src/jalview/ws/jws1/SeqSearchWSClient.java

|o*jalview/src/jalview/ws/jws1/SeqSearchWSThread.java

|o*jalview/src/jalview/ws/jws1/WS1Client.java

|o*jalview/src/jalview/ws/jws1/WSJob.java

|o*jalview/src/jalview/ws/jws2/AWS2Thread.java

|o*jalview/src/jalview/ws/jws2/JabaParamStore.java

|o*jalview/src/jalview/ws/jws2/JabaPreset.java

|o*jalview/src/jalview/ws/jws2/JabaWsServerQuery.java

|o*jalview/src/jalview/ws/jws2/Jws2Client.java

|o*jalview/src/jalview/ws/jws2/Jws2Discoverer.java

|o*jalview/src/jalview/ws/jws2/JWs2Job.java

|o*jalview/src/jalview/ws/jws2/MsaWSClient.java

|o*jalview/src/jalview/ws/jws2/MsaWSThread.java

|o*jalview/src/jalview/ws/jws2/ParameterUtils.java

|o*jalview/src/jalview/ws/jws2/dm/JabaOption.java

|o*jalview/src/jalview/ws/jws2/dm/JabaParameter.java

|o*jalview/src/jalview/ws/jws2/dm/JabaValueConstrain.java

|o*jalview/src/jalview/ws/jws2/dm/JabaWsParamSet.java

|o*jalview/src/jalview/ws/params/ArgumentI.java

|o*jalview/src/jalview/ws/params/InvalidArgumentException.java

|o*jalview/src/jalview/ws/params/OptionI.java

|o*jalview/src/jalview/ws/params/ParamDatastoreI.java

|o*jalview/src/jalview/ws/params/ParameterI.java

|o*jalview/src/jalview/ws/params/ParamManager.java

|o*jalview/src/jalview/ws/params/ValueConstrainI.java

|o*jalview/src/jalview/ws/params/WsParamSetI.java

|o*jalview/src/jalview/ws/params/simple/BooleanOption.java

|o*jalview/src/jalview/ws/params/simple/IntegerParameter.java

|o*jalview/src/jalview/ws/params/simple/Option.java

|o*jalview/src/jalview/ws/params/simple/Parameter.java

|o*jalview/src/jalview/ws/params/simple/StringChoiceParameter.java

|o*jalview/src/jalview/ws/rest/AlignmentProcessor.java

|o*jalview/src/jalview/ws/rest/HttpResultSet.java

|o*jalview/src/jalview/ws/rest/InputType.java

|o*jalview/src/jalview/ws/rest/NoValidInputDataException.java

|o*jalview/src/jalview/ws/rest/RestClient.java

|o*jalview/src/jalview/ws/rest/RestJob.java

|o*jalview/src/jalview/ws/rest/RestJobThread.java

|o*jalview/src/jalview/ws/rest/RestServiceDescription.java

|o*jalview/src/jalview/ws/rest/params/Alignment.java

|o*jalview/src/jalview/ws/rest/params/AnnotationFile.java

|o*jalview/src/jalview/ws/rest/params/JobConstant.java

|o*jalview/src/jalview/ws/rest/params/SeqGroupIndexVector.java

|o*jalview/src/jalview/ws/rest/params/SeqIdVector.java

|o*jalview/src/jalview/ws/rest/params/SeqVector.java

|o*jalview/src/jalview/ws/rest/params/Tree.java

|o*jalview/src/jalview/ws/seqfetcher/ASequenceFetcher.java

|o*jalview/src/jalview/ws/seqfetcher/DbSourceProxy.java

|o*jalview/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java

|o*jalview/src/MCview/AppletPDBCanvas.java

|o*jalview/src/MCview/AppletPDBViewer.java

|o*jalview/src/MCview/Atom.java

|o*jalview/src/MCview/Bond.java

|o*jalview/src/MCview/MCMatrix.java

|o*jalview/src/MCview/PDBCanvas.java

|o*jalview/src/MCview/PDBChain.java

|o*jalview/src/MCview/PDBfile.java

|o*jalview/src/MCview/PDBViewer.java

|o*jalview/src/MCview/Residue.java

|o*jalview/src/MCview/Zsort.java

|o*jalview/src/org/biojava/dasobert/das/DAS_Feature_Handler.java

|o*jalview/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java

|o*jalview/src/org/biojava/dasobert/das/DAS_Sequence_Handler.java

|o*jalview/src/org/biojava/dasobert/das/FeatureThread.java

|o*jalview/src/org/biojava/dasobert/das/SequenceThread.java

|o*jalview/src/org/biojava/dasobert/das2/Das2Capability.java

|o*jalview/src/org/biojava/dasobert/das2/Das2CapabilityImpl.java

|o*jalview/src/org/biojava/dasobert/das2/Das2Source.java

|o*jalview/src/org/biojava/dasobert/das2/Das2SourceImpl.java

|o*jalview/src/org/biojava/dasobert/das2/DasSourceConverter.java

|o*jalview/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java

|o*jalview/src/org/biojava/dasobert/das2/io/DasSourceReader.java

|o*jalview/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java

|o*jalview/src/org/biojava/dasobert/dasregistry/Das1Source.java

|o*jalview/src/org/biojava/dasobert/dasregistry/Das2Validator.java

|o*jalview/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java

|o*jalview/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java

|o*jalview/src/org/biojava/dasobert/dasregistry/DasSource.java

|o*jalview/src/org/biojava/dasobert/dasregistry/DasSourceComparator.java

|o*jalview/src/org/biojava/dasobert/eventmodel/AbstractDasEvent.java

|o*jalview/src/org/biojava/dasobert/eventmodel/FeatureEvent.java

|o*jalview/src/org/biojava/dasobert/eventmodel/FeatureListener.java

|o*jalview/src/org/biojava/dasobert/eventmodel/ObjectListener.java

|o*jalview/src/org/biojava/dasobert/eventmodel/SequenceEvent.java

|o*jalview/src/org/biojava/dasobert/eventmodel/SequenceListener.java

|o*jalview/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java

|o*jalview/src/org/biojava/dasobert/feature/AbstractSegment.java

|o*jalview/src/org/biojava/dasobert/feature/FeatureComparator.java

|o*jalview/src/org/biojava/dasobert/feature/FeatureMapComparator.java

|o*jalview/src/org/biojava/dasobert/feature/FeatureTrack.java

|o*jalview/src/org/biojava/dasobert/feature/FeatureTrackConverter.java

|o*jalview/src/org/biojava/dasobert/feature/FeatureTrackImpl.java

|o*jalview/src/org/biojava/dasobert/feature/HistogramFeature.java

|o*jalview/src/org/biojava/dasobert/feature/HistogramSegment.java

|o*jalview/src/org/biojava/dasobert/feature/Segment.java

|o*jalview/src/org/biojava/dasobert/feature/SegmentComparator.java

|o*jalview/src/org/biojava/dasobert/feature/SegmentImpl.java

|o*jalview/src/org/jibble/epsgraphics/EpsDocument.java

|o*jalview/src/org/jibble/epsgraphics/EpsException.java

|o*jalview/src/org/jibble/epsgraphics/EpsGraphics2D.java

|o*jalview/src/uk/ac/ebi/picr/model/CrossReference.java

|o*jalview/src/uk/ac/ebi/picr/model/CrossReference_Helper.java

|o*jalview/src/uk/ac/ebi/picr/model/UPEntry.java

|o*jalview/src/uk/ac/ebi/picr/model/UPEntry_Helper.java

|o*jalview/src/uk/ac/ebi/www/Data.java

|o*jalview/src/uk/ac/ebi/www/InputParams.java

|o*jalview/src/uk/ac/ebi/www/WSFile.java

|o*jalview/src/uk/ac/ebi/www/WSWUBlast.java

|o*jalview/src/uk/ac/ebi/www/WSWUBlastService.java

|o*jalview/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java

|o*jalview/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java

|o*jalview/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java

|o*jalview/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java

|o*jalview/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java

|o*jalview/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java

|o*jalview/src/vamsas/IMsaWS.java

|o*jalview/src/vamsas/objects/simple/Alignment.java

|o*jalview/src/vamsas/objects/simple/Alignment_Helper.java

|o*jalview/src/vamsas/objects/simple/JpredResult.java

|o*jalview/src/vamsas/objects/simple/JpredResult_Helper.java

|o*jalview/src/vamsas/objects/simple/MsaResult.java

|o*jalview/src/vamsas/objects/simple/MsaResult_Helper.java

|o*jalview/src/vamsas/objects/simple/Msfalignment.java

|o*jalview/src/vamsas/objects/simple/Msfalignment_Helper.java

|o*jalview/src/vamsas/objects/simple/Object.java

|o*jalview/src/vamsas/objects/simple/Object_Helper.java

|o*jalview/src/vamsas/objects/simple/Result.java

|o*jalview/src/vamsas/objects/simple/Result_Helper.java

|o*jalview/src/vamsas/objects/simple/Secstructpred.java

|o*jalview/src/vamsas/objects/simple/Secstructpred_Helper.java

|o*jalview/src/vamsas/objects/simple/SeqSearchResult.java

|o*jalview/src/vamsas/objects/simple/SeqSearchResult_Helper.java

|o*jalview/src/vamsas/objects/simple/Sequence.java

|o*jalview/src/vamsas/objects/simple/Sequence_Helper.java

|o*jalview/src/vamsas/objects/simple/SequenceSet.java

|o*jalview/src/vamsas/objects/simple/SequenceSet_Helper.java

|o*jalview/src/vamsas/objects/simple/WsJobId.java

|\*jalview/src/vamsas/objects/simple/WsJobId_Helper.java

\+Directory Hierarchy