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

A

AA - Static variable in interface apollo.datamodel.SequenceI

AAMultiSequenceAlignerPanel - Class in apollo.gui.detailviewers.sequencealigner.AAPanel

The main class for the Amino Acid view.

AAMultiSequenceAlignerPanel(GuiCurationState, Strand, ReadingFrame) - Constructor for class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel

Constructor

AB_INITIO_LABEL - Static variable in class apollo.dataadapter.ensj.view.TypesPanel

ABINITIO - Static variable in class apollo.dataadapter.ensj.model.TypesModel

AbstractApolloAdapter - Class in apollo.dataadapter

All the dataadapters now subclass AbstractApolloAdapter, which new data adapters should do as well.

AbstractApolloAdapter() - Constructor for class apollo.dataadapter.AbstractApolloAdapter

AbstractLazySequence - Class in apollo.datamodel.seq

i wonder if this should move to dataadapter package as its a sequence loader basically - so it loads stuff just like a data adapter

AbstractLazySequence(String, Controller) - Constructor for class apollo.datamodel.seq.AbstractLazySequence

AbstractLazySequence.LazyLoadControlledObject - Class in apollo.datamodel.seq

AbstractLazySequence.LazyLoadControlledObject(Controller) - Constructor for class apollo.datamodel.seq.AbstractLazySequence.LazyLoadControlledObject

AbstractParser - Class in apollo.dataadapter.analysis

AbstractParser() - Constructor for class apollo.dataadapter.analysis.AbstractParser

AbstractScrollablePanel - Class in apollo.gui.detailviewers.sequencealigner

AbstractScrollablePanel() - Constructor for class apollo.gui.detailviewers.sequencealigner.AbstractScrollablePanel

AbstractSequence - Class in apollo.datamodel

AbstractSequence(String) - Constructor for class apollo.datamodel.AbstractSequence

AbstractTierPanel - Class in apollo.gui.detailviewers.sequencealigner

AbstractTierPanel() - Constructor for class apollo.gui.detailviewers.sequencealigner.AbstractTierPanel

accept(Visitor) - Method in class apollo.datamodel.AnnotatedFeature

General implementation of Visitor pattern.

accept(Visitor) - Method in class apollo.datamodel.AssemblyFeature

accept(Visitor) - Method in class apollo.datamodel.CurationSet

General implementation of Visitor pattern.

accept(Visitor) - Method in class apollo.datamodel.Evidence

General implementation of Visitor pattern.

accept(Visitor) - Method in class apollo.datamodel.FeatureSet

General implementation of Visitor pattern.

accept(Visitor) - Method in class apollo.datamodel.SeqFeature

General implementation of Visitor pattern.

accept(Visitor) - Method in interface apollo.datamodel.SeqFeatureI

A general utility method to accept Visitors.

accept(Visitor) - Method in class apollo.datamodel.StrandedFeatureSet

General implementation of Visitor pattern.

accept(Visitor) - Method in class apollo.gui.drawable.DrawableSeqFeature

General implementation of Visitor pattern.

accept(File) - Method in class apollo.gui.GenericFileFilter

Whether the given file is accepted by this filter

accept(File) - Method in class apollo.util.ExampleFileFilter

Return true if this file should be shown in the directory pane, false if it shouldn't.

ACCESSION - Static variable in class apollo.dataadapter.otter.parser.TagHandler

ActionEventRouter - Class in apollo.dataadapter.ensj.controller

Generic class to forward action events onto central handler.

ActionEventRouter(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.ActionEventRouter

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.chado.ChadoAdapterGUI

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI.HistoryListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI.ProxyListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.das2.DAS2AdapterGUI.HistoryListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.das2.DAS2AdapterGUI.ProxyListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.EnsCGIAdapterGUI.ChrStartEndListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj.controller.ActionEventRouter

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj.view.AnnotationsPanel

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.DataSourceConfigInteractionListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowAnnotationConfigurationActionListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowDataSourceConfigurationActionListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowTypesActionListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.AnnotationSourceChooser.FindDataSetsListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel.ChooserActionListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel.DatabaseFindListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel.EnsemblDBSelectionListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel.HostListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.DriverDialog

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI.DataSourceChangeListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.GbrowseAdapterGUI.ChrStartEndListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.graph.GraphAdapterGUI.ColorActionListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.AlignBlockChooser.OKButtonListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.builder.BuilderAdapterGUI.ModelChangeListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI.DnaAlignTypesButtonActionListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI.FullPanelListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI.ShowDataSourceConfigurationActionListener

actionPerformed(ActionEvent) - Method in class apollo.dataadapter.synteny.SyntenyMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.AddFilterAction

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.AddResultFilterAction

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.CreateExonAction

Performs the insertion

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.CreateIntronAction

Performs the insertion

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.DeleteExonAction

Performs the deletion

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.DisplaySequenceAction

Brings up the display sequence window

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.FrameShiftAction

Performs the insertion

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.MergeExonAction

Performs the merge

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.SequenceEditAction

Performs the sequence edit

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.SetEndAction

Performs the update

actionPerformed(ActionEvent) - Method in class apollo.gui.detailviewers.sequencealigner.actions.SetTranslationStartAction

Performs the update

actionPerformed(ActionEvent) - Method in class apollo.gui.event.MethodRunnerActionListener

Runs the method named in the constructor.

actionPerformed(ActionEvent) - Method in class apollo.gui.FindPanel

Handles all buttons and fields, does name, position, and sequence searching

actionPerformed(ActionEvent) - Method in class apollo.gui.FullSyntenyPanel

actionPerformed(ActionEvent) - Method in class apollo.gui.genomemap.NavigationBar

actionPerformed(ActionEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

Action event listener

actionPerformed(ActionEvent) - Method in class apollo.gui.GlyphChooser

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.AnalysisMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.AnnotationMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.EditMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.FileMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.GraphMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.HelpMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.LinksMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.PeptideMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.PropertyMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.ShowMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.SyntenyLinkMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.SyntenyViewMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.ThresholdMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.TierPopupMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.TiersMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.TreeMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.TypesMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.menus.ViewMenu

actionPerformed(ActionEvent) - Method in class apollo.gui.PropertyPanel

actionPerformed(ActionEvent) - Method in class apollo.gui.ProxyDialog

actionPerformed(ActionEvent) - Method in class apollo.gui.TableColumnChooser

actionPerformed(ActionEvent) - Method in class apollo.gui.tweeker.Tweeker

actionPerformed(ActionEvent) - Method in class apollo.gui.TypePanel

adapter - Variable in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

ADAPTER - Static variable in class apollo.dataadapter.synteny.builder.Model

adapter - Variable in class apollo.gui.ProgressFrame

ADAPTER_CLASSES - Static variable in class apollo.dataadapter.synteny.builder.Model

ADAPTER_SET - Static variable in class apollo.dataadapter.synteny.builder.Model

ADAPTER_TYPES - Static variable in class apollo.dataadapter.synteny.builder.Model

adapterClassName - Variable in class apollo.dataadapter.chado.ChadoDatabase

Fully-qualified name of a Java class that extends apollo.dataadapter.chado.jdbc.JdbcChadoAdapter; used to implement DBMS-specific features or optimizations.

AdapterModel - Class in apollo.dataadapter.synteny.builder

AdapterModel(String, String, String) - Constructor for class apollo.dataadapter.synteny.builder.AdapterModel

adaptorName - Variable in class apollo.dataadapter.ensj19.EnsJAdapterGUI.DataTypeButton

ADD - Static variable in class apollo.editor.FeatureChangeEvent

Replace these with TransactionOperation!

ADD - Static variable in class apollo.editor.TransactionOperation

add(Comparator<T>) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.MultiComparatorArrayList

add(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel

add(int, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel

add(ViewI, Object) - Method in class apollo.gui.genomemap.ApolloPanel

Add a View to the views.

add(ViewI) - Method in class apollo.gui.genomemap.ApolloPanel

add(ViewI, Object) - Method in class apollo.gui.genomemap.LaidoutViewContainer

add(SelectionItem) - Method in class apollo.gui.Selection

I took out the boolean force, add is always an add and if its already it does nothing, in other words have it always be force == true, i dont think force==false was used at all Took out the return value of SelectionItem - dont think it was used.

add(SelectionItem, boolean) - Method in class apollo.gui.Selection

add(FeatureList, Object, boolean) - Method in class apollo.gui.Selection

add(FeatureList, Object) - Method in class apollo.gui.Selection

add(Selection, boolean) - Method in class apollo.gui.Selection

add(Selection) - Method in class apollo.gui.Selection

add(Object) - Method in class apollo.util.FeatureIterator

add(Object) - Method in class apollo.util.FeatureList

addFeature should be used in lieu of add.

ADD_RESULT_GENES_AS_ANNOTATIONS - Static variable in class apollo.dataadapter.StateInformation

ADD_RESULT_GENES_LABEL - Static variable in class apollo.dataadapter.ensj.view.OptionsPanel

ADD_TRANSCRIPT_SUPPORT - Static variable in class apollo.dataadapter.StateInformation

ADD_TRANSCRIPT_SUPPORT_LABEL - Static variable in class apollo.dataadapter.ensj.view.OptionsPanel

addActionListener(ActionListener) - Method in class apollo.dataadapter.synteny.builder.Controller

addActionListener(ActionListener) - Method in class apollo.gui.ChromosomeField

addActionRouter(JButton, String) - Method in class apollo.dataadapter.ensj.controller.Controller

addActionRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.controller.Controller

addActionRouter(JButton, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI

addActionRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI

addAdapterModel(String, AdapterModel) - Method in class apollo.dataadapter.synteny.builder.Model

addAdapterSet(String) - Method in class apollo.dataadapter.synteny.builder.Model

addAlignable(SeqFeatureI) - Method in class apollo.util.FeatureList

addAlignFeature(SequenceI, SeqFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

Adds feature to an existing SeqWrapper if it doesnt overlap with it, otherwise creates a new SeqWrapper for it,

addAlignFeature(SequenceI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

Adds feature to an existing SeqWrapper if it doesn't overlap with it, otherwise creates a new SeqWrapper for it,

addAlignPair(FeaturePairI, FeatureSetI) - Method in class apollo.dataadapter.analysis.AlignmentParser

addAll(Collection<? extends SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel

addAll(int, Collection<? extends SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel

addAll(FeatureList) - Method in class apollo.util.FeatureList

Adds all feats that are new, that it doesnt already have.

addAllFeatures(FeatureList) - Method in class apollo.util.FeatureList

addAnalysisType(String) - Method in class apollo.config.FeatureProperty

addAnalysisType(FeatureProperty, String) - Method in class apollo.config.TierProperty

addAnnot(Vector, boolean) - Method in class apollo.editor.AnnotationEditor

This method is a complete edit for adding a new gene.

addAnnotation(Vector, boolean, String) - Method in class apollo.editor.AnnotationEditor

addAnnotationComment(String) - Method in class apollo.config.Style

Add a canned annotation comment.

addAnnotationEditor(AnnotationEditor, boolean) - Method in class apollo.dataadapter.CurationState

addAnnotationEditor(AnnotationEditor, boolean) - Method in class apollo.gui.synteny.GuiCurationState

addAnnotations(Collection<SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

Adds a collection of annotations to the list of annotations (but not the annotation panel)

addAttributeValue(String, String) - Method in class apollo.dataadapter.gff3.GFF3Entry

Add an attribute

addCapability(String, String) - Method in class apollo.dataadapter.das.simple.SimpleDASDsn

e.g.

addCellEditorListener(CellEditorListener) - Method in class apollo.gui.DisabledEditor

addChange(AnnotationChangeEvent) - Method in class apollo.editor.ChangeList

Add change to end of changes list

addChangeList(ChangeList) - Method in class apollo.editor.ChangeList

addCheckbox(JCheckBox) - Method in class apollo.dataadapter.FileTabPanel

addChildren(SeqFeatureI) - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser

Find all children of this parent and add them to the parent seqfeature

addColumn(ColumnProperty) - Method in class apollo.config.FeatureProperty

addComment(String) - Method in class apollo.config.FeatureProperty

addComment(String) - Method in class apollo.config.TierProperty

addComment(SeqFeatureI, AddTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Comment strings look like this: Only one EST supports this alternative transcript::DATE:Mon Feb 26 18:08:49 CET 2007::TS:1172509728919 With the author in the pub table

addComment(long, Comment) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Add a comment to the database

addComment(Comment) - Method in class apollo.datamodel.AnnotatedFeature

addComment(int, Comment) - Method in class apollo.datamodel.AnnotatedFeature

addComment(Comment) - Method in interface apollo.datamodel.AnnotatedFeatureI

addComment(int, Comment) - Method in interface apollo.datamodel.AnnotatedFeatureI

addComments(AnnotatedFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Add all comments from an AnnotatedFeatureI object

addContigFeatures(CurationSet, List, Location) - Method in class apollo.dataadapter.ensj.DataFetcher

addController(Controller) - Method in class apollo.gui.MultiController

addCurationSet(Object, CurationSet) - Method in class apollo.datamodel.CurationSet

addCutSites(Vector, Vector, Color) - Method in class apollo.gui.genomemap.ScaleView

addDataChangeListenerToDataSourceConfigPanels() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI

addDataListener(DataListener) - Method in class apollo.dataadapter.DummySequenceAdapter

addDataListener(DataListener) - Method in class apollo.dataadapter.EfetchSequenceAdapter

addDbXref(SeqFeatureI, AddTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

addDbXref(long, DbXref) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

addDbXref(String, String) - Method in class apollo.datamodel.AbstractSequence

addDbXref(String, String, int) - Method in class apollo.datamodel.AbstractSequence

addDbXref(DbXref) - Method in class apollo.datamodel.AbstractSequence

addDbXref(DbXref) - Method in class apollo.datamodel.Identifier

addDbXref(DbXref) - Method in class apollo.datamodel.SeqFeature

addDbXref(DbXref) - Method in interface apollo.datamodel.SeqFeatureI

addDbXref(String, String, int) - Method in interface apollo.datamodel.SequenceI

addDbXref(String, String) - Method in interface apollo.datamodel.SequenceI

addDbXref(DbXref) - Method in interface apollo.datamodel.SequenceI

addDbxrefs(AnnotatedFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Add all dbxrefs from an AnnotatedFeatureI object

addDecorations(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableGeneSeqFeature

Draws in translated sequence if feature is an ExonI, its zoomed in, seq is available, and it is in a coding region

addDecorations(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableResultSeqFeature

addDecorations(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature

draw in label and codons

addDisplayComponents() - Method in class apollo.dataadapter.analysis.AnalysisPanel

Default display type entry component is JComboBox

addDitagFeatures(CurationSet, List, Location, List) - Method in class apollo.dataadapter.ensj.DataFetcher

addDnaAlignFeatures(CurationSet, List, Location, List) - Method in class apollo.dataadapter.ensj.DataFetcher

addDrawable(Drawable) - Method in class apollo.gui.drawable.DrawableFeatureSet

addDrawable(Drawable) - Method in interface apollo.gui.drawable.DrawableSetI

addEditRegion() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

puts up vertical lines in szap(main window) indicating what region that is currently displayed

addEvidence(String, String, int) - Method in class apollo.datamodel.AnnotatedFeature

addEvidence(String) - Method in class apollo.datamodel.AnnotatedFeature

addEvidence(String, int) - Method in class apollo.datamodel.AnnotatedFeature

addEvidence(Evidence) - Method in class apollo.datamodel.AnnotatedFeature

addEvidence(String) - Method in interface apollo.datamodel.AnnotatedFeatureI

addEvidence(String, int) - Method in interface apollo.datamodel.AnnotatedFeatureI

addEvidence(Evidence) - Method in interface apollo.datamodel.AnnotatedFeatureI

addEvidence(Evidence) - Method in class apollo.datamodel.EvidenceSet

addEvidenceExons() - Method in class apollo.editor.AnnotationEditor

The default method to add evidence to exons.

addEvidenceExonsAllowed() - Method in class apollo.editor.AnnotationEditor

Determine if the current selection sets are compatible with the the default adding evidence to exons method.

addEvidencePanel(EvidencePanel) - Method in class apollo.gui.evidencepanel.EvidencePanelContainer

addExon(SeqFeatureI, String, Date, Long, int, ChadoFeature, boolean) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter

Add an exon to the database.

addExon(SeqFeatureI, String, Date, Long, int, ChadoFeature, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Add an exon to a transcript, inserting the exon into the database if it does not already exist.

addExon(ExonI) - Method in class apollo.datamodel.Transcript

If exon overlaps with other exons then it merges them, otherwise adds exon to transcript

addExons() - Method in class apollo.editor.AnnotationEditor

The default addExons which adds exons to a transcript.

addExons(Transcript, Vector) - Method in class apollo.editor.AnnotationEditor

The version of addExons which actually does the work.

addExonsAllowed() - Method in class apollo.editor.AnnotationEditor

addExtension(String) - Method in class apollo.gui.GenericFileFilter

Adds a file extension for filtering

addExtension(String) - Method in class apollo.util.ExampleFileFilter

Adds a filetype "dot" extension to filter against.

addExternalDataChangeListener(ActionListener) - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel

Sometimes we want to know when the user has started modifying the datasource, from _outside_ this panel.

addExternalDataSourceChangeListener(ActionListener) - Method in class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel

The input listener is added to each data source config panel.

addFeature() - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser

addFeature(SeqFeatureI) - Method in class apollo.datamodel.FeatureSet

Add feature to end of features list, recalc low and high

addFeature(SeqFeatureI, boolean) - Method in class apollo.datamodel.FeatureSet

addFeature(SeqFeatureI) - Method in class apollo.datamodel.SeqFeature

no-op.

addFeature(SeqFeatureI, boolean) - Method in class apollo.datamodel.SeqFeature

no-op - overridden by FeatureSet

addFeature(SeqFeatureI) - Method in interface apollo.datamodel.SeqFeatureI

Add child feature

addFeature(SeqFeatureI, boolean) - Method in interface apollo.datamodel.SeqFeatureI

Add feature at sorted position

addFeature(SeqFeatureI) - Method in class apollo.datamodel.StrandedFeatureSet

Features must be added in sort order, if this turns out to be too slow, then we will need to figure out another way to keep them all sorted (5prime to 3prime that is)

addFeature(SeqFeatureI, boolean) - Method in class apollo.datamodel.StrandedFeatureSet

addFeature(SeqFeatureI) - Method in class apollo.datamodel.Transcript

addFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel

Adds feature to an existing SeqWrapper if it doesnt overlap with it, otherwise creates a new SeqWrapper for it,

addFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

Adds feature to an existing SeqWrapper if it doesnt overlap with it, otherwise creates a new SeqWrapper for it,

addFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.HomogeneousPanel

addFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel

addFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.Tier

Adds the feature to this Tier

addFeature(SeqFeatureI) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI

addFeature(Drawable, Transformer) - Method in class apollo.gui.genomemap.FeatureTier

Calls addFeature on its FeatureSet with the DrawableSeqFeature and the sort flag set to true, this will cause the DSFs to be sorted Since it only allows DrawableSeqFeatures to be added shouldnt the fset be a DrawableFeatureSet instead of just a FeatureSet? Then getFeatureSet could return a DrawableFeatureSet and we wouldnt have to cast it There doesnt seem to be a reason at the moment to let it other features than dsfs - am i right about this?

addFeature(SeqFeatureI) - Method in class apollo.util.FeatureList

Adds SeqFeatureI if not already in list

addFeatureDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableFeatureSet

Create a drawable for sf(createDrawable) and add it as a child (addDrawable).

addFeatureDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableGeneFeatureSet

addFeatureDrawable(SeqFeatureI) - Method in interface apollo.gui.drawable.DrawableSetI

addFeaturePair(FeaturePairI) - Method in class apollo.util.FeatureList

addFeatureProperty(FeatureProperty) - Method in class apollo.config.TierProperty

addFeatures(Collection<SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.Tier

Adds a collection of features to this tier

addFeatures(Collection<SeqFeatureI>) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI

addFeatureToPanel(SeqFeatureI, MultiTierPanel) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

addField(String, Component) - Method in class apollo.gui.annotinfo.FeatureEditPanel

addField(JComponent, Component) - Method in class apollo.gui.annotinfo.FeatureEditPanel

addFieldName(String) - Method in class apollo.dataadapter.mysql.Table

addFieldsPanelBottomGlue() - Method in class apollo.gui.annotinfo.FeatureEditPanel

pad out bottom of fields panel, for layout - otherwise syns can get huge

AddFilterAction - Class in apollo.gui.detailviewers.sequencealigner.actions

AddFilterAction(MultiSequenceAlignerPanel, AddFilterPanel.TYPES) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.AddFilterAction

AddFilterPanel - Class in apollo.gui.detailviewers.sequencealigner.menus

AddFilterPanel(MultiSequenceAlignerPanel, AddFilterPanel.TYPES) - Constructor for class apollo.gui.detailviewers.sequencealigner.menus.AddFilterPanel

AddFilterPanel.TYPES - Enum in apollo.gui.detailviewers.sequencealigner.menus

addFirst(ViewI, Object) - Method in class apollo.gui.genomemap.LaidoutViewContainer

addGene(FeatureSetI, FeatureSetI, FeatureSetI) - Method in class apollo.dataadapter.analysis.GeneFinderParser

addGene(SeqFeatureI, String, Date, ChadoFeature, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Add a gene to the chado database.

addGeneOrTranscript() - Method in class apollo.editor.AnnotationEditor

The default addGeneOrTranscript.

addGeneOrTranscript(boolean) - Method in class apollo.editor.AnnotationEditor

addGeneOrTranscriptAllowed() - Method in class apollo.editor.AnnotationEditor

Determine whether it's OK to do an add gene or transcript.

addGenePredictionResults(Connection, String[], StrandedFeatureSet, FeatureLocImplementation, SequenceI) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Deprecated. use chadoProgram array instead of string array

addGenePredictionResults(Connection, ChadoProgram[], StrandedFeatureSet, FeatureLocImplementation, SequenceI) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Retrieve gene predictions and add them to parentFeatSet as SeqFeatures.

addGenePredictionResults(Connection, ChadoProgram[], StrandedFeatureSet, FeatureLocImplementation, SequenceI, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Retrieve gene predictions and add them to parentFeatSet as SeqFeatures.

addGenes(StrandedFeatureSet, Location, List, boolean, String) - Method in class apollo.dataadapter.ensj.DataFetcher

Retrieves ensJ genes/transcripts/exons, converts them into seq features and adds them to the curation set.

addGraph(ScoreCalculator, boolean, Color) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

addHighlightRegion(BaseScrollable, Color, boolean) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

addHighlights(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableFeatureSet

addHighlights(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature

highlights edges and box around if isHighlighted

addHighlights(Graphics, Rectangle, Transformer, TierManagerI) - Method in class apollo.gui.drawable.Triangle

addIsProblematicCheckbox() - Method in class apollo.gui.annotinfo.FeatureEditPanel

addItemListener(ItemListener) - Method in class apollo.dataadapter.ensj19.SourceChooserWithHistory

addKaryotype(Karyotype) - Method in class apollo.dataadapter.KaryotypeAdapter

addKeyRouter(JTextField, String) - Method in class apollo.dataadapter.ensj.controller.Controller

addKeyRouter(Component, String) - Method in class apollo.dataadapter.ensj.controller.Controller

addKeyRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.controller.Controller

addKeyRouter(JTextField, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI

addKeyRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI

addKeyRouter(Component, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI

addKeyword(String) - Method in class apollo.datamodel.AssemblyFeature

addLayoutComponent(Component, Object) - Method in class apollo.gui.genomemap.ApolloLayoutManager

addLayoutComponent(String, Component) - Method in class apollo.gui.synteny.SyntenyLayout

addLayoutView(ViewI, Object) - Method in class apollo.gui.genomemap.ApolloLayoutManager

addLink(FeaturePairI) - Method in class apollo.datamodel.LinkSet

addLink(Link) - Method in class apollo.datamodel.LinkSet

addLinkPanel(SyntenyLinkPanel) - Method in class apollo.gui.synteny.SyntenyPanel

addLinks(LinkSet) - Method in class apollo.datamodel.LinkSet

addListener(EventListener) - Method in class apollo.gui.Controller

addListener(RubberbandListener) - Method in class apollo.gui.genomemap.Rubberband

addMessage(String, String) - Method in class apollo.gui.PrefsPanel

addNewAnnot(String) - Method in class apollo.editor.AnnotationEditor

addNote(String, PeptideNote) - Method in class apollo.dataadapter.genbank.GenbankValidator

addNotify() - Method in class apollo.gui.annotinfo.FeatureEditorDialog

addNotify() - Method in class apollo.gui.ControlledPanel

override Component.addNotify, called when added to parent.

addNotify() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

addNotify() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel.DefaultRowHeader

This is where the row numbers JLabels get created

addNotify() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

addNotify() - Method in class apollo.gui.featuretree.FeatureTreeFrame

addNotify() - Method in class apollo.gui.FindPanel

addOccurance() - Method in class apollo.analysis.filter.HuffNode

addOneLevelAnnotations(Connection, SequenceI, StrandedFeatureSet, FeatureLocImplementation, boolean, boolean, boolean) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

add annotations with only one level, like transposons (for now) and annotated tiling paths, promoters & what not.

addOverlappingAllowed() - Method in class apollo.editor.AnnotationEditor

addOverlappingGene(Vector) - Method in class apollo.editor.AnnotationEditor

This method creates a new gene from the features, whether or not they overlap an existing gene.

addPanel(AbstractTierPanel) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel

Adds a new

addPanel(StrandedZoomableApolloPanel) - Method in class apollo.gui.synteny.SyntenyPanel

addParameter(String, String) - Method in class apollo.config.Style

Whenever we add a new parameter to the style file, we've been adding methods in Style.java to set/get some variable--it's getting annoying.

addPopupRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.controller.Controller

addPopupRouter(JComboBox, String) - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI

addPredictionTranscripts(StrandedFeatureSet, Location, List) - Method in class apollo.dataadapter.ensj.DataFetcher

addPrimaryKeyColumnValue(String, HashMap) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

addPropertiesWithPrefix(Properties, String, Properties) - Method in class apollo.dataadapter.analysis.AnalysisAdapterGUI

addProperty(String, String) - Method in class apollo.analysis.SeqAnalysisBase

addProperty(String, String) - Method in interface apollo.analysis.SeqAnalysisI

set the value of a property

addProperty(String, String) - Method in class apollo.dataadapter.chado.ChadoTransaction

addProperty(String, String) - Method in class apollo.dataadapter.synteny.builder.AdapterModel

addProperty(String, String) - Method in class apollo.datamodel.FeaturePair

addProperty(String, String) - Method in class apollo.datamodel.seq.GenbankSequence

addProperty(String, String) - Method in class apollo.datamodel.SeqFeature

addProperty(String, String) - Method in interface apollo.datamodel.SeqFeatureI

addProperty(String, String) - Method in class apollo.datamodel.Synonym

addProperty(String, String, int) - Method in class apollo.editor.Transaction

Add a new value to the Vector for this property name.

addPropSchemeChangeListener(PropSchemeChangeListener) - Method in class apollo.config.PropertyScheme

addProteinAlignFeatures(CurationSet, List, Location, List) - Method in class apollo.dataadapter.ensj.DataFetcher

addProteinAlignments(Connection, String, StrandedFeatureSet, FeatureLocImplementation) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Retrieve a set of protein alignments from Chado and convert them into instances of apollo.datmodel.FeaturePair.

addProteinAnnotations(CurationSet, List, List) - Method in class apollo.dataadapter.ensj.DataFetcher

addRefFeature(String, SeqFeatureI) - Method in class apollo.datamodel.SeqFeature

addRemark(String) - Method in class apollo.datamodel.AssemblyFeature

addRepeatFeatures(CurationSet, List, Location) - Method in class apollo.dataadapter.ensj.DataFetcher

Add all repeat features into the input set.

addResult(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

Adds a result to this panel so that it can be displayed.

AddResultFilterAction - Class in apollo.gui.detailviewers.sequencealigner.actions

AddResultFilterAction(MultiSequenceAlignerPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.AddResultFilterAction

addResultGenesAsAnnotations() - Method in class apollo.dataadapter.ensj.model.OptionsModel

addResults(Set<SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

Adds all results in a set to this panel so that they can be displayed.

addResults(Collection<SeqFeatureI>) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

Adds a collection of results to the list of results (but not to the result panel)

addReturnedObject(Object) - Method in class apollo.dataadapter.otter.parser.OtterContentHandler

addScore(Score) - Method in class apollo.datamodel.FeaturePair

addScore(double) - Method in class apollo.datamodel.FeaturePair

addScore(String, double) - Method in class apollo.datamodel.FeaturePair

addScore(String, String) - Method in class apollo.datamodel.FeaturePair

addScore(Score) - Method in class apollo.datamodel.SeqFeature

addScore(double) - Method in class apollo.datamodel.SeqFeature

addScore(String, double) - Method in class apollo.datamodel.SeqFeature

addScore(String, String) - Method in class apollo.datamodel.SeqFeature

addScore(Score) - Method in interface apollo.datamodel.SeqFeatureI

addScore(double) - Method in interface apollo.datamodel.SeqFeatureI

addScore(String, double) - Method in interface apollo.datamodel.SeqFeatureI

addScore(String, String) - Method in interface apollo.datamodel.SeqFeatureI

addScrollBar() - Method in class apollo.gui.genomemap.TierView

addSearchHits(Connection, ChadoProgram[], boolean, boolean, boolean, boolean, boolean, SequenceI, StrandedFeatureSet, String, boolean, FeatureLocImplementation) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Retrieve a set of search hits (e.g.

addSelectedToHistory() - Method in class apollo.dataadapter.GuiTabPanel

Puts currently selected item at top of history list

addSelectionListener(SelectableI) - Method in class apollo.gui.SelectionItem

addSequence(SequenceI) - Method in class apollo.datamodel.CurationSet

addSequence(SequenceI, int, String, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

addSequenceEdit(SequenceEdit, String, Date) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter

Add a sequence edit to the database.

addSequenceEdit(SequenceEdit, String, Date) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

addSequenceEdit(SequenceEdit) - Method in class apollo.datamodel.AbstractSequence

addSequenceEdit(SequenceEdit) - Method in interface apollo.datamodel.SequenceI

addSequencingErrorPosition(String, int, String) - Method in class apollo.datamodel.AbstractSequence

The position of the genomic sequencing error is in genomic coordinates.

addSequencingErrorPosition(String, int, String) - Method in interface apollo.datamodel.SequenceI

addSimpleFeatures(CurationSet, List, Location, List) - Method in class apollo.dataadapter.ensj.DataFetcher

addSite(int) - Method in class apollo.gui.genomemap.Sites

addSpeciesComparison(SpeciesComparison) - Method in class apollo.datamodel.CompositeDataHolder

addSubject(String, String, String) - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser

Add the subject id and range to the feature as properties.

addSupportToTranscripts() - Method in class apollo.dataadapter.ensj.model.OptionsModel

addSynonym(AnnotatedFeatureI, String) - Method in class apollo.config.DefaultNameAdapter

returns an add transaction for adding synonym to annot.

addSynonym(SeqFeatureI, AddTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

addSynonym(long, String) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Add a synonym to the database

addSynonym(String) - Method in class apollo.datamodel.AnnotatedFeature

addSynonym used to refuse (quite reasonably) to add synonyms that are the same as the name of the feature, but Chado XML is rather fond of those reflexive synonyms, so go ahead and add them, what the heck.

addSynonym(int, String) - Method in class apollo.datamodel.AnnotatedFeature

addSynonym(Synonym) - Method in class apollo.datamodel.AnnotatedFeature

addSynonym(String) - Method in interface apollo.datamodel.AnnotatedFeatureI

addSynonym(int, String) - Method in interface apollo.datamodel.AnnotatedFeatureI

addSynonym(Synonym) - Method in interface apollo.datamodel.AnnotatedFeatureI

addSynonym(String) - Method in class apollo.datamodel.Identifier

addSynonym(int, String) - Method in class apollo.datamodel.Identifier

addSynonym(Synonym) - Method in class apollo.datamodel.Identifier

addSynonym(int, Synonym) - Method in class apollo.datamodel.Identifier

addSynonymGui() - Method in class apollo.gui.annotinfo.FeatureEditPanel

addSynonyms(AnnotatedFeatureI) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Add all synonyms from an AnnotatedFeatureI object

addSyntenyRegionForChromosome(String, SyntenyRegion) - Method in class apollo.dataadapter.GFFSyntenyAdapter

addSyntenyRegionForChromosome(String, SyntenyRegion) - Method in class apollo.dataadapter.SyntenyAdapter

addSyntenyRegionForChromosome(String, SyntenyRegion) - Method in interface apollo.dataadapter.SyntenyAdapterI

addSyntenyRegionsForChromosome(String, Vector) - Method in class apollo.dataadapter.SyntenyAdapter

addSyntenyResultMenuItem() - Method in class apollo.config.Style

Whether to add a menu item to the result popup menu that will bring up the selected feature as the other species in synteny

addSyntenySpeciesNumDropdown() - Method in class apollo.config.Style

Whether to add link query radio buttons to synteny adap gui

addTable(Table) - Method in class apollo.dataadapter.mysql.Database

addTier(SequenceI, int, String, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

Adds a new tier to the panel.

addTierManagerListener(TierManagerListener) - Method in class apollo.gui.TierManager

addTierType(TierProperty) - Method in class apollo.config.PropertyScheme

addToCurationSet() - Method in class apollo.dataadapter.AbstractApolloAdapter

addToCurationSet() - Method in class apollo.dataadapter.analysis.AnalysisAdapter

from ApolloDataAdapterI interface.

addToCurationSet() - Method in interface apollo.dataadapter.ApolloDataAdapterI

addToCurationSet() - Method in class apollo.dataadapter.chado.ChadoAdapter

addToCurationSet() - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter

Like getCurationSet--used for layering new data.

addToCurationSet() - Method in class apollo.dataadapter.ensj.EnsJAdapter

addToCurationSet() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter

addToCurationSet() - Method in class apollo.dataadapter.gamexml.GAMEAdapter

Called if user is layering additional GAME data on top of whatever's already been loaded

addToCurationSet() - Method in class apollo.dataadapter.gff3.GFF3Adapter

Add GFF3 data to currently existing CurationSet

addToCurationSet(Color) - Method in class apollo.dataadapter.graph.GraphAdapter

Add graph data

addToCurationSet() - Method in class apollo.main.DataLoader

Layer data onto curationset (if multi species active species cur set)

addToCurrentSelection(Selection) - Method in class apollo.gui.SelectionManager

Just adds newSelection to the current selection.

addToFeature(String) - Method in class apollo.dataadapter.genbank.PublicDbFeature

addToPanel(JComponent) - Method in class apollo.dataadapter.analysis.AnalysisPanel

addTopLevelAnnot(SeqFeatureI, String, Date, ChadoFeature) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter

Add a top level annotation to the database.

addTopLevelAnnot(SeqFeatureI, String, Date, ChadoFeature) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Add a top level annotation to the chado database.

AddTransaction - Class in apollo.editor

Transaction for adding a SeqFeatureI.

AddTransaction() - Constructor for class apollo.editor.AddTransaction

AddTransaction(SeqFeatureI) - Constructor for class apollo.editor.AddTransaction

AddTransaction(SeqFeatureI, TransactionSubpart) - Constructor for class apollo.editor.AddTransaction

AddTransaction(SeqFeatureI, TransactionSubpart, Object) - Constructor for class apollo.editor.AddTransaction

AddTransaction(Object, SeqFeatureI, TransactionSubpart, Object) - Constructor for class apollo.editor.AddTransaction

AddTransaction(SeqFeatureI, TransactionSubpart, Object, int) - Constructor for class apollo.editor.AddTransaction

AddTransaction(Object, SeqFeatureI, TransactionSubpart, Object, int) - Constructor for class apollo.editor.AddTransaction

addTransaction(Transaction) - Method in class apollo.editor.AnnotationChangeEvent

If compound change event, add trans to compound transaction AnnotationCompoundEvent overrides no-op

addTransaction(Transaction) - Method in class apollo.editor.AnnotationChangeLog

addTransaction(Transaction) - Method in class apollo.editor.AnnotationCompoundEvent

addTransaction(CompoundTransaction) - Method in class apollo.editor.AnnotationCompoundEvent

addTransaction(Transaction) - Method in class apollo.editor.CompoundTransaction

Add a child Transaction to this CompoundTransaction object.

addTransaction(CompoundTransaction) - Method in class apollo.editor.CompoundTransaction

Adds the children of the compound trans NOT the CompoundTransaction itself.

addTransaction(Transaction) - Method in class apollo.editor.TransactionManager

addTranscript(Transcript, String, Date, Long, long, ChadoFeature, boolean) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoWriter

Add a transcript to the database.

addTranscript(Transcript, String, Date, Long, long, ChadoFeature, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Add a transcript to the chado database.

addTranscript() - Method in class apollo.editor.AnnotationEditor

If called with no args, addTranscript checks which gene was selected and adds the transcript to that gene.

addTranscriptAllowed() - Method in class apollo.editor.AnnotationEditor

Whether allowed to add transcript, just calls addEvidenceExonsAllowed as conditions are same

addTranscriptComment(String) - Method in class apollo.config.Style

Add a canned transcript comment.

addUpdateProperty(String, String) - Method in class apollo.dataadapter.chado.ChadoUpdateTransaction

addVector(Vector) - Method in class apollo.util.FeatureList

addViewListener(ViewListener) - Method in class apollo.gui.genomemap.LinearView

addViewListener(ViewListener) - Method in interface apollo.gui.genomemap.ViewI

Add a View event listener

addVisibilityListener(VisibilityListener) - Method in class apollo.gui.genomemap.LinearView

addWindowListener(WindowListener) - Method in class apollo.gui.TypePanel

adjustEdges() - Method in class apollo.datamodel.FeatureSet

Set low and high according to lowest and highest coord in kids

adjustEdges(SeqFeatureI) - Method in class apollo.datamodel.FeatureSet

If span has higher high and or lower low than current, reset high/low

adjustEdges() - Method in interface apollo.datamodel.FeatureSetI

adjustEdges(SeqFeatureI) - Method in interface apollo.datamodel.FeatureSetI

adjustmentValueChanged(AdjustmentEvent) - Method in class apollo.gui.detailviewers.sequencealigner.HorizontalScrollBarAdjustmentListener

assumes that the scrollbar adjustment values have the same bounds as the number of pixels in the component in the viewport

adjustmentValueChanged(AdjustmentEvent) - Method in class apollo.gui.detailviewers.sequencealigner.VerticalScrollBarAdjustmentListener

assumes that the scrollbar adjustment values have the same bounds as the number of pixels in the component in the viewport

adjustmentValueChanged(AdjustmentEvent) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

adjustmentValueChanged(AdjustmentEvent) - Method in class apollo.gui.genomemap.TierView

AFTER_LOAD - Static variable in class apollo.gui.event.LazyLoadEvent

aggregateSizeChange - Variable in class apollo.gui.TierManager

AGGRESSIVE_GENE_NAMING - Static variable in class apollo.dataadapter.StateInformation

AGGRESSIVE_NAMING_LABEL - Static variable in class apollo.dataadapter.ensj.view.OptionsPanel

aggressiveGeneNaming() - Method in class apollo.dataadapter.ensj.model.OptionsModel

Ala - Static variable in class apollo.seq.ResidueProperties

align_seq - Variable in class apollo.dataadapter.analysis.AlignmentParser

AlignBlockChooser - Class in apollo.dataadapter.synteny

I am popped up by the compara adapter if the user is required to choose between different align blocks that a fixed genomic range is mapped to - for instance, if human chr A:x-y maps to mosquito chr B:l-m, AND mosquito chr C: p-q, then we need the user to choose between these regions before we can display the alignments from human<->mosquito.

AlignBlockChooser(HashMap) - Constructor for class apollo.dataadapter.synteny.AlignBlockChooser

AlignBlockChooser.OKButtonListener - Class in apollo.dataadapter.synteny

AlignBlockChooser.OKButtonListener() - Constructor for class apollo.dataadapter.synteny.AlignBlockChooser.OKButtonListener

alignmentIsPeptide() - Method in class apollo.datamodel.SeqFeature

Returns true if alignment is peptide sequence, false if nucleotide This is for the hit alignment(not query).

alignmentIsPeptide() - Method in interface apollo.datamodel.SeqFeatureI

Sequence of the alignment of hit to query, previously stored in hit features subject_alignment property.

AlignmentParser - Class in apollo.dataadapter.analysis

AlignmentParser() - Constructor for class apollo.dataadapter.analysis.AlignmentParser

allowedSet - Variable in class apollo.dataadapter.StateInformation

allowsMovement - Variable in class apollo.gui.genomemap.ApolloPanel

allowsTierDrags() - Method in class apollo.gui.genomemap.AnnotationView

allowsTierDrags() - Method in class apollo.gui.genomemap.SiteView

allowsTierDrags() - Method in class apollo.gui.genomemap.TierView

allowsTierDrags() - Method in interface apollo.gui.genomemap.TierViewI

Whether this view allows tier dragging

ALLSTOPS - Static variable in interface apollo.gui.drawable.DrawableAnnotationConstants

Show all stop codons which are in phase.

AllTests - Class in apollo.dataadapter.gff3

AllTests() - Constructor for class apollo.dataadapter.gff3.AllTests

AllTests - Class in apollo.util

AllTests() - Constructor for class apollo.util.AllTests

allTypes - Variable in class apollo.config.TiersIO

AlternateEnsJSequence - Class in apollo.dataadapter.ensj

AlternateEnsJSequence(String, Controller, Location, Properties) - Constructor for class apollo.dataadapter.ensj.AlternateEnsJSequence

AlternateEnsJSequence - Class in apollo.dataadapter.ensj19

AlternateEnsJSequence(String, Controller, LinearLocation, Properties) - Constructor for class apollo.dataadapter.ensj19.AlternateEnsJSequence

amend_RNA(StringBuffer) - Method in class apollo.datamodel.SeqFeature

AminoAcidBaseRenderer - Class in apollo.gui.detailviewers.sequencealigner.renderers

AminoAcidBaseRenderer(int, Orientation) - Constructor for class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidBaseRenderer

AminoAcidRenderer - Class in apollo.gui.detailviewers.exonviewer

AminoAcidRenderer(int, int, int, SeqAlignPanel) - Constructor for class apollo.gui.detailviewers.exonviewer.AminoAcidRenderer

AminoAcidRenderer - Class in apollo.gui.detailviewers.sequencealigner.renderers

AminoAcidRenderer(ReadingFrame) - Constructor for class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidRenderer

AminoAcidRendererOLD - Class in apollo.gui.detailviewers.sequencealigner

AminoAcidRendererOLD(int, int, int, SeqAlignPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.AminoAcidRendererOLD

AminoAcidRendererSpaced - Class in apollo.gui.detailviewers.sequencealigner.renderers

AminoAcidRendererSpaced(int) - Constructor for class apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidRendererSpaced

ANALYSIS - Static variable in class apollo.editor.ResultChangeEvent

analysis_type - Variable in class apollo.analysis.filter.AnalysisInput

analysis_types - Variable in class apollo.config.FeatureProperty

analysis_types - Variable in class apollo.config.TierProperty

AnalysisAdapter - Class in apollo.dataadapter.analysis

AnalysisAdapter() - Constructor for class apollo.dataadapter.analysis.AnalysisAdapter

AnalysisAdapterGUI - Class in apollo.dataadapter.analysis

Most of the smarts here are actually in AnalysisPanel and its subclasses This just holds the game panels in its tabbed pane

AnalysisAdapterGUI(IOOperation, CurationSet) - Constructor for class apollo.dataadapter.analysis.AnalysisAdapterGUI

AnalysisAdaptor - Class in apollo.dataadapter.gbrowse

AnalysisAdaptor(MySQLDatabase) - Constructor for class apollo.dataadapter.gbrowse.AnalysisAdaptor

AnalysisDataAdapterI - Interface in apollo.analysis

DataAdapterI interface Used to load annotated and non-annotated data from whatever datasource

AnalysisFilter - Class in apollo.analysis.filter

AnalysisFilter() - Constructor for class apollo.analysis.filter.AnalysisFilter

AnalysisFilterI - Interface in apollo.analysis.filter

AnalysisGUI - Class in apollo.analysis

Provides GUI for running different analysis tools and importing the results into Apollo.

AnalysisGUI() - Constructor for class apollo.analysis.AnalysisGUI

Constructor.

AnalysisGUI(int, int) - Constructor for class apollo.analysis.AnalysisGUI

Constructor.

AnalysisGUI(int, int, int) - Constructor for class apollo.analysis.AnalysisGUI

Constructor.

AnalysisGUI(int, int, int, FeatureList) - Constructor for class apollo.analysis.AnalysisGUI

Constructor.

AnalysisInput - Class in apollo.analysis.filter

This contains all of the filtering parameters to use on a set of raw output from a computational analysis of the sequence.

AnalysisInput() - Constructor for class apollo.analysis.filter.AnalysisInput

AnalysisMenu - Class in apollo.gui.menus

has menu items for gc plot and restriction enzyme.

AnalysisMenu() - Constructor for class apollo.gui.menus.AnalysisMenu

AnalysisPanel - Class in apollo.dataadapter.analysis

This is only used by AnalysisAdapterGUI.

AnalysisPanel.displayTierItemListener - Class in apollo.dataadapter.analysis

Where will the blast analysis results appear, name that tier.

AnalysisPanel.displayTierItemListener() - Constructor for class apollo.dataadapter.analysis.AnalysisPanel.displayTierItemListener

AnalysisPanel.fileItemListener - Class in apollo.dataadapter.analysis

Which file contains the analysis results

AnalysisPanel.fileItemListener() - Constructor for class apollo.dataadapter.analysis.AnalysisPanel.fileItemListener

AnalysisParserI - Interface in apollo.dataadapter.analysis

anchor(Point) - Method in class apollo.gui.genomemap.Rubberband

anchorPt - Variable in class apollo.gui.genomemap.Rubberband

annot_columns - Static variable in class apollo.gui.evidencepanel.EvidencePanel

AnnotatedFeature - Class in apollo.datamodel

One thought Im having is that annotation stuff would be a HASA instead of a ISA for SeqFeatureI.

AnnotatedFeature() - Constructor for class apollo.datamodel.AnnotatedFeature

AnnotatedFeature(SeqFeatureI) - Constructor for class apollo.datamodel.AnnotatedFeature

AnnotatedFeature(FeatureSetI, String) - Constructor for class apollo.datamodel.AnnotatedFeature

AnnotatedFeatureI - Interface in apollo.datamodel

ANNOTATION - Static variable in class apollo.editor.TransactionClass

AnnotationAddEvent - Class in apollo.editor

AnnotationChangeEvent for add

AnnotationAddEvent(Object, AnnotatedFeatureI) - Constructor for class apollo.editor.AnnotationAddEvent

A feature has been added, e.g.

AnnotationAddEvent(Object, AnnotatedFeatureI, TransactionSubpart) - Constructor for class apollo.editor.AnnotationAddEvent

A subpart has been added, e.g.

AnnotationAddEvent(Object, AnnotatedFeatureI, TransactionSubpart, boolean) - Constructor for class apollo.editor.AnnotationAddEvent

AnnotationChangeEvent - Class in apollo.editor

A controller managed event class which signals when a change is made to a set of annotations and what type of change occurred.

AnnotationChangeEvent(Object) - Constructor for class apollo.editor.AnnotationChangeEvent

Solely for edit session done event

AnnotationChangeEvent(Object, AnnotatedFeatureI) - Constructor for class apollo.editor.AnnotationChangeEvent

No subpart

AnnotationChangeEvent(Object, AnnotatedFeatureI, TransactionSubpart) - Constructor for class apollo.editor.AnnotationChangeEvent

With subpart

AnnotationChangeListener - Interface in apollo.editor

AnnotationChangeLog - Class in apollo.editor

DELETE THIS - replace by TransactionManager - i think i got all references - test that it works out and delete! Logs AnnotationChangeEvents which are fired when edits occur.

AnnotationChangeLog() - Constructor for class apollo.editor.AnnotationChangeLog

AnnotationCompoundEvent - Class in apollo.editor

AnnotationCompoundEvent(CompoundTransaction) - Constructor for class apollo.editor.AnnotationCompoundEvent

Constructor It defaults the transaction to not undo

AnnotationDeleteEvent - Class in apollo.editor

AnnotationDeleteEvent(Object, AnnotatedFeatureI, SeqFeatureI) - Constructor for class apollo.editor.AnnotationDeleteEvent

Delete whole feature.

AnnotationDeleteEvent(Object, AnnotatedFeatureI, TransactionSubpart) - Constructor for class apollo.editor.AnnotationDeleteEvent

Delete subpart (comment, synonym)

AnnotationDeleteEvent(Object, AnnotatedFeatureI, TransactionSubpart, boolean) - Constructor for class apollo.editor.AnnotationDeleteEvent

AnnotationEditor - Class in apollo.editor

A class for performing edits on the annotations.

AnnotationEditor(GuiCurationState, FeatureSetI) - Constructor for class apollo.editor.AnnotationEditor

The AnnotationEditor constructor.

annotationEditor - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel

annotationEditor - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

AnnotationEditor.FeatChangeData - Class in apollo.editor

Helper class for keeping track of changed top level annots

AnnotationEditor.FeatChangeData() - Constructor for class apollo.editor.AnnotationEditor.FeatChangeData

AnnotationEditorMouseListener - Class in apollo.gui.detailviewers.sequencealigner

Class to handle mouse interactions for an annotation panel NOTE: It can be hard to keep track of what coordinate system you are working in.

AnnotationEditorMouseListener(MultiTierPanel, GuiCurationState, MultiSequenceAlignerPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.AnnotationEditorMouseListener

Constructor

AnnotationEnsJAdapter - Class in apollo.dataadapter.ensj19

AnnotationEnsJAdapter() - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapter

AnnotationEnsJAdapterGUI - Class in apollo.dataadapter.ensj19

AnnotationEnsJAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI

AnnotationEnsJAdapterGUI.DataSourceConfigInteractionListener - Class in apollo.dataadapter.ensj19

If the user chooses a particular ensembl database from the default filechooser, we will update the other databases with our best guess (if we can find one) for the maps and variation databases.

AnnotationEnsJAdapterGUI.DataSourceConfigInteractionListener() - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.DataSourceConfigInteractionListener

AnnotationEnsJAdapterGUI.ShowAnnotationConfigurationActionListener - Class in apollo.dataadapter.ensj19

Space saver - Toggles the annotation source chooser to be visible/not.

AnnotationEnsJAdapterGUI.ShowAnnotationConfigurationActionListener() - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowAnnotationConfigurationActionListener

AnnotationEnsJAdapterGUI.ShowDataSourceConfigurationActionListener - Class in apollo.dataadapter.ensj19

Space saver - Toggles the data source chooser to be visible/not.

AnnotationEnsJAdapterGUI.ShowDataSourceConfigurationActionListener() - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowDataSourceConfigurationActionListener

AnnotationEnsJAdapterGUI.ShowTypesActionListener - Class in apollo.dataadapter.ensj19

Sets the Include Panel contained in the types panel to visible and re-packs the dialog - this makes it look like the dialog has expanded with those options

AnnotationEnsJAdapterGUI.ShowTypesActionListener() - Constructor for class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowTypesActionListener

AnnotationFeatureComparator - Class in apollo.gui.detailviewers.sequencealigner

AnnotationFeatureComparator() - Constructor for class apollo.gui.detailviewers.sequencealigner.AnnotationFeatureComparator

annotationFilter(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel

annotationFilter(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel

annotationFilter(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

I don't think this is used in any way...

AnnotationHeaderMouseListener - Class in apollo.gui.detailviewers.sequencealigner.listeners

AnnotationHeaderMouseListener(MultiSequenceAlignerPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.listeners.AnnotationHeaderMouseListener

AnnotationMenu - Class in apollo.gui.menus

Note that this is actually the popup menu you get when you right-click after selecting an annotation.

AnnotationMenu(GuiCurationState, ApolloPanelI, AnnotationView, Selection, Point) - Constructor for class apollo.gui.menus.AnnotationMenu

Selection is the selection for the whole ApolloPanel (not just the AnnotView)

AnnotationRenderer - Class in apollo.gui.detailviewers.sequencealigner.renderers

AnnotationRenderer(GuiCurationState) - Constructor for class apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer

AnnotationReplaceEvent - Class in apollo.editor

This class is temporary in theory.

AnnotationReplaceEvent(Object, AnnotatedFeatureI, AnnotatedFeatureI) - Constructor for class apollo.editor.AnnotationReplaceEvent

AnnotationRighClickMenu - Class in apollo.gui.detailviewers.sequencealigner

This is the popup menu that gets displayed when you right click on an annotation.

AnnotationRighClickMenu(GuiCurationState, MultiTierPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu

Constructor

annotationRoot - Variable in class apollo.datamodel.AnnotatedFeature

AnnotationsModel - Class in apollo.dataadapter.ensj.model

AnnotationsModel() - Constructor for class apollo.dataadapter.ensj.model.AnnotationsModel

AnnotationSourceChooser - Class in apollo.dataadapter.ensj19

Presents the user with a choice of file or server input for the annotation source.

AnnotationSourceChooser() - Constructor for class apollo.dataadapter.ensj19.AnnotationSourceChooser

AnnotationSourceChooser(Vector, Vector, Vector) - Constructor for class apollo.dataadapter.ensj19.AnnotationSourceChooser

AnnotationSourceChooser.FindDataSetsListener - Class in apollo.dataadapter.ensj19

AnnotationSourceChooser.FindDataSetsListener() - Constructor for class apollo.dataadapter.ensj19.AnnotationSourceChooser.FindDataSetsListener

AnnotationSourceChooser.RemoveDatasetsListenerForPort - Class in apollo.dataadapter.ensj19

AnnotationSourceChooser.RemoveDatasetsListenerForPort() - Constructor for class apollo.dataadapter.ensj19.AnnotationSourceChooser.RemoveDatasetsListenerForPort

AnnotationSourceChooser.RemoveDatasetsListenerForServer - Class in apollo.dataadapter.ensj19

AnnotationSourceChooser.RemoveDatasetsListenerForServer() - Constructor for class apollo.dataadapter.ensj19.AnnotationSourceChooser.RemoveDatasetsListenerForServer

AnnotationsPanel - Class in apollo.dataadapter.ensj.view

AnnotationsPanel(View) - Constructor for class apollo.dataadapter.ensj.view.AnnotationsPanel

AnnotationUpdateEvent - Class in apollo.editor

AnnotationUpdateEvent(UpdateTransaction) - Constructor for class apollo.editor.AnnotationUpdateEvent

New way of doing annotation change events - they are just carriers of transactions.

AnnotationUpdateEvent(Object, AnnotatedFeatureI, TransactionSubpart) - Constructor for class apollo.editor.AnnotationUpdateEvent

AnnotationUpdateEvent(Object, AnnotatedFeatureI, TransactionSubpart, boolean) - Constructor for class apollo.editor.AnnotationUpdateEvent

AnnotationView - Class in apollo.gui.genomemap

A view to display annotations in

AnnotationView(JComponent, String, SelectionManager, GuiCurationState) - Constructor for class apollo.gui.genomemap.AnnotationView

annotationView - Variable in class apollo.gui.genomemap.ResultView

annotDrag(DragViewI, Vector, boolean, StringBuffer) - Method in class apollo.gui.genomemap.AnnotationView

annotNumber - Static variable in class apollo.config.GmodNameAdapter

AnnotSessionDoneEvent - Class in apollo.editor

This event indicates that the editor is done with a series of edits.

AnnotSessionDoneEvent(Object) - Constructor for class apollo.editor.AnnotSessionDoneEvent

do we need annot top or changed feature?

Apollo - Class in apollo.main

Apollo() - Constructor for class apollo.main.Apollo

apollo.analysis - package apollo.analysis

apollo.analysis.filter - package apollo.analysis.filter

apollo.bop - package apollo.bop

apollo.config - package apollo.config

apollo.dataadapter - package apollo.dataadapter

apollo.dataadapter.analysis - package apollo.dataadapter.analysis

apollo.dataadapter.chado - package apollo.dataadapter.chado

apollo.dataadapter.chado.jdbc - package apollo.dataadapter.chado.jdbc

apollo.dataadapter.chadoxml - package apollo.dataadapter.chadoxml

apollo.dataadapter.das - package apollo.dataadapter.das

Defines the interfaces to support the reading of DAS datasources by Apollo.

apollo.dataadapter.das.simple - package apollo.dataadapter.das.simple

Provides simple implementations of the interfaces defined in the apollo.dataadapter.das package.

apollo.dataadapter.das2 - package apollo.dataadapter.das2

apollo.dataadapter.debug - package apollo.dataadapter.debug

apollo.dataadapter.ensj - package apollo.dataadapter.ensj

apollo.dataadapter.ensj.controller - package apollo.dataadapter.ensj.controller

apollo.dataadapter.ensj.model - package apollo.dataadapter.ensj.model

apollo.dataadapter.ensj.view - package apollo.dataadapter.ensj.view

apollo.dataadapter.ensj19 - package apollo.dataadapter.ensj19

apollo.dataadapter.exception - package apollo.dataadapter.exception

apollo.dataadapter.flychadoxml - package apollo.dataadapter.flychadoxml

apollo.dataadapter.flygamexml - package apollo.dataadapter.flygamexml

apollo.dataadapter.gamexml - package apollo.dataadapter.gamexml

apollo.dataadapter.gbrowse - package apollo.dataadapter.gbrowse

apollo.dataadapter.genbank - package apollo.dataadapter.genbank

apollo.dataadapter.gff3 - package apollo.dataadapter.gff3

apollo.dataadapter.graph - package apollo.dataadapter.graph

apollo.dataadapter.mysql - package apollo.dataadapter.mysql

apollo.dataadapter.otter - package apollo.dataadapter.otter

apollo.dataadapter.otter.parser - package apollo.dataadapter.otter.parser

apollo.dataadapter.sample - package apollo.dataadapter.sample

apollo.dataadapter.synteny - package apollo.dataadapter.synteny

apollo.dataadapter.synteny.builder - package apollo.dataadapter.synteny.builder

apollo.datamodel - package apollo.datamodel

apollo.datamodel.seq - package apollo.datamodel.seq

apollo.editor - package apollo.editor

apollo.external - package apollo.external

apollo.gui - package apollo.gui

apollo.gui.annotinfo - package apollo.gui.annotinfo

apollo.gui.detailviewers - package apollo.gui.detailviewers

apollo.gui.detailviewers.blixem - package apollo.gui.detailviewers.blixem

apollo.gui.detailviewers.exonviewer - package apollo.gui.detailviewers.exonviewer

apollo.gui.detailviewers.seqexport - package apollo.gui.detailviewers.seqexport

apollo.gui.detailviewers.sequencealigner - package apollo.gui.detailviewers.sequencealigner

apollo.gui.detailviewers.sequencealigner.AAPanel - package apollo.gui.detailviewers.sequencealigner.AAPanel

apollo.gui.detailviewers.sequencealigner.actions - package apollo.gui.detailviewers.sequencealigner.actions

apollo.gui.detailviewers.sequencealigner.comparators - package apollo.gui.detailviewers.sequencealigner.comparators

apollo.gui.detailviewers.sequencealigner.DNAPanel - package apollo.gui.detailviewers.sequencealigner.DNAPanel

apollo.gui.detailviewers.sequencealigner.filters - package apollo.gui.detailviewers.sequencealigner.filters

apollo.gui.detailviewers.sequencealigner.listeners - package apollo.gui.detailviewers.sequencealigner.listeners

apollo.gui.detailviewers.sequencealigner.menus - package apollo.gui.detailviewers.sequencealigner.menus

apollo.gui.detailviewers.sequencealigner.overview - package apollo.gui.detailviewers.sequencealigner.overview

apollo.gui.detailviewers.sequencealigner.renderers - package apollo.gui.detailviewers.sequencealigner.renderers

apollo.gui.drawable - package apollo.gui.drawable

apollo.gui.event - package apollo.gui.event

apollo.gui.evidencepanel - package apollo.gui.evidencepanel

apollo.gui.featuretree - package apollo.gui.featuretree

apollo.gui.genomemap - package apollo.gui.genomemap

apollo.gui.menus - package apollo.gui.menus

apollo.gui.synteny - package apollo.gui.synteny

apollo.gui.tweeker - package apollo.gui.tweeker

apollo.io - package apollo.io

apollo.main - package apollo.main

apollo.seq - package apollo.seq

apollo.seq.io - package apollo.seq.io

apollo.test - package apollo.test

apollo.util - package apollo.util

apollo.util.interval - package apollo.util.interval

apollo_panel - Variable in class apollo.gui.genomemap.LinearView

ApolloAdapterException - Exception in apollo.dataadapter

ApolloAdapterException(String) - Constructor for exception apollo.dataadapter.ApolloAdapterException

ApolloAdapterException(String, Exception) - Constructor for exception apollo.dataadapter.ApolloAdapterException

ApolloAdapterException(Exception) - Constructor for exception apollo.dataadapter.ApolloAdapterException

ApolloControlServer - Class in apollo.external

this class kicks off the servlet.

ApolloControlServer() - Constructor for class apollo.external.ApolloControlServer

ApolloControlServlet - Class in apollo.external

take in http request for a location and load it - for now hardwired to game adapter loading fly actually i dont think thats true anymore - i think this just scrolls & zooms to the region if its within range, rather than causing a whole reload as reloading in apollo isnt zippy like igb so it would be too laggy url that it responds to looks something like this http://localhost:8085/ApolloControl?seqid=chr2R&start=10000&end=12000 maybe add ?organism=dmel

ApolloControlServlet() - Constructor for class apollo.external.ApolloControlServlet

ApolloDataAdapterGUI - Interface in apollo.dataadapter

ApolloDataAdapterI - Interface in apollo.dataadapter

DataAdapterI interface Used to load annotated and non-annotated data from whatever datasource Could this implement org.bdgp.io.VisualDataAdapter or are there apollo adapters with no UI?

ApolloDataI - Interface in apollo.datamodel

DataLoader returns an ApolloDataI which can be queried whether its holding a CurationSet or CompositeDataHolder, which can then be retrieved.

ApolloFrame - Class in apollo.gui

CompositeApolloFrame subclass is now the working instantiation of ApolloFrame.

ApolloFrame() - Constructor for class apollo.gui.ApolloFrame

constructor for singleton.

ApolloJalviewEventBridge - Class in apollo.gui

Converts events from apollo to jalview and vice versa

ApolloJalviewEventBridge(Controller, Controller, AlignFrame) - Constructor for class apollo.gui.ApolloJalviewEventBridge

ApolloLaundry - Class in apollo.test

ApolloLaundry() - Constructor for class apollo.test.ApolloLaundry

ApolloLayoutManager - Class in apollo.gui.genomemap

An Abstract base ApolloLayoutManager class

ApolloLayoutManager() - Constructor for class apollo.gui.genomemap.ApolloLayoutManager

ApolloLoaderI - Interface in apollo.gui

Interface for data loader to layer data on to curation set?

ApolloMetalScrollBarUI - Class in apollo.gui

ApolloMetalScrollBarUI() - Constructor for class apollo.gui.ApolloMetalScrollBarUI

ApolloNameAdapterI - Interface in apollo.config

ApolloPanel - Class in apollo.gui.genomemap

This class is a container to hold and manage the various Views which are needed by Apollo.

ApolloPanelHolderI - Interface in apollo.gui.genomemap

An interface that holds ApolloPanels.

ApolloPanelI - Interface in apollo.gui.genomemap

This was invented to eliminate all of the casting that was going on.

ApolloRunner - Class in apollo.gui

ApolloRunner() - Constructor for class apollo.gui.ApolloRunner

ApolloScrollBar - Class in apollo.gui

ApolloScrollBar() - Constructor for class apollo.gui.ApolloScrollBar

ApolloTest - Class in apollo.test

ApolloTest(String) - Constructor for class apollo.test.ApolloTest

This is for test case.

appearsToBeChadoXML(String, BufferedReader) - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter

Check whether the input appears to be chadoXML by looking for the line

appendCharacterBuffer(String) - Method in class apollo.dataadapter.otter.parser.TagHandler

appendElements(Collection<? extends T>, Collection<? super T>) - Static method in class apollo.util.CollectionUtil

Append elements from src to dest.

applyLayout(JIniFile, boolean) - Method in class apollo.gui.ApolloFrame

applyLayout(JIniFile, String, boolean) - Method in class apollo.gui.evidencepanel.EvidencePanel

applyLayout(JIniFile, boolean) - Method in class apollo.gui.evidencepanel.EvidencePanelContainer

applyLayout(JIniFile, String, boolean) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

applyLayout(JIniFile, boolean) - Method in class apollo.gui.synteny.SyntenyPanel

applyVisibilityFromLayout(JIniFile, String) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

areAnnotationViewsVisible() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

areAnyTiersLabeled() - Method in class apollo.gui.genomemap.FeatureTierManager

areAnyTiersLabeled() - Method in interface apollo.gui.genomemap.FeatureTierManagerI

areLimitsSet() - Method in class apollo.gui.genomemap.LinearView

areLimitsSet() - Method in interface apollo.gui.genomemap.ViewI

areLinksShadedByPercId() - Method in class apollo.gui.synteny.SyntenyPanel

areOpaqueLinksUsed() - Method in class apollo.gui.synteny.SyntenyPanel

areOverlapping(SeqFeatureI, SeqFeatureI) - Method in class apollo.config.NoOverlap

Just returns false

areOverlapping(SeqFeatureI, SeqFeatureI) - Method in class apollo.config.ORF_Overlap

areOverlapping(SeqFeatureI, SeqFeatureI) - Method in interface apollo.config.OverlapI

areOverlapping(SeqFeatureI, SeqFeatureI) - Method in class apollo.config.SimpleOverlap

The simple overlap checking function.

areOverlapping(SeqFeatureI, SeqFeatureI) - Method in class apollo.editor.AnnotationEditor

areOverlapping determines if two SeqFeatureIs overlap using the currently defined gene definition (from Config.getGeneDefinition().

areResultViewsVisible() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

areSameLocation(SeqFeatureI, SeqFeatureI) - Method in class apollo.dataadapter.genbank.GenbankRead

areYouSure(String) - Static method in class apollo.main.LoadUtil

Puts up a dialog asking user the question provided (which usually is some variant on "Are you sure?").

Arg - Static variable in class apollo.seq.ResidueProperties

ArrayListTransferHandler - Class in apollo.gui

ArrayListTransferHandler() - Constructor for class apollo.gui.ArrayListTransferHandler

ArrayListTransferHandler.ArrayListTransferable - Class in apollo.gui

ArrayListTransferHandler.ArrayListTransferable(ArrayList) - Constructor for class apollo.gui.ArrayListTransferHandler.ArrayListTransferable

askRenameGameConfig(String, String) - Static method in class apollo.config.Style

7/2005: Special backwards-compatibility hand-holding: game.style and game.tiers were recently renamed fly.style (which imports game.style) and fly.tiers, but some users may still have a private game.style or game.tiers in their .apollo directory.

Asn - Static variable in class apollo.seq.ResidueProperties

Asp - Static variable in class apollo.seq.ResidueProperties

ASSEMBLY_END - Static variable in class apollo.dataadapter.otter.parser.TagHandler

ASSEMBLY_START - Static variable in class apollo.dataadapter.otter.parser.TagHandler

ASSEMBLY_TYPE - Static variable in class apollo.dataadapter.otter.parser.TagHandler

AssemblyFeature - Class in apollo.datamodel

A class to represent SeqFeatures which have been mapped to a static golden path- the usual start/end is assumed to be in chromosome coords, but the assembly start/end specific to this subclass are in coords relative to the feature.

AssemblyFeature() - Constructor for class apollo.datamodel.AssemblyFeature

AssemblyFeature(int, String) - Constructor for class apollo.datamodel.AssemblyFeature

AssemblyFeatureI - Interface in apollo.datamodel

assignAnnotationName() - Method in class apollo.editor.AnnotationEditor

assignAnnotationNameAllowed() - Method in class apollo.editor.AnnotationEditor

atof(String) - Static method in class apollo.util.Format

Converts a string of digits to an double

atoi(String) - Static method in class apollo.util.Format

Converts a string of digits (decimal, octal or hex) to an integer

atol(String) - Static method in class apollo.util.Format

Converts a string of digits (decimal, octal or hex) to a long integer

attachAnnot(AnnotatedFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel

can be transcript or 1 level annot

attachAnnot(AnnotatedFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

can be transcript or 1 level annot

attachEnsemblDatabaseDropdownListener() - Method in class apollo.dataadapter.ensj19.DataSourceConfigurationPanel

attachFeatureToSequence(int, SeqFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

attachFeatureToSequence(int, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

attachListeners() - Method in class apollo.analysis.SeqAnalysisGUI

attachListeners() - Method in class apollo.gui.detailviewers.exonviewer.BaseFineEditor

attachListeners() - Method in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor

attachListeners() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerFrame

attachListeners() - Method in class apollo.gui.GenericFileAdapterGUI

attachRendererToSequence(int, BaseRenderer) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

attachRendererToTier(int, BaseRenderer) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

Attaches a new BaseRenderer to the given tier

attachTranscripts(Vector) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel

Expects a vector of Transcripts or 1 level annots.

attachTranscripts(Vector) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

Expects a vector of Transcripts or 1 level annots.

AUTHOR - Static variable in class apollo.dataadapter.otter.parser.TagHandler

AUTHOR - Static variable in class apollo.dataadapter.StateInformation

author - Variable in class apollo.editor.Transaction

AUTHOR_EMAIL - Static variable in class apollo.dataadapter.otter.parser.TagHandler

AUTHOR_EMAIL - Static variable in class apollo.dataadapter.StateInformation

autonomousHSPs(boolean) - Method in class apollo.analysis.filter.AnalysisInput

autopromote - Variable in class apollo.analysis.filter.AnalysisInput

AutoSaveThread - Class in apollo.gui

AutoSaveThread(String, int) - Constructor for class apollo.gui.AutoSaveThread

B

backBuffer - Variable in class apollo.gui.genomemap.ApolloPanel

backBufferHeight - Variable in class apollo.gui.genomemap.ApolloPanel

backBufferWidth - Variable in class apollo.gui.genomemap.ApolloPanel

backgroundColour - Variable in class apollo.gui.genomemap.LinearView

BaseAdaptor - Class in apollo.dataadapter.mysql

BaseAdaptor() - Constructor for class apollo.dataadapter.mysql.BaseAdaptor

BaseAdaptor(MySQLDatabase) - Constructor for class apollo.dataadapter.mysql.BaseAdaptor

BaseEditorPanel - Class in apollo.gui.detailviewers.exonviewer

BaseEditorPanel(GuiCurationState, BaseFineEditor, boolean, int, int, SeqFeatureI) - Constructor for class apollo.gui.detailviewers.exonviewer.BaseEditorPanel

Need lowestBase for offset of sequence

BaseEditorPanel - Class in apollo.gui.detailviewers.sequencealigner

BaseEditorPanel(GuiCurationState, BaseFineEditor, boolean, int, int, SeqFeatureI) - Constructor for class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

Need lowestBase for offset of sequence

BaseFilter<T> - Class in apollo.gui.detailviewers.sequencealigner.filters

BaseFilter() - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.BaseFilter

BaseFilter(boolean) - Constructor for class apollo.gui.detailviewers.sequencealigner.filters.BaseFilter

baseFineEditor - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel

BaseFineEditor - Class in apollo.gui.detailviewers.exonviewer

baseFineEditor - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

BaseFineEditor - Class in apollo.gui.detailviewers.sequencealigner

BaseFineEditorHorizontalColHeader - Class in apollo.gui.detailviewers.sequencealigner

Draws the horizontal header at the top of the EDE which displays the base number which is currently in view.

BaseFineEditorHorizontalColHeader(BaseEditorPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.BaseFineEditorHorizontalColHeader

BaseFineEditorRowHeader - Class in apollo.gui.detailviewers.exonviewer

BaseFineEditorRowHeader(BaseEditorPanel) - Constructor for class apollo.gui.detailviewers.exonviewer.BaseFineEditorRowHeader

BaseFineEditorRowHeader - Class in apollo.gui.detailviewers.sequencealigner

BaseFineEditorRowHeader(BaseEditorPanel) - Constructor for class apollo.gui.detailviewers.sequencealigner.BaseFineEditorRowHeader

BaseFocusEvent - Class in apollo.gui.event

BaseFocusEvent(Object, int, SeqFeatureI) - Constructor for class apollo.gui.event.BaseFocusEvent

Constructor for position focus event, request to center on focus

BaseFocusEvent(Object, Region) - Constructor for class apollo.gui.event.BaseFocusEvent

BaseFocusListener - Interface in apollo.gui.event

BaseGFFAdapter - Class in apollo.dataadapter

I'm a variant of a GFFAdapter that does NO translation of the features I read into sets of features (ie no post-processing of the data).

BaseGFFAdapter(String) - Constructor for class apollo.dataadapter.BaseGFFAdapter

BaseGFFAdapter() - Constructor for class apollo.dataadapter.BaseGFFAdapter

BASEPAIR_RANGE - Static variable in class apollo.dataadapter.DataInputType

basepairRangeToPixelRange(RangeI) - Method in class apollo.gui.Transformer

This takes care of doing the inclusion at the end of base pair ranges and compensates for xOrientation.

basePairToPos(int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

basePairToPos(int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

basePairToTierPosition(int) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel

Converts from base pair to tier position

BaseRenderer - Interface in apollo.gui.detailviewers.exonviewer

BaseRenderer - Interface in apollo.gui.detailviewers.sequencealigner.renderers

BaseRendererFactory - Class in apollo.gui.detailviewers.sequencealigner

BaseRendererFactory() - Constructor for class apollo.gui.detailviewers.sequencealigner.BaseRendererFactory

BaseRendererI - Interface in apollo.gui.detailviewers.sequencealigner.renderers

BaseScrollable - Interface in apollo.gui

BasicWindowListener - Class in apollo.gui.event

BasicWindowListener() - Constructor for class apollo.gui.event.BasicWindowListener

BEFORE_LOAD - Static variable in class apollo.gui.event.LazyLoadEvent

beforeFivePrimeEnd(SeqFeatureI) - Method in class apollo.datamodel.FeatureSet

Returns true if the feature passed in has a 3 prime end that is more 5prime than this feature.

beginTierDrag(MouseEvent) - Method in class apollo.gui.genomemap.FeatureView

beginTierDrag(MouseEvent) - Method in class apollo.gui.genomemap.TierView

beginTierDrag(MouseEvent) - Method in interface apollo.gui.genomemap.TierViewI

Start a tier drag

beginTransaction() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Begin a transaction using the current JDBC Connection.

bgColor - Static variable in class apollo.gui.annotinfo.FeatureEditorDialog

bgColor - Static variable in class apollo.gui.detailviewers.seqexport.SeqExport

binarySearch(Vector, Comparator, Object, boolean) - Static method in class apollo.util.SeqFeatureUtil

biotype - Variable in class apollo.datamodel.SeqFeature

BIOTYPE - Static variable in class apollo.gui.DetailInfo

BLACK - Static variable in class apollo.util.interval.RbNode

blankLine(String) - Method in class apollo.config.TiersIO

BlastFilterPanel - Class in apollo.analysis.filter

BlastFilterPanel(Color) - Constructor for class apollo.analysis.filter.BlastFilterPanel

BlastHandler - Class in apollo.analysis

BlastHandler() - Constructor for class apollo.analysis.BlastHandler

BlastParser - Class in apollo.dataadapter.analysis

BlastParser() - Constructor for class apollo.dataadapter.analysis.BlastParser

BlastXMLParser - Class in apollo.analysis

BlastXMLParser() - Constructor for class apollo.analysis.BlastXMLParser

BlastXMLParser.BlastXMLParserException - Exception in apollo.analysis

BlastXMLParser.BlastXMLParserException(String) - Constructor for exception apollo.analysis.BlastXMLParser.BlastXMLParserException

BlastXMLParserTest - Class in apollo.analysis

BlastXMLParserTest() - Constructor for class apollo.analysis.BlastXMLParserTest

BlatParser - Class in apollo.dataadapter.analysis

BlatParser() - Constructor for class apollo.dataadapter.analysis.BlatParser

BlixemRunner - Class in apollo.gui.detailviewers.blixem

BlixemRunner(CurationSet, Vector, int, int) - Constructor for class apollo.gui.detailviewers.blixem.BlixemRunner

blueGreen - Static variable in class apollo.config.FeatureProperty

BookmarkMenu - Class in apollo.gui.menus

This menu allows for the bookmarking of annots.

bop - Class in apollo.bop

bop() - Constructor for class apollo.bop.bop

BopException - Exception in apollo.dataadapter.exception

BopException() - Constructor for exception apollo.dataadapter.exception.BopException

BopException(String) - Constructor for exception apollo.dataadapter.exception.BopException

BopException(String, String) - Constructor for exception apollo.dataadapter.exception.BopException

BopException(String, Exception) - Constructor for exception apollo.dataadapter.exception.BopException

BopException(String, String, Exception) - Constructor for exception apollo.dataadapter.exception.BopException

BOTH - Static variable in class apollo.gui.genomemap.ApolloLayoutManager

BOTHENDS - Static variable in interface apollo.gui.drawable.DrawableAnnotationConstants

Indicates both ends of a feature.

boxBounds - Variable in class apollo.gui.drawable.DrawableSeqFeature

Allocate a rectangle to put bounding box in because instantiation // is so slow.

breakSingle(String) - Static method in class apollo.dataadapter.genbank.GenbankFormatter

Formats a string so that it does not run beyond a specified line length.

breakSingle(String, int) - Static method in class apollo.dataadapter.genbank.GenbankFormatter

brown - Static variable in class apollo.config.FeatureProperty

browseButton - Variable in class apollo.gui.GenericFileAdapterGUI

browseFiles(JComboBox) - Method in class apollo.dataadapter.genbank.GenbankAdapterGUI

Called from browse button, sets browser with currently selected path if there is one, and then calls browser to get a file.

browseFiles(JComboBox) - Method in class apollo.gui.GenericFileAdapterGUI

Called from browse button, sets browser with currently selected path if there is one, and then calls browser to get a file

BUFFER_SIZE - Static variable in class apollo.dataadapter.synteny.SyntenyComparaAdapter

buildEditList() - Method in class apollo.datamodel.FeatureSet

buildEditList() - Method in interface apollo.datamodel.FeatureSetI

BuilderAdapter - Class in apollo.dataadapter.synteny.builder

BuilderAdapter() - Constructor for class apollo.dataadapter.synteny.builder.BuilderAdapter

BuilderAdapterGUI - Class in apollo.dataadapter.synteny.builder

BuilderAdapterGUI(IOOperation, Model) - Constructor for class apollo.dataadapter.synteny.builder.BuilderAdapterGUI

BuilderAdapterGUI.ModelChangeListener - Class in apollo.dataadapter.synteny.builder

BuilderAdapterGUI.ModelChangeListener() - Constructor for class apollo.dataadapter.synteny.builder.BuilderAdapterGUI.ModelChangeListener

buildFeatures(StrandedFeatureSet, Hashtable, int, PropertyScheme) - Method in class apollo.dataadapter.FeatureSetBuilder

buildFeaturesHash(Vector, Hashtable, Hashtable) - Method in class apollo.dataadapter.ensj.EnsJFeatureSetBuilder

buildFeaturesHash(Vector, Hashtable, Hashtable) - Method in class apollo.dataadapter.FeatureSetBuilder

buildGUI() - Method in class apollo.analysis.filter.BlastFilterPanel

buildGUI() - Method in class apollo.analysis.filter.GenscanFilterPanel

buildGUI() - Method in class apollo.analysis.filter.NoFilterPanel

buildGUI() - Method in class apollo.analysis.filter.Sim4FilterPanel

buildGUI() - Method in class apollo.analysis.SeqAnalysisGUI

buildGUI() - Method in class apollo.dataadapter.analysis.AnalysisPanel

buildGUI() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI

buildGUI() - Method in class apollo.dataadapter.EnsCGIAdapterGUI

buildGUI() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI

buildGUI() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI

buildGUI() - Method in class apollo.dataadapter.FileTabPanel

Add in browse button

buildGUI() - Method in class apollo.dataadapter.flychadoxml.LocationChadoPanel

buildGUI() - Method in class apollo.dataadapter.flygamexml.LocationGAMEPanel

buildGUI() - Method in class apollo.dataadapter.GbrowseAdapterGUI

buildGUI() - Method in class apollo.dataadapter.gff3.GFF3AdapterGUI

buildGUI() - Method in class apollo.dataadapter.GFFAdapterGUI

buildGUI() - Method in class apollo.dataadapter.graph.GraphAdapterGUI

buildGUI() - Method in class apollo.dataadapter.GuiTabPanel

buildGUI() - Method in class apollo.dataadapter.otter.OtterAdapterGUI

buildGUI() - Method in class apollo.dataadapter.otter.OtterXMLAdapterGUI

buildGUI() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI

buildGUI() - Method in class apollo.gui.GenericFileAdapterGUI

buildGUI() - Method in class apollo.gui.ProgressFrame

buildGUI() - Method in class apollo.gui.SliderWindow

buildGUIForReading() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI

buildGUIForReading() - Method in class apollo.dataadapter.genbank.GenbankAdapterGUI

Loops through TabPanels and inserts into tabbed pane, Also hafta add our own buttons, since DataAdapterChooser does not add buttons for AbstractIntDataAdapUIs although i think there should be a way for an AbstractIntDAI to say hey i want those buttons like boolean addOKCancelButtons()

buildGUIForWriting() - Method in class apollo.dataadapter.genbank.GenbankAdapterGUI

buildIncludePanel() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI

buildLocationPanel() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI

buildMenu() - Method in class apollo.gui.menus.FileMenu

buildmRNAEditList() - Method in class apollo.datamodel.SeqFeature

buildORFEditList() - Method in class apollo.datamodel.FeatureSet

buildPAM() - Static method in class apollo.seq.ResidueProperties

C

c - Variable in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer

c - Variable in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer

cacheAnalysisTable() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance

cacher - Variable in class apollo.datamodel.seq.AbstractLazySequence

CacheSeqIdLoader - Class in apollo.datamodel.seq

This presently will only work with parent as GAMESequence.

CacheSeqIdLoader(GAMESequence) - Constructor for class apollo.datamodel.seq.CacheSeqIdLoader

CacheSequenceLoader - Class in apollo.datamodel.seq

CacheSequenceLoader(LazySequenceI) - Constructor for class apollo.datamodel.seq.CacheSequenceLoader

CacheSequenceLoader.SequenceRange - Class in apollo.datamodel.seq

CacheSequenceLoader.SequenceRange(String, int, int) - Constructor for class apollo.datamodel.seq.CacheSequenceLoader.SequenceRange

cacheUI(IOOperation, DataAdapterUI) - Method in class apollo.dataadapter.AbstractApolloAdapter

calcTickInterval(int[]) - Static method in class apollo.gui.genomemap.PlotUtil

calcTickInterval(int[], Graphics, Transformer, Vector) - Static method in class apollo.gui.genomemap.PlotUtil

calcTranslationStartForLongestPeptide() - Method in class apollo.datamodel.FeatureSet

This sets the start at a standard start codon that gives the longest peptide (which may not be the first start codon).

calcTranslationStartForLongestPeptide() - Method in interface apollo.datamodel.TranslationI

calculateHighlightRect(StrandedZoomableApolloPanel.HighlightWrapper) - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

calculateTierNumber(Point) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanelHeaderTable

Calculates the tier number for a given point

canAddFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.HomogeneousPanel

canAddFeature(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel

canBeAddedToSequence(SeqWrapper, SeqFeatureI) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

Checks if there are any overlaps between features in sw and feature, if so return false, else true

cancelCellEditing() - Method in class apollo.gui.DisabledEditor

canHandleSelection(FeatureSelectionEvent, Object) - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

Does all the handle selection checks

canHaveChildren() - Method in class apollo.datamodel.Exon

canHaveChildren() - Method in class apollo.datamodel.FeatureSet

This method determines if there are any child SeqFeatures in this set (FeatureSets are NOT included).

canHaveChildren() - Method in class apollo.datamodel.Range

If SeqFeature is an instanceof FeatureSetI and FeatureSetI.hasChildFeatures is true then true.

canHaveChildren() - Method in interface apollo.datamodel.RangeI

If RangeI is an instanceof FeatureSetI and FeatureSetI.hasChildFeatures is true then return true.

canImport(JComponent, DataFlavor[]) - Method in class apollo.gui.ArrayListTransferHandler

canRender(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer

canRender(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.ResultRenderer

canRender(SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer

canWriteData() - Method in class apollo.dataadapter.AbstractApolloAdapter

Whether write operation is supported by data adapter

canWriteData() - Method in interface apollo.dataadapter.ApolloDataAdapterI

Whether write operation is supported by data adapter

canWriteToDirectory(String) - Static method in class apollo.util.IOUtil

Check whether specified directory is writeable

CaseInsensitiveStringHash - Class in apollo.util

CaseInsensitiveStringHash(int, float) - Constructor for class apollo.util.CaseInsensitiveStringHash

CaseInsensitiveStringHash(int) - Constructor for class apollo.util.CaseInsensitiveStringHash

CaseInsensitiveStringHash() - Constructor for class apollo.util.CaseInsensitiveStringHash

cDNA - Variable in class apollo.datamodel.Transcript

CDNA_NAME - Static variable in class apollo.editor.TransactionSubpart

CDS_END_NOT_FOUND - Static variable in class apollo.dataadapter.otter.parser.TagHandler

CDS_START_NOT_FOUND - Static variable in class apollo.dataadapter.otter.parser.TagHandler

CENTER_OUTLINE - Static variable in class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer

CENTER_OUTLINE - Static variable in class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer

CENTER_OUTLINE - Static variable in class apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer

centerOnScreen(Component) - Static method in class apollo.gui.ApolloFrame

centers component on screen - put in a util class?

certainly_bad - Static variable in class apollo.analysis.filter.TwilightFilter

certainly_good - Static variable in class apollo.analysis.filter.TwilightFilter

CGI - Class in apollo.dataadapter

CGI(String, int, String, Hashtable, PrintStream, String) - Constructor for class apollo.dataadapter.CGI

CGI(String, int, String, Hashtable, PrintStream) - Constructor for class apollo.dataadapter.CGI

CGI(String, int, String, PrintStream) - Constructor for class apollo.dataadapter.CGI

CGI(String, String, PrintStream) - Constructor for class apollo.dataadapter.CGI

CHADO_DB - Static variable in class apollo.dataadapter.chado.ChadoAdapter

chado_dbs - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI

List of Chado databases read by the ChadoAdapter from its configuration file.

ChadoAdapter - Class in apollo.dataadapter.chado

A data adapter that allows Apollo to communicate with a Chado-compliant relational database.

ChadoAdapter() - Constructor for class apollo.dataadapter.chado.ChadoAdapter

ChadoAdapterGUI - Class in apollo.dataadapter.chado

In the Apollo data adapter specification each data adapter has two parts: a class that implements the graphical user interface, and a class that interacts with the data source (as directed by the user via the GUI).

ChadoAdapterGUI(IOOperation, ChadoDatabase[]) - Constructor for class apollo.dataadapter.chado.ChadoAdapterGUI

ChadoAdHocFlatFileWriter - Class in apollo.dataadapter.chado

Writes a curation set to an ad-hoc chado-based flat file format.

ChadoAdHocFlatFileWriter() - Constructor for class apollo.dataadapter.chado.ChadoAdHocFlatFileWriter

ChadoDatabase - Class in apollo.dataadapter.chado

Connection and configuration information for a Chado database.

ChadoDatabase() - Constructor for class apollo.dataadapter.chado.ChadoDatabase

Default constructor.

ChadoDatabase(String, String, String, String, String, String) - Constructor for class apollo.dataadapter.chado.ChadoDatabase

chadoDb - Variable in class apollo.dataadapter.chado.ChadoDatabase

Name of the specific Chado database instance/schema on the database server.

chadoDb - Variable in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Schema/database name of the Chado database instance.

chadoDbPrompt - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI

chadoDbTextField - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI

chadoFeatureExists(Connection, String, String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Check whether a particular feature exists in a given Chado database.

chadoFeatureExists(Connection, String, String, StringBuilder) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Check whether a particular feature exists in a given Chado database.

ChadoInstance - Interface in apollo.dataadapter.chado.jdbc

An interface whose goal is to capture all the observed differences between disparate sites' (e.g., FlyBase, TIGR) chado database usage.

ChadoJdbcNameAdapter - Class in apollo.config

ChadoJdbcNameAdapter() - Constructor for class apollo.config.ChadoJdbcNameAdapter

ChadoProgram - Class in apollo.dataadapter.chado.jdbc

A set of chado.analysis rows that have the same value in their 'program' column.

ChadoProgram(String, String, String, boolean) - Constructor for class apollo.dataadapter.chado.jdbc.ChadoProgram

ChadoProgram(String, boolean) - Constructor for class apollo.dataadapter.chado.jdbc.ChadoProgram

ChadoProgram(String) - Constructor for class apollo.dataadapter.chado.jdbc.ChadoProgram

ChadoTransaction - Class in apollo.dataadapter.chado

Class that represents the chado XML counterpart of an Apollo transaction.

ChadoTransaction() - Constructor for class apollo.dataadapter.chado.ChadoTransaction

ChadoTransaction.Operation - Class in apollo.dataadapter.chado

INNER CLASS Operation

ChadoTransactionTransformer - Class in apollo.dataadapter.chado

This class is used to translate Apollo Transaction objects to Chado Transaction objects.

ChadoTransactionTransformer() - Constructor for class apollo.dataadapter.chado.ChadoTransactionTransformer

ChadoTransactionXMLTemplate - Class in apollo.dataadapter.chadoxml

This class is used to process xml template for transactions.

ChadoTransactionXMLTemplate(String) - Constructor for class apollo.dataadapter.chadoxml.ChadoTransactionXMLTemplate

ChadoTransactionXMLTemplate(String, String, String) - Constructor for class apollo.dataadapter.chadoxml.ChadoTransactionXMLTemplate

ChadoTransactionXMLWriter - Class in apollo.dataadapter.chadoxml

This class is used to write Transaction objects to Chado transaction XML.

ChadoTransactionXMLWriter() - Constructor for class apollo.dataadapter.chadoxml.ChadoTransactionXMLWriter

Default constructor

ChadoUpdateTransaction - Class in apollo.dataadapter.chado

ChadoUpdateTransaction() - Constructor for class apollo.dataadapter.chado.ChadoUpdateTransaction

ChadoUpdateTransaction(String, String) - Constructor for class apollo.dataadapter.chado.ChadoUpdateTransaction

chadoVersion - Variable in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Chado schema version - should this be merged with chado instance?

ChadoXmlAdapter - Class in apollo.dataadapter.chadoxml

A FlyBase-specific reader for Chado XML files.

ChadoXmlAdapter() - Constructor for class apollo.dataadapter.chadoxml.ChadoXmlAdapter

Must have empty constructor to work with org.bdgp.io.DataAdapterRegistry instance creation from config string

ChadoXmlAdapterGUI - Class in apollo.dataadapter.chadoxml

ChadoXmlUtils - Class in apollo.dataadapter.chadoxml

ChadoXmlUtils() - Constructor for class apollo.dataadapter.chadoxml.ChadoXmlUtils

ChadoXmlWrite - Class in apollo.dataadapter.chadoxml

ChadoXmlWrite: writes Chado XML to a file.

ChadoXmlWrite() - Constructor for class apollo.dataadapter.chadoxml.ChadoXmlWrite

ChainedRepaintEvent - Class in apollo.gui.event

ChainedRepaintEvent(Object) - Constructor for class apollo.gui.event.ChainedRepaintEvent

ChainedRepaintListener - Interface in apollo.gui.event

CHANGE_DATABASE - Static variable in class apollo.dataadapter.ensj.controller.Controller

ChangeDatabaseHandler - Class in apollo.dataadapter.ensj.controller

The user has typed into the host, port etc database fields, so we clear off the ensembl-db list selected ensembl-db.

ChangeDatabaseHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.ChangeDatabaseHandler

changeEnd(SeqFeatureI, int, int, int) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel

changeEnd(SeqFeatureI, int, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

ChangeList - Class in apollo.editor

TransactionManager does the real coalescing for saving transactions.

ChangeList(Controller) - Constructor for class apollo.editor.ChangeList

for gene edit panel

changeStart(SeqFeatureI, int, int, int) - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel

changeStart(SeqFeatureI, int, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

changeTierHeight(int) - Method in class apollo.gui.genomemap.AnnotationView

changeTierHeight(int) - Method in class apollo.gui.genomemap.TierView

changeTierHeights(int) - Method in class apollo.gui.genomemap.ApolloPanel

changeTypeColor(FeatureView, Selection) - Method in class apollo.gui.genomemap.FeatureTierManager

Pop up the color chooser for the selected feature type

changeYOrientation() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

characters(char[], int, int) - Method in class apollo.dataadapter.das.simple.DASDsnContentHandler

characters(char[], int, int) - Method in class apollo.dataadapter.das.simple.DASEntryPointContentHandler

characters(char[], int, int) - Method in class apollo.dataadapter.das.simple.DASFeatureContentHandler

characters(char[], int, int) - Method in class apollo.dataadapter.das.simple.DASSequenceContentHandler

characters(char[], int, int) - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser

implementing sax handler interface

characters(char[], int, int) - Method in class apollo.dataadapter.das2.SegmentParser

characters(char[], int, int) - Method in class apollo.dataadapter.das2.SourceParser

characters(char[], int, int) - Method in class apollo.dataadapter.gamexml.XMLParser

characters(char[], int, int) - Method in class apollo.dataadapter.otter.parser.OtterContentHandler

charAt(int) - Method in class apollo.gui.detailviewers.sequencealigner.Tier

Returns the base on the reference sequence for a given position

charAt(int) - Method in interface apollo.gui.detailviewers.sequencealigner.TierI

charHeight - Variable in class apollo.gui.TierManager

checkAdjacent(Transcript, Vector) - Method in class apollo.editor.AnnotationEditor

Determines if two exons are adjacent to one another in the transcript.

checkBoolean(String, String) - Method in class apollo.config.Style

checkCuration(CurationSet, DataOutputStream) - Method in class apollo.dataadapter.genbank.GenbankValidator

Writing G

checkFeature(FeatureSetI, String, String) - Method in class apollo.dataadapter.genbank.GenbankValidator

checkFocusDrivenEdits() - Method in class apollo.gui.annotinfo.FeatureEditPanel

Focus driven edits occur in textboxes -> synonyms, names, and ids.

checkFocusDrivenEdits() - Method in class apollo.gui.annotinfo.GeneEditPanel

Focus driven edits occur in textboxes -> synonyms, names, and ids.

checkForLocation(DataInput) - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance

If dataInput is a location, change its SO type to be getLocationSeqType()

checkFormat(SeqFeatureI, String) - Method in interface apollo.config.ApolloNameAdapterI

Returns true if id jibes with seq feature's ID format.

checkFormat(SeqFeatureI, String) - Method in class apollo.config.ChadoJdbcNameAdapter

Returns true if id jibes with seq feature's ID format.

checkFormat(SeqFeatureI, String) - Method in class apollo.config.DefaultNameAdapter

Returns true if seq feature's ID format is ok.

checkFormat(SeqFeatureI, String) - Method in class apollo.config.ParameciumNameAdapter

Returns true if id jibes with seq feature's ID format.

checkFormat(SeqFeatureI, String) - Method in class apollo.config.TigrAnnotNameAdapter

checkFreeMemory() - Method in class apollo.gui.CheckMemoryThread

CheckMemoryThread - Class in apollo.gui

CheckMemoryThread(long) - Constructor for class apollo.gui.CheckMemoryThread

checkName(String, Class) - Method in interface apollo.config.ApolloNameAdapterI

checkName(String, Class) - Method in class apollo.config.ChadoJdbcNameAdapter

checkName(String, Class) - Method in class apollo.config.DefaultNameAdapter

checkName(String, Class) - Method in class apollo.config.ParameciumNameAdapter

checkName(String, Class) - Method in class apollo.config.TigrAnnotNameAdapter

checkRefFeatures(FeatureSetI) - Static method in class apollo.dataadapter.debug.DisplayTool

checkValidColor(String, String) - Method in class apollo.config.Style

child_0 - Variable in class apollo.analysis.filter.HuffNode

child_1 - Variable in class apollo.analysis.filter.HuffNode

CHILD_TYPE - Static variable in class apollo.dataadapter.synteny.builder.AdapterModel

childrenReady(SeqFeatureI) - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser

Returns true if all children of this feature have already been read in

CHIMERA_GAP - Static variable in class apollo.analysis.filter.AnalysisFilter

chooseTab(String) - Method in class apollo.dataadapter.flychadoxml.FlyChadoXmlAdapterGUI

chooseTab(String) - Method in class apollo.dataadapter.flygamexml.FlyGAMEAdapterGUI

CHROMOSOME - Static variable in class apollo.dataadapter.otter.parser.TagHandler

Chromosome - Class in apollo.datamodel

Chromosome(String, String, Vector) - Constructor for class apollo.datamodel.Chromosome

Chromosome(String, String, int) - Constructor for class apollo.datamodel.Chromosome

Chromosome(String, String, int, int, int) - Constructor for class apollo.datamodel.Chromosome

chromosome - Variable in class apollo.datamodel.GenomicRange

ChromosomeAdapter - Class in apollo.dataadapter

ChromosomeAdapter(String) - Constructor for class apollo.dataadapter.ChromosomeAdapter

ChromosomeAdapter() - Constructor for class apollo.dataadapter.ChromosomeAdapter

ChromosomeBand - Class in apollo.datamodel

ChromosomeBand(String, String, int, int, String) - Constructor for class apollo.datamodel.ChromosomeBand

ChromosomeDrawer - Class in apollo.dataadapter.synteny

ChromosomeDrawer(Chromosome, Vector, Hashtable, boolean) - Constructor for class apollo.dataadapter.synteny.ChromosomeDrawer

ChromosomeField - Class in apollo.gui

Chromsome field is either a combo box or text field depending on if config has a chromosome vector

ChromosomeField() - Constructor for class apollo.gui.ChromosomeField

ChromosomeField(Vector) - Constructor for class apollo.gui.ChromosomeField

ChromosomePanel - Class in apollo.dataadapter.synteny

ChromosomePanel(Chromosome, Vector) - Constructor for class apollo.dataadapter.synteny.ChromosomePanel

ChromosomePanel(Chromosome, Vector, StatusBar) - Constructor for class apollo.dataadapter.synteny.ChromosomePanel

ChromosomePanel(Chromosome, Vector, Hashtable, StatusBar) - Constructor for class apollo.dataadapter.synteny.ChromosomePanel

ChromosomePanel(Chromosome, Vector, Hashtable, StatusBar, AbstractDataAdapterUI, String, String) - Constructor for class apollo.dataadapter.synteny.ChromosomePanel

CigarUtil - Class in apollo.util

CigarUtil() - Constructor for class apollo.util.CigarUtil

CLASS - Static variable in class apollo.dataadapter.synteny.builder.Model

clean() - Method in class apollo.dataadapter.gamexml.XMLParser

cleanUp(CurationSet, String, AnalysisInput) - Method in class apollo.analysis.filter.AnalysisFilter

cleanUp(CurationSet, String, AnalysisInput) - Method in interface apollo.analysis.filter.AnalysisFilterI

All filters on computed results must support this interface.

cleanUp(Vector, FeatureSetI, FeatureSetI, int, AnalysisFilter) - Static method in class apollo.analysis.filter.Coverage

cleanUp() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

cleanup extra components when closing down

cleanupByType(FeatureSetI, String) - Method in class apollo.analysis.filter.AnalysisFilter

Experimental--not currently being used.

cleanUpTwilightZone(FeaturePairI, FeaturePairI, boolean, boolean) - Method in class apollo.analysis.filter.TwilightFilter

clear() - Method in class apollo.datamodel.LinkSet

clear() - Method in class apollo.editor.TransactionManager

clear(boolean) - Method in class apollo.gui.Controller

Clear called by handleDataLoadEvent with clearOnDataLoadEvent set to true, for species controllers not master controllers also called by CurationState when removed

clear() - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

clear() - Method in class apollo.gui.detailviewers.sequencealigner.MultiTierPanel

clear() - Method in class apollo.gui.detailviewers.sequencealigner.overview.IntervalComponent

clear() - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

clear() - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel

clear() - Method in class apollo.gui.detailviewers.sequencealigner.Tier

clear() - Method in interface apollo.gui.detailviewers.sequencealigner.TierI

clear() - Method in class apollo.gui.evidencepanel.EvidencePanelContainer

clear(boolean) - Method in class apollo.gui.genomemap.AnnotationView

clear() - Method in class apollo.gui.genomemap.FeatureView

sets internal vars to null: fset, dfset, visibleDrawables, graphics should it set them to empty vectors instead of null? T

clear(boolean) - Method in class apollo.gui.genomemap.FeatureView

clear() - Method in class apollo.gui.genomemap.GraphView

clear() - Method in class apollo.gui.genomemap.LinearView

clear() - Method in class apollo.gui.genomemap.ManagedView

clear(boolean) - Method in class apollo.gui.genomemap.ResultView

Clear out mem leaks

clear() - Method in class apollo.gui.genomemap.ScaleView

clear() - Method in class apollo.gui.genomemap.TierView

clear() - Method in interface apollo.gui.genomemap.ViewI

clear() - Method in class apollo.gui.menus.AnnotationMenu

Clean up dangling references (mem leaks)

clear() - Method in class apollo.gui.menus.TierPopupMenu

Clean up dangling references (mem leaks)

clear() - Method in class apollo.gui.Selection

This does deselection.

clear() - Method in class apollo.util.CaseInsensitiveStringHash

CLEAR_EDIT - Static variable in interface apollo.datamodel.SequenceI

I question if CLEAR_EDIT shouold be a separate type - its just a deletion of the above types - refactor?

CLEAR_SEQ_REGIONS - Static variable in class apollo.dataadapter.ensj.controller.Controller

clearActionListeners() - Method in class apollo.dataadapter.synteny.builder.Controller

clearAll() - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser

clearAnnotations() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel

clearAnnotations() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel

clearAnnotations() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

removes all the annotations from the annotation list and the annotation panel

clearCache() - Method in class apollo.datamodel.seq.CacheSequenceLoader

clearComments() - Method in class apollo.datamodel.AnnotatedFeature

clearComments() - Method in interface apollo.datamodel.AnnotatedFeatureI

clearCutSites() - Method in class apollo.gui.genomemap.ScaleView

clearData() - Method in interface apollo.gui.genomemap.ApolloPanelHolderI

clearData() - Method in class apollo.gui.genomemap.StrandedZoomableApolloPanel

clearEdges() - Method in class apollo.gui.genomemap.ApolloPanel

clearEdges() - Method in class apollo.gui.genomemap.FeatureView

clearFeature() - Method in class apollo.dataadapter.das2.DAS2FeatureSaxParser

clearFeatures() - Method in class apollo.gui.genomemap.DrawableTierManager

Clears features from tiers, and clear tiers

clearFeatures() - Method in interface apollo.gui.genomemap.FeatureTierManagerI

clearFeatures() - Method in class apollo.gui.genomemap.FeatureView

just clears out features from view

clearFindsButton - Variable in class apollo.gui.detailviewers.exonviewer.BaseFineEditor

clearFindsButton - Variable in class apollo.gui.detailviewers.sequencealigner.BaseFineEditor

clearHighlights() - Method in class apollo.gui.genomemap.FeatureView

clearKids() - Method in class apollo.datamodel.FeatureSet

clearKids() - Method in class apollo.datamodel.SeqFeature

by default no kids - no-op

clearKids() - Method in interface apollo.datamodel.SeqFeatureI

clear out allkids - if have any

clearLog4JDiagnosticContext() - Static method in class apollo.main.Apollo

Clears/removes the Log4J Nested Diagnostic Context (NDC) for a Thread.

clearOldData() - Method in class apollo.dataadapter.AbstractApolloAdapter

This has to be called in the subclass.getCurationSet (super.clearOldData()) to do the new data notification(clears old features) - also it notifies Config of style change.

clearProperties() - Method in class apollo.datamodel.SeqFeature

clearProperties() - Method in interface apollo.datamodel.SeqFeatureI

clearProperties() - Method in class apollo.datamodel.Synonym

clearRect(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics

clearResidues() - Method in class apollo.datamodel.AbstractSequence

sets residues to empty string

clearResidues() - Method in class apollo.datamodel.Sequence

clearResidues() - Method in interface apollo.datamodel.SequenceI

clears out residues (set to empty string)

clearResults() - Method in class apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel

clearResults() - Method in class apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel

clearResults() - Method in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

removes all of the results from the results list and the result panel

clearSelected() - Method in class apollo.gui.genomemap.Sites

clearSelection() - Method in class apollo.gui.genomemap.ApolloPanel

clearSelection() - Method in interface apollo.gui.genomemap.ApolloPanelI

clearSelections() - Method in class apollo.gui.genomemap.SiteView

Clear all selections in all Sites

clearSelections() - Method in class apollo.gui.SelectionManager

clear() is called on the currently selected Selection.

clearSeqChoiceComboBox() - Method in class apollo.dataadapter.chado.ChadoAdapterGUI

Reset the seqChoiceComboBox to its original state; called when the current database changes.

ClearSeqRegionsHandler - Class in apollo.dataadapter.ensj.controller

The user has selected a new coordinate system, so I flush the known seq-regions and update.

ClearSeqRegionsHandler(Controller, String) - Constructor for class apollo.dataadapter.ensj.controller.ClearSeqRegionsHandler

clearSites() - Method in class apollo.gui.genomemap.Sites

clearStateInformation() - Method in class apollo.dataadapter.AbstractApolloAdapter

This SHOULD reset all the contents of the stateInformation being held by an adapter: with setStateInformation, this is not guaranteed.

clearStateInformation() - Method in class apollo.dataadapter.BaseGFFAdapter

clearStateInformation() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter

clearStateInformation() - Method in class apollo.dataadapter.das2.DAS2Adapter

clearStateInformation() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter

clearStateInformation() - Method in class apollo.dataadapter.ensj19.EnsJAdapter

clearStateInformation() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapter

clearStateInformation() - Method in class apollo.dataadapter.synteny.SyntenyAdapter

Does nothing yet, because the state info isn't being used on this adapter yet.

clearSynonyms() - Method in class apollo.datamodel.AnnotatedFeature

clearSynonyms() - Method in interface apollo.datamodel.AnnotatedFeatureI

clearSynonyms() - Method in class apollo.datamodel.Identifier

clearTransactions() - Method in class apollo.editor.AnnotationChangeLog

if new data is loaded transactions need to be cleared out.

clip - Variable in class apollo.gui.genomemap.FastClippingGraphics

ClipboardUtil - Class in apollo.util

ClipboardUtil() - Constructor for class apollo.util.ClipboardUtil

clipRect(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics

clone() - Method in class apollo.config.ColumnProperty

clone() - Method in class apollo.config.FeatureProperty

this needs to be a deep clone not a shallow one

clone() - Method in class apollo.config.TierProperty

clone() - Method in class apollo.datamodel.AnnotatedFeature

clone() - Method in class apollo.datamodel.Comment

to get a field-by-field replica of this feature

clone() - Method in class apollo.datamodel.FeatureSet

to get a field-by-field replica of this feature

clone() - Method in class apollo.datamodel.Identifier

clone() - Method in class apollo.datamodel.SeqFeature

to get a field-by-field replica of this feature

clone() - Method in interface apollo.datamodel.SeqFeatureI

to get a field-by-field replica of this feature

clone() - Method in class apollo.gui.Transformer

cloneAnnot() - Method in class apollo.datamodel.AnnotatedFeature

cloneAnnot() - Method in interface apollo.datamodel.AnnotatedFeatureI

cloneComment() - Method in class apollo.datamodel.Comment

cloneFeature() - Method in class apollo.datamodel.SeqFeature

cloneFeature() - Method in interface apollo.datamodel.SeqFeatureI

clones feature

cloneInstance() - Method in interface apollo.dataadapter.chado.jdbc.ChadoInstance

cloneList() - Method in class apollo.util.FeatureList

Returns a FeatureList that contains seq feature clones of all features in current list.

cloneSynonym() - Method in class apollo.datamodel.Synonym

close() - Method in class apollo.dataadapter.CGI

close() - Method in interface apollo.gui.EditWindowI

closeConnection(Connection) - Method in class apollo.dataadapter.ensj.controller.EventHandler

closeMode() - Method in class apollo.dataadapter.otter.parser.OtterContentHandler

coalesce() - Method in class apollo.editor.TransactionManager

Coalesce all Transaction instances in this TransactionManager.

CODING - Static variable in interface apollo.datamodel.CodingPropertiesI

CODING_PROPERTIES - Static variable in class apollo.gui.DetailInfo

CodingPropertiesI - Interface in apollo.datamodel

codonHash - Static variable in class apollo.seq.ResidueProperties

codonTranslate(String) - Static method in class apollo.seq.ResidueProperties

coincidence - Variable in class apollo.analysis.filter.AnalysisInput

collapse - Variable in class apollo.analysis.filter.AnalysisInput

collapseAll() - Method in class apollo.gui.featuretree.FeatureTreePanel

collapseResults(boolean) - Method in class apollo.analysis.filter.AnalysisInput

collapseResults() - Method in class apollo.analysis.filter.AnalysisInput

collapseTier(String) - Method in class apollo.gui.genomemap.FeatureTierManager

collapseTier(FeatureView, ApolloPanelI) - Method in class apollo.gui.genomemap.FeatureTierManager

The next few methods are used by TierPopupMenu and AnnotationMenu

collapseTier(String) - Method in interface apollo.gui.genomemap.FeatureTierManagerI

CollectionUtil - Class in apollo.util

This class provides static utility methods for handling Collections.

CollectionUtil() - Constructor for class apollo.util.CollectionUtil

collectShadows() - Method in class apollo.gui.genomemap.DragView

colName - Variable in class apollo.dataadapter.chado.jdbc.TableColumn

color - Static variable in class apollo.gui.FindPanel

color - Variable in class apollo.util.interval.RbNode

colorAllAnnotsByOwner() - Method in class apollo.config.Style

colorIndex - Static variable in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

colorList - Static variable in class apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel

colour - Variable in class apollo.config.FeatureProperty

colourHash - Static variable in class apollo.config.FeatureProperty

cols - Variable in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

cols - Variable in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

The number of base pairs displayed in a single row

ColumnApolloLayout - Class in apollo.gui.genomemap

An ApolloLayoutManager which lays out its views in a single column.

ColumnApolloLayout() - Constructor for class apollo.gui.genomemap.ColumnApolloLayout

ColumnProperty - Class in apollo.config

ColumnProperty(String) - Constructor for class apollo.config.ColumnProperty

ColumnProperty(String, int) - Constructor for class apollo.config.ColumnProperty

ColumnProperty(ColumnProperty) - Constructor for class apollo.config.ColumnProperty

columns - Variable in class apollo.config.FeatureProperty

comboBox - Variable in class apollo.dataadapter.GuiTabPanel

CommandLine - Class in apollo.main

Class for dealing with command line options.

commandLineXmlFileFormatIsConfigged() - Static method in class apollo.config.Config

Returns true if commandLineXmlFileFormat is nonnull and is "game" or "chado"

Comment - Class in apollo.datamodel

Comment() - Constructor for class apollo.datamodel.Comment

Comment(String, String, String, long) - Constructor for class apollo.datamodel.Comment

COMMENT - Static variable in class apollo.editor.TransactionClass

COMMENT - Static variable in class apollo.editor.TransactionSubpart

comments - Variable in class apollo.config.FeatureProperty

comments - Variable in class apollo.config.TierProperty

comments - Variable in class apollo.config.TiersIO

commitAccessions(boolean) - Method in class apollo.dataadapter.genbank.GenbankAdapter

commitAddTransaction(String, AddTransaction, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

commitChanges(CurationSet) - Method in class apollo.dataadapter.AbstractApolloAdapter

commitChanges(CompositeDataHolder) - Method in class apollo.dataadapter.AbstractApolloAdapter

SyntenyAdapter and SerialDiskAdapter override this

commitChanges(Object) - Method in class apollo.dataadapter.AbstractApolloAdapter

commitChanges(Object, boolean, boolean) - Method in class apollo.dataadapter.AbstractApolloAdapter

GAMEAdapter and ChadoXMLAdapter can specify whether to save annots and whether to save results

commitChanges(CurationSet, boolean, boolean) - Method in class apollo.dataadapter.AbstractApolloAdapter

commitChanges(CompositeDataHolder, boolean, boolean) - Method in class apollo.dataadapter.AbstractApolloAdapter

commitChanges(CurationSet) - Method in interface apollo.dataadapter.ApolloDataAdapterI

writes the changes from a featureChangeLog to a writeable datasource.

commitChanges(CompositeDataHolder) - Method in interface apollo.dataadapter.ApolloDataAdapterI

Write out composite data holder to multiple data adapters (only SyntenyAdapter actually implements this)

commitChanges(Object) - Method in interface apollo.dataadapter.ApolloDataAdapterI

Straight from DataAdapterGUI.doOp.

commitChanges(Object, boolean, boolean) - Method in interface apollo.dataadapter.ApolloDataAdapterI

GAMEAdapter and ChadoXMLAdapter can specify whether to save annots and whether to save results

commitChanges(CurationSet) - Method in class apollo.dataadapter.BaseGFFAdapter

commitChanges(CurationSet) - Method in class apollo.dataadapter.chado.ChadoAdapter

Writes back curation set via jdbc, using the curations sets transactions

commitChanges(CurationSet) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

commitChanges(CurationSet) - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter

Main method for writing ChadoXML file

commitChanges(CurationSet, boolean, boolean) - Method in class apollo.dataadapter.chadoxml.ChadoXmlAdapter

Main method for writing ChadoXML file

commitChanges(CurationSet) - Method in class apollo.dataadapter.das.simple.SimpleDASAdapter

commitChanges(CurationSet) - Method in class apollo.dataadapter.das2.DAS2Adapter

Main method for writing DAS2XML file

commitChanges(CurationSet) - Method in class apollo.dataadapter.EnsCGIAdapter

commitChanges(CurationSet) - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapter

Write the (now edited) curation set back to the otter server or file, depending on what was nominated.

commitChanges(CurationSet) - Method in class apollo.dataadapter.ensj19.EnsJAdapter

commitChanges(CurationSet) - Method in class apollo.dataadapter.gamexml.GAMEAdapter

commitChanges(CurationSet, boolean, boolean) - Method in class apollo.dataadapter.gamexml.GAMEAdapter

Writes XML If the input type is not FILE, prompts user for a file to save to.

commitChanges(CurationSet) - Method in class apollo.dataadapter.GbrowseAdapter

commitChanges(CurationSet, boolean) - Method in class apollo.dataadapter.genbank.GenbankAdapter

Write GenBank report in tabular or human-readable format, as requested

commitChanges(CurationSet) - Method in class apollo.dataadapter.gff3.GFF3Adapter

Commit data

commitChanges(CurationSet) - Method in class apollo.dataadapter.otter.OtterAdapter

commitChanges(CurationSet) - Method in class apollo.dataadapter.otter.OtterXMLAdapter

commitChanges(CurationSet) - Method in class apollo.dataadapter.SerialDiskAdapter

commitChanges(CompositeDataHolder) - Method in class apollo.dataadapter.SerialDiskAdapter

If multi cur set, appends curset name to filename - or should it appends the cur set # so its retrievable?

commitChanges(CompositeDataHolder) - Method in class apollo.dataadapter.synteny.SyntenyAdapter

Write out composite data holder to multiple data adapters - called by DataLoader/FileMenu not SynAdapGUI

commitChanges(CurationSet) - Method in class apollo.dataadapter.synteny.SyntenyAdapter

I think this is now pase and should be deleted - always gets a CompositeDataHolder now - this is actually not called by SyntenyAdapterGUI.doOp(WRITE) - calls child adapter guis doOp this is called by DataLoader though

commitDeleteTransaction(String, DeleteTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

commitTransaction() - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Commit a transaction using the current JDBC Connection.

commitTransaction(String, int, Transaction, boolean) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

commitTransactions(TransactionManager) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

Write a set of transactions to the database using adapter

commitTransactions(TransactionManager) - Method in class apollo.dataadapter.TransactionOutputAdapter

The client to this class should call this method to commit (save or write changes to the database) transactions.

commitTransformedTransactions(List) - Method in class apollo.dataadapter.chado.jdbc.JDBCTransactionWriter

This takes a list of chado transactions (not apollo transactions) and commits them

commitTransformedTransactions(List) - Method in class apollo.dataadapter.chadoxml.ChadoTransactionXMLWriter

commitTransformedTransactions(List) - Method in class apollo.dataadapter.TransactionOutputAdapter

A subclass to this class should implement this method to provide its own behaviors.

commitUpdateParentTransaction(String, UpdateParentTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

commitUpdateTransaction(String, UpdateTransaction) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

CompactFeaturePlaceFinder - Class in apollo.gui.detailviewers.sequencealigner

This class encapsulates a 'compact' place finding algorithm.

CompactFeaturePlaceFinder() - Constructor for class apollo.gui.detailviewers.sequencealigner.CompactFeaturePlaceFinder

Comparable - Interface in apollo.datamodel

Comparator - Interface in apollo.util

ComparatorBase<T> - Class in apollo.gui.detailviewers.sequencealigner.comparators

ComparatorBase() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorBase

ComparatorFactory - Class in apollo.gui.detailviewers.sequencealigner.comparators

ComparatorFactory() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorFactory

ComparatorFactory.TYPE - Enum in apollo.gui.detailviewers.sequencealigner.comparators

ComparatorReverse<T> - Class in apollo.gui.detailviewers.sequencealigner.comparators

ComparatorReverse(Comparator<T>) - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorReverse

ComparatorSeqFeatureDisplayType - Class in apollo.gui.detailviewers.sequencealigner.comparators

ComparatorSeqFeatureDisplayType() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureDisplayType

ComparatorSeqFeatureFrame - Class in apollo.gui.detailviewers.sequencealigner.comparators

ComparatorSeqFeatureFrame() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureFrame

ComparatorSeqFeatureLength - Class in apollo.gui.detailviewers.sequencealigner.comparators

ComparatorSeqFeatureLength() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureLength

ComparatorSeqFeatureName - Class in apollo.gui.detailviewers.sequencealigner.comparators

ComparatorSeqFeatureName() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureName

ComparatorSeqFeatureScore - Class in apollo.gui.detailviewers.sequencealigner.comparators

ComparatorSeqFeatureScore() - Constructor for class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureScore

compare(Object, Object) - Method in class apollo.gui.detailviewers.sequencealigner.AnnotationFeatureComparator

compare(T, T) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorBase

compare(T, T) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorReverse

compare(SeqFeatureI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureDisplayType

compare(SeqFeatureI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureFrame

compare(SeqFeatureI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureLength

compare(SeqFeatureI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureName

compare(SeqFeatureI, SeqFeatureI) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureScore

compare(T, T) - Method in class apollo.gui.detailviewers.sequencealigner.comparators.MultiComparatorArrayList

compare(Object, Object) - Method in class apollo.gui.detailviewers.sequencealigner.ResultFeatureComparator

compare(Object, Object) - Method in class apollo.gui.evidencepanel.TablePanel.MegaComparator

compare(Object, Object) - Method in interface apollo.util.Comparator

compare(Object, Object) - Method in class apollo.util.FeatureAlphabeticalComparator

compare(Object, Object) - Method in class apollo.util.FeatureComparator

compareDoubles(Double, Double) - Method in class apollo.gui.evidencepanel.TablePanel.MegaComparator

compareIntegers(Integer, Integer) - Method in class apollo.gui.evidencepanel.TablePanel.MegaComparator

compareRanges(Range, Range) - Method in class apollo.gui.evidencepanel.TablePanel.MegaComparator

compareStrings(String, String) - Method in class apollo.gui.evidencepanel.TablePanel.MegaComparator

compareTo(Object) - Method in interface apollo.datamodel.Comparable

compareTo(Object) - Method in class apollo.datamodel.SeqFeature

compareTo(Object) - Method in interface apollo.datamodel.SeqFeatureI

compareTo(Object) - Method in class apollo.util.interval.Interval

complain(String) - Method in class apollo.config.Style

Print message to stderr

completeGUIInitialization() - Method in class apollo.gui.ApolloFrame

This is only called once, from ApolloRunner when the gui is first coming up, after the first dataset is loaded (CAF.loadData())

componentInit() - Method in class apollo.gui.FindPanel

componentInit() - Method in class apollo.gui.SeqMatchPanel

CompositeApolloFrame - Class in apollo.gui.synteny

The synteny panels need to display many stranded-zoomable-apollo-panels at once, (unlike the standard apollo frame).

CompositeApolloFrame.MacApplicationSupport - Class in apollo.gui.synteny

CompositeApolloFrame.MacApplicationSupport() - Constructor for class apollo.gui.synteny.CompositeApolloFrame.MacApplicationSupport

CompositeDataHolder - Class in apollo.datamodel

Holds multiple curation sets for synteny.

CompositeDataHolder() - Constructor for class apollo.datamodel.CompositeDataHolder

CompositeDataHolder(SpeciesComparison) - Constructor for class apollo.datamodel.CompositeDataHolder

CompositeDataHolder(CurationSet) - Constructor for class apollo.datamodel.CompositeDataHolder

Puts composite curation sets into species comparisons

CompositeDataSourceConfigurationPanel - Class in apollo.dataadapter.ensj19

This is a panel which composes a number of the standard DataSourceConfiguration panels - one for the results, one for variations, one for sequences.

CompositeDataSourceConfigurationPanel(String[]) - Constructor for class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel

Automatically takes the first chooser name passed in as the default.

CompositeDataSourceConfigurationPanel(String[], boolean) - Constructor for class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel

CompositeDataSourceConfigurationPanel() - Constructor for class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel

CompositeDataSourceConfigurationPanel.ChooserActionListener - Class in apollo.dataadapter.ensj19

Exposes the chosen panel, hides the one that was previously chosen

CompositeDataSourceConfigurationPanel.ChooserActionListener() - Constructor for class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel.ChooserActionListener

CompositeDataSourceConfigurationPanel.DatabaseFindListener - Class in apollo.dataadapter.ensj19

When the user hits "find" on the _default_ data config panel, we need to find all core ensembl databases, as well as variations.

CompositeDataSourceConfigurationPanel.DatabaseFindListener() - Constructor for class apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel.DatabaseFindListener

CompoundTransaction - Class in apollo.editor

A CompoundTransaction contains a list of Transactions (children).

CompoundTransaction(Object) - Constructor for class apollo.editor.CompoundTransaction

phase out -> require source!

Compress - Class in apollo.analysis.filter

Compress() - Constructor for class apollo.analysis.filter.Compress

compress(String, int, boolean) - Static method in class apollo.analysis.filter.Compress

compress_threshold - Variable in class apollo.analysis.filter.BlastFilterPanel

compressedCodonHash - Static variable in class apollo.seq.ResidueProperties

computeMD5Checksum(String) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

Config - Class in apollo.config

A class with static data members and static methods for setting and retrieving configuration information for the apollo gui.

Config() - Constructor for class apollo.config.Config

confirmSaved(Object[], DataLoader) - Static method in class apollo.main.LoadUtil

should this be done on a per curationState basis?

connect() - Method in class apollo.dataadapter.mysql.MySQLDatabase

connect() - Method in class apollo.dataadapter.mysql.MySQLInstance

connection - Variable in class apollo.dataadapter.CGI

CONNECTION_STRING - Static variable in class apollo.dataadapter.StateInformation

constraints - Variable in class apollo.dataadapter.GuiTabPanel

construct() - Method in class apollo.gui.SwingWorker

Compute the value to be returned by the get method.

ContainerView - Class in apollo.gui.genomemap

ContainerView(JComponent, String, boolean) - Constructor for class apollo.gui.genomemap.ContainerView

ContainerViewI - Interface in apollo.gui.genomemap

contains(RangeI) - Method in class apollo.datamodel.CurationSet

Overrides Range.contains.

contains(Link) - Method in class apollo.datamodel.LinkSet

contains(RangeI) - Method in class apollo.datamodel.Range

contains(int) - Method in class apollo.datamodel.Range

contains(RangeI) - Method in interface apollo.datamodel.RangeI

Returns true if range of sf is entierly within this RangeI

contains(int) - Method in interface apollo.datamodel.RangeI

contains(Object) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel

contains(Point, Transformer, TierManagerI) - Method in class apollo.gui.drawable.DrawableSeqFeature

contains(Object) - Method in class apollo.util.CaseInsensitiveStringHash

containsAll(Collection<?>) - Method in class apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel

containsCoding() - Method in class apollo.datamodel.Exon

Convenience function that uses getCodingProperties() and returns true if its codingProperty has coding

containsCoding() - Method in interface apollo.datamodel.ExonI

Returns true if exon contains any coding region.

containsFeature(SeqFeatureI) - Method in class apollo.gui.Selection

Returns true if there is a SelectionItem in Selection with sf

containsFeature(SeqFeatureI, SeqFeatureI) - Static method in class apollo.util.SeqFeatureUtil

Returns true if container contains query (or is query)

containsKey(String) - Method in class apollo.util.CaseInsensitiveStringHash

CONTIG - Static variable in class apollo.dataadapter.DataInputType

CONTIG_LABEL - Static variable in class apollo.dataadapter.ensj.view.TypesPanel

ControlledObjectI - Interface in apollo.gui

Interface defining methods required to add a Controller to an object getControllerWindow and needs AutoRemoval used by Controller to remove listeners when their controller window is closing.

ControlledPanel - Class in apollo.gui

An extension of JPanel to make automatic Controller window management possible.

ControlledPanel() - Constructor for class apollo.gui.ControlledPanel

Controller - Class in apollo.dataadapter.ensj.controller

Controller(Model, View) - Constructor for class apollo.dataadapter.ensj.controller.Controller

Controller - Class in apollo.dataadapter.synteny.builder

Controller(Model, View) - Constructor for class apollo.dataadapter.synteny.builder.Controller

Controller - Class in apollo.gui

An event controller forwarding multiple types of event to registered listeners.

Controller() - Constructor for class apollo.gui.Controller

controller - Variable in class apollo.gui.genomemap.ApolloPanel

controller - Variable in class apollo.gui.genomemap.ContainerView

controller - Variable in class apollo.gui.genomemap.TierView

controller - Variable in class apollo.gui.NonWindowControlledObject

controller - Variable in class apollo.gui.TierManager

ControllerDebugListener - Class in apollo.gui

ControllerDebugListener(Controller) - Constructor for class apollo.gui.ControllerDebugListener

convertFromBaseOrientedToInterbase() - Method in class apollo.datamodel.Range

convertFromBaseOrientedToInterbase() - Method in interface apollo.datamodel.RangeI

Converts base oriented range to interbase range

convertFromInterbaseToBaseOriented() - Method in class apollo.datamodel.Range

convertFromInterbaseToBaseOriented() - Method in interface apollo.datamodel.RangeI

Converts interbase range to base oriented range

convertLogicalNameToSpeciesName(String) - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapter

Use the synteny style to convert from logical to actual species names.

coord_seq - Variable in class apollo.dataadapter.analysis.AlignmentParser

COORD_SYSTEM - Static variable in class apollo.dataadapter.ensj.EnsJAdapter

copyAnnotatedGenesIntoResultTier(StrandedFeatureSet, StrandedFeatureSet, String, SequenceI) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

A method that copies all the annotated protein-coding genes into a result tier.

copyArea(int, int, int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics

copyElements(Collection<? extends T>, Collection<? super T>, boolean) - Static method in class apollo.util.CollectionUtil

Copy elements from src to dest.

copyFile(String, String) - Static method in class apollo.util.IOUtil

copyOnWrite - Variable in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

copySeqToClipboard(Sequence) - Static method in class apollo.util.ClipboardUtil

should this go in SequenceUtil?

copyTextToClipboard(String) - Static method in class apollo.util.ClipboardUtil

count - Variable in class apollo.analysis.filter.HuffNode

Coverage - Class in apollo.analysis.filter

Coverage() - Constructor for class apollo.analysis.filter.Coverage

creaateIntronMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu

create() - Method in class apollo.gui.genomemap.FastClippingGraphics

create(int, int, int, int) - Method in class apollo.gui.genomemap.FastClippingGraphics

CREATE_BUTTON - Static variable in class apollo.dataadapter.synteny.builder.Controller

CREATE_SET_BUTTON - Static variable in class apollo.dataadapter.synteny.builder.Controller

createAdaptersAndGUIs(String) - Method in class apollo.dataadapter.synteny.builder.Model

createAnnotation() - Method in class apollo.editor.AnnotationEditor

createAnnotation(String) - Method in class apollo.editor.AnnotationEditor

The default createAnnotation method for creating an unsupported annotation.

createAnnotation(int, int, String) - Method in class apollo.editor.AnnotationEditor

This method puts up a dialog asking for the size of the new exon, and then calls #createAnnotation(int,int,int).

createAnnotation(int, int, int, String) - Method in class apollo.editor.AnnotationEditor

This method uses #addAnnotation(Vector,false,type) to create an unsupported transcript or gene, or one level?

createAnnotationAllowed() - Method in class apollo.editor.AnnotationEditor

Determine whether or not the SelectionSets are compatible with creating an unsupported (no evidence) annotation.

createBorder(String) - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI

createCacher() - Method in class apollo.datamodel.seq.AbstractLazySequence

Overriden by GAMESequence

createCacher() - Method in class apollo.datamodel.seq.GAMESequence

createChangeList() - Method in class apollo.gui.annotinfo.FeatureEditPanel

createClassFromName(String) - Method in class apollo.config.FeatureProperty

createDefaultFeatureProperty() - Method in class apollo.config.PropertyScheme

createDialog() - Method in class apollo.gui.detailviewers.sequencealigner.menus.AddFilterPanel

createDragView(MouseEvent, Selection) - Method in class apollo.gui.genomemap.TierView

createDragView(MouseEvent, Selection) - Method in interface apollo.gui.genomemap.TierViewI

Interface of method required for starting a drag from this TierView

createDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableEnsemblFeatureSet

createDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableFeatureSet

createDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableGeneFeatureSet

createDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawablePhaseHighlightGeneFeatureSet

createDrawable(SeqFeatureI) - Method in class apollo.gui.drawable.DrawableResultFeatureSet

createDrawable(SeqFeatureI) - Static method in class apollo.gui.drawable.DrawableUtil

Creates and returns a DrawableFeatureSet from a FeatureSetI.

CreateExonAction - Class in apollo.gui.detailviewers.sequencealigner.actions

An Action class for creating a single base exon within an intron region.

CreateExonAction(String, GuiCurationState, AnnotationEditor) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.CreateExonAction

Constructor

createExonMenuItem - Variable in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel

createExonMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu

createExonMenuItem - Variable in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

createFeature(OBOParser) - Method in class apollo.dataadapter.gff3.GFF3Entry

Create the implementing class of AnnotatedFeatureI given the type

createFinder(FeaturePlaceFinder.Type) - Static method in class apollo.gui.detailviewers.sequencealigner.FeaturePlaceFinder

createFP() - Method in class apollo.dataadapter.analysis.BlatParser

createGlyph(String) - Static method in class apollo.gui.drawable.DrawableUtil

Glyph name may be whole path (apollo.gui.drawable.Zigzag), just the class name(Zigzag)

createGraphics(Graphics, int, int, int, int) - Method in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

createGraphics(Graphics, int, int, int, int) - Method in class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

CreateIntronAction - Class in apollo.gui.detailviewers.sequencealigner.actions

An Action class for creating a single base intron within an exon region.

CreateIntronAction(String, GuiCurationState, AnnotationEditor) - Constructor for class apollo.gui.detailviewers.sequencealigner.actions.CreateIntronAction

Constructor

createLinksFromSpeciesComp(SpeciesComparison) - Method in interface apollo.dataadapter.synteny.LinkerI

createMenuManager(ApolloFrame) - Static method in class apollo.gui.menus.MenuManager

createNameAdapter() - Method in class apollo.config.FeatureProperty

createNameFromClass(Object) - Method in class apollo.config.FeatureProperty

Given a class, e.g.

createPopupMenu(ApolloPanelI, MouseEvent) - Method in class apollo.gui.genomemap.AnnotationView

createPopupMenu(ApolloPanelI, MouseEvent) - Method in class apollo.gui.genomemap.FeatureView

This is overridden by ResultView and AnnotView - make abstract?

createPopupMenu(ApolloPanelI, MouseEvent) - Method in class apollo.gui.genomemap.ResultView

createRightClickMenu() - Method in class apollo.gui.detailviewers.exonviewer.BaseEditorPanel

createRightClickMenu() - Method in class apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

createSrcFeatureIDTransaction(String, String) - Method in class apollo.dataadapter.chado.ChadoTransactionTransformer

createStateInformation() - Method in interface apollo.dataadapter.ApolloDataAdapterGUI

createStateInformation() - Method in class apollo.dataadapter.das.simple.SimpleDASAdapterGUI

createStateInformation() - Method in class apollo.dataadapter.das2.DAS2AdapterGUI

createStateInformation() - Method in class apollo.dataadapter.ensj.EnsJAdapterGUI

Convert the Model (which has all the UI's state information) into a properties object to be passed to the dataadapter.

createStateInformation() - Method in class apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI

We make sure (in addition to the superclass's setStateInfo) that we have added the names of the chosen annotation input and output files.

createStateInformation() - Method in class apollo.dataadapter.ensj19.EnsJAdapterGUI

createStateInformation() - Method in class apollo.dataadapter.gff3.GFF3AdapterGUI

createStateInformation() - Method in class apollo.dataadapter.GFFAdapterGUI

createStateInformation() - Method in class apollo.dataadapter.graph.GraphAdapterGUI

createStateInformation() - Method in class apollo.dataadapter.synteny.builder.BuilderAdapterGUI

createStateInformation() - Method in class apollo.dataadapter.synteny.SyntenyComparaAdapterGUI

add on the hit-information to the query-information already in there.

createStyle(String) - Static method in class apollo.config.Config

If already have style for styleFilename, return that.

createTransferable(JComponent) - Method in class apollo.gui.ArrayListTransferHandler

createUnixShellCommand(SeqAnalysisLocal) - Method in class apollo.analysis.BlastHandler

different analysis programs require different ways of running them this method is only called by SeqAnalysisLocal

createUnixShellCommand(SeqAnalysisLocal) - Method in class apollo.analysis.GenericProgramHandler

different analysis programs require different ways of running them assumes a command line is made by programPath programParams inputSequence [datasourcePath]

createUnixShellCommand(SeqAnalysisLocal) - Method in interface apollo.analysis.ProgramHandlerI

different analysis programs require different ways of running them

curated - Variable in class apollo.config.TierProperty

curation - Variable in class apollo.dataadapter.analysis.AnalysisPanel

curation - Variable in class apollo.gui.genomemap.SiteView

curation_set - Variable in class apollo.dataadapter.AbstractApolloAdapter

CurationManager - Class in apollo.gui.synteny

Holds CurationState objects.

curationSet - Variable in class apollo.analysis.SeqAnalysisBase

CurationSet - Class in apollo.datamodel

I am the central holder of renderable data - results, annotations etc.

CurationSet() - Constructor for class apollo.datamodel.CurationSet

CurationSet(StrandedFeatureSetI, StrandedFeatureSetI, String) - Constructor for class apollo.datamodel.CurationSet

curationSet - Variable in class apollo.test.ApolloTest

curationSetIsLoaded(boolean) - Method in class apollo.gui.Controller

CurationState - Class in apollo.dataadapter

CurationState(int) - Constructor for class apollo.dataadapter.CurationState

current_job_id - Variable in class apollo.bop.JDBCPipelineAdapter

CUSTOM - Static variable in class apollo.gui.genomemap.StrandedZoomableApolloPanel

CUSTOM_DB_PROMPT - Static variable in class apollo.dataadapter.chado.ChadoAdapterGUI

Prompt for the pull-down menu that allows the user to select a Chado database from among those read from the Chado adapter's configuration file.

CUSTOM_SEQ_PROMPT - Static variable in class apollo.dataadapter.chado.ChadoAdapterGUI

Prompt for the area in which the user can enter the ID of the sequence he/she wishes to load.

CutSite - Class in apollo.gui.tweeker

CutSite(int, int, RestrictionEnzyme) - Constructor for class apollo.gui.tweeker.CutSite

Cys - Static variable in class apollo.seq.ResidueProperties

CYTOLOGY - Static variable in class apollo.dataadapter.DataInputType

D

DAS2Adapter - Class in apollo.dataadapter.das2

I implement a AbstractDataAdapter, allowing Apollo to get information from DAS datasources, using 'simple' implementions of DASServerI, DASDsn etc.

DAS2Adapter() - Constructor for class apollo.dataadapter.das2.DAS2Adapter

DAS2AdapterGUI - Class in apollo.dataadapter.das2

This actually constructs a completely different GUI for reading vs.

DAS2AdapterGUI() - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI

DAS2AdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI

DAS2AdapterGUI.DSNListener - Class in apollo.dataadapter.das2

DAS2AdapterGUI.DSNListener() - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI.DSNListener

DAS2AdapterGUI.HistoryListener - Class in apollo.dataadapter.das2

DAS2AdapterGUI.HistoryListener() - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI.HistoryListener

DAS2AdapterGUI.ProxyListener - Class in apollo.dataadapter.das2

This listener gets fired when the user wants to set a Proxy Server for the session

DAS2AdapterGUI.ProxyListener() - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI.ProxyListener

DAS2AdapterGUI.ServerListener - Class in apollo.dataadapter.das2

DAS2AdapterGUI.ServerListener() - Constructor for class apollo.dataadapter.das2.DAS2AdapterGUI.ServerListener

DAS2FeatureSaxParser - Class in apollo.dataadapter.das2

Parser that reads features from das2xml and stores them in Apollo datamodels (the top level of which is a CurationSet).

DAS2FeatureSaxParser() - Constructor for class apollo.dataadapter.das2.DAS2FeatureSaxParser

DAS2Request - Class in apollo.dataadapter.das2

Adapted from das/simple/SimpleDASServer I don't understand why that class was called "server", since it's client-side.

DAS2Request(String) - Constructor for class apollo.dataadapter.das2.DAS2Request

You must pass in the URL of a DAS-reference server, used in all further requests.

DAS2Writer - Class in apollo.dataadapter.das2

writeXML: writes DAS2XML to a file

DAS2Writer() - Constructor for class apollo.dataadapter.das2.DAS2Writer

DASDsn - Interface in apollo.dataadapter.das

DASDsnContentHandler - Class in apollo.dataadapter.das.simple

I am the ContentHandler used when SimpleDASServer parses the result of a 'dsn' call to a das data source.

DASDsnContentHandler() - Constructor for class apollo.dataadapter.das.simple.DASDsnContentHandler

DASEntryPointContentHandler - Class in apollo.dataadapter.das.simple

I am the ContentHandler used when SimpleDASServer parses the result of a 'entry_points' call to a das data source and dsn.

DASEntryPointContentHandler() - Constructor for class apollo.dataadapter.das.simple.DASEntryPointContentHandler

DASFeature - Interface in apollo.dataadapter.das

DASFeatureContentHandler - Class in apollo.dataadapter.das.simple

I am the ContentHandler used when SimpleDASServer parses the result of a 'features' call to a das data source (with a specified dsn and segment).

DASFeatureContentHandler() - Constructor for class apollo.dataadapter.das.simple.DASFeatureContentHandler

DASFeatureContentHandler(DASServerI, DASDsn, HashMap, HashMap, long, long) - Constructor for class apollo.dataadapter.das.simple.DASFeatureContentHandler

DASLazySequence - Class in apollo.dataadapter.das

I am a Sequence class for implementing lazy load using a DASServer

DASLazySequence(String, Controller, RangeI, DASServerI, DASDsn, DASSegment) - Constructor for class apollo.dataadapter.das.DASLazySequence

DASSegment - Interface in apollo.dataadapter.das

I represent the contained in a Segment (as defined by the DAS-spec) needed by Apollo to request features for the segment, and display the features of the segment.

DASSequence - Interface in apollo.dataadapter.das

I represent the data contained in a dna sequence (as defined by the DAS-spec) needed by Apollo to display a sequence.

DASSequenceContentHandler - Class in apollo.dataadapter.das.simple

I am the ContentHandler used when SimpleDASServer parses the result of a 'dna' call to a das data source (passing in dsn and segment).

DASSequenceContentHandler() - Constructor for class apollo.dataadapter.das.simple.DASSequenceContentHandler

DASSequenceContentHandler(DASServerI, DASDsn, DASSegment[]) - Constructor for class apollo.dataadapter.das.simple.DASSequenceContentHandler

DASServerI - Interface in apollo.dataadapter.das

I represent the capability of a general DASServer, as required by Apollo to make das-data requests.

data - Variable in class apollo.dataadapter.CGI

DATA_ADAPTER - Static variable in class apollo.dataadapter.StateInformation

DATA_FILE_NAME - Static variable in class apollo.dataadapter.StateInformation

DATA_RETRIEVE_BEGIN - Static variable in class apollo.dataadapter.DataLoadEvent

DATA_RETRIEVE_DONE - Static variable in class apollo.dataadapter.DataLoadEvent

dataAdapterIsAvailable(IOOperation) - Static method in class apollo.config.Config

dataArray - Variable in class apollo.io.FileParse

database - Variable in class apollo.analysis.filter.AnalysisInput

Database - Class in apollo.dataadapter.mysql

Database(String, String, String, String) - Constructor for class apollo.dataadapter.mysql.Database

Database(String, String, String, String, int) - Constructor for class apollo.dataadapter.mysql.Database

DATABASE - Static variable in class apollo.dataadapter.StateInformation

databaseChoicePrompt - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI

databaseComboBox - Variable in class apollo.dataadapter.chado.ChadoAdapterGUI

databaseHasStyle(String) - Method in class apollo.config.Style

Returns true if have style for db

DatabaseModel - Class in apollo.dataadapter.ensj.model

DatabaseModel() - Constructor for class apollo.dataadapter.ensj.model.DatabaseModel

DatabasePanel - Class in apollo.dataadapter.ensj.view

DatabasePanel(View) - Constructor for class apollo.dataadapter.ensj.view.DatabasePanel

DataFetcher - Class in apollo.dataadapter.ensj

I am just a separate helper class to stop the EnsJAdapter from becoming too huge.

DataFetcher(EnsJAdapter) - Constructor for class apollo.dataadapter.ensj.DataFetcher

DataInput - Class in apollo.dataadapter

This lumps together DataInputType and getInput String in ApolloDataAdapterI.

DataInput(DataInputType, String) - Constructor for class apollo.dataadapter.DataInput

DataInput(String, String) - Constructor for class apollo.dataadapter.DataInput

DataInput(String, String, String) - Constructor for class apollo.dataadapter.DataInput

DataInput(String, String, String, String) - Constructor for class apollo.dataadapter.DataInput

Constructor for a location with Strings for chrom, start, & end & so type

DataInput(DataInputType) - Constructor for class apollo.dataadapter.DataInput

DataInput(String) - Constructor for class apollo.dataadapter.DataInput

DataInputType - Class in apollo.dataadapter

A value class for the different types of Data input

DataInputType.UnknownTypeException - Exception in apollo.dataadapter

DataListener - Interface in apollo.dataadapter

Interface to get notification when an adapter is about to create new data Should this be merged with DataLoadListener? YES! and go through controller perhaps Controller should go in a different package than gui? Should there be one method with a DataEvent that distinguishes beginning and ending load? 7.26.04 This has been merged with DataLoadListener.

DataLoader - Class in apollo.main

This class handles loading of data into Apollo.

DataLoader() - Constructor for class apollo.main.DataLoader

DataLoadEvent - Class in apollo.dataadapter

DataLoadEvent are sent out on new data being loaded.

DataLoadEvent(Object, int) - Constructor for class apollo.dataadapter.DataLoadEvent

If type is DATA_RETRIEVE_BEGIN then we dont have apolloData nor region yet

DataLoadEvent(Object, CurationSet) - Constructor for class apollo.dataadapter.DataLoadEvent

dataLoadingDone() - Method in interface apollo.dataadapter.DataListener

DataLoadListener - Interface in apollo.dataadapter

DataModelConversionUtil - Class in apollo.dataadapter.ensj

DataModelConversionUtil() - Constructor for class apollo.dataadapter.ensj.DataModelConversionUtil

dataRetrievalBeginning() - Method in class apollo.dataadapter.DataLoadEvent

New data is about to be fetched and made.

dataRetrievalDone() - Method in class apollo.dataadapter.DataLoadEvent

New data has been retrieved/created.

DataSourceConfigurationPanel - Class in apollo.dataadapter.ensj19

This panel allows the user to configure the parameters necessary for the EnsJ-interface to an ensembl database.

DataSourceConfigurationPanel() - Constructor for class apollo.dataadapter.ensj19.DataSourceConfigurationPanel

DataSourceConfigurationPanel(String) - Constructor for class apollo.dataadapter.ensj19.DataSourceConfigurationPanel

DataSourceConfigurationPanel.DataChangeListener - Class in apollo.dataadapter.ensj19

Triggered when the user types into any data field

DataSourceConfigurationPanel.DataChangeListener() - Constructor for class apollo.dataadapter.ensj19.DataSourceConfigurationPanel.DataChangeListener

DataSourceConfigurationPanel.EnsemblDBSelectionListener - Class in apollo.dataadapter.ensj19

Triggered when the user selects a particular database

DataSourceConfigurationPanel.EnsemblDBSelectionListener() - Constructor for class apollo.dataadapter.ensj19.DataSourceConfigurationPanel.EnsemblDBSelectionListener

DataSourceConfigurationPanel.HostListener - Class in apollo.dataadapter.ensj19

Triggered when the user pushes the "find" button

DataSourceConfigurationPanel.HostListener() - Constructor for class apollo.dataadapter.ensj19.DataSourceConfigurationPanel.HostListener

DataUtil - Class in apollo.datamodel.seq

date - Variable in class apollo.editor.Transaction

date_formats - Static variable in class apollo.util.DateUtil

dateNoTime(Date) - Static method in class apollo.util.DateUtil

Return a date in the format 18-JAN-2004 (Used by GenbankReport)

DateUtil - Class in apollo.util

DateUtil() - Constructor for class apollo.util.DateUtil

db - Variable in class apollo.dataadapter.mysql.BaseAdaptor

DBAdaptor - Class in apollo.dataadapter.gbrowse

DBAdaptor(MySQLDatabase) - Constructor for class apollo.dataadapter.gbrowse.DBAdaptor

dbname - Variable in class apollo.dataadapter.GbrowseAdapter

DbXref - Class in apollo.datamodel

DbXref(String, String, String) - Constructor for class apollo.datamodel.DbXref

DbXref(String, String, String, boolean) - Constructor for class apollo.datamodel.DbXref

DBXREF - Static variable in class apollo.editor.TransactionSubpart

debug - Variable in class apollo.analysis.filter.AnalysisInput

DEBUG - Static variable in class apollo.config.Config

Debug mode for Apollo developers; references to this variable are scattered throughout the Apollo code.

debug - Variable in class apollo.gui.genomemap.FeatureTierManager

debug - Variable in class apollo.gui.genomemap.LinearView

debug_str - Variable in class apollo.analysis.filter.AnalysisInput

debugFeature(SeqFeatureI, SeqFeatureI, String, boolean) - Method in class apollo.analysis.filter.AnalysisFilter

debugFeature(SeqFeatureI, String) - Method in class apollo.analysis.filter.AnalysisFilter

debugFeature(SeqFeatureI, String, boolean) - Method in class apollo.analysis.filter.AnalysisFilter

debugFilter(String) - Method in class apollo.analysis.filter.AnalysisInput

DebugLazySequence - Class in apollo.datamodel.seq

DebugLazySequence(String, Controller, String) - Constructor for class apollo.datamodel.seq.DebugLazySequence

debugName(SeqFeatureI) - Method in class apollo.analysis.filter.AnalysisFilter

debugName(SeqFeatureI) - Method in class apollo.dataadapter.analysis.Sim4Parser

debugName(SeqFeatureI) - Static method in class apollo.dataadapter.gamexml.GAMESave

DECORATED - Static variable in class apollo.gui.drawable.DrawableSeqFeature

decrementGeneTranscriptRanks(Long, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

decrementTierHeight() - Method in class apollo.gui.genomemap.TierView

decrementTierHeight() - Method in interface apollo.gui.genomemap.TierViewI

decrementTierHeight() - Method in class apollo.gui.TierManager

decrementTierHeight() - Method in interface apollo.gui.TierManagerI

decrementTranscriptExonRanks(Long, long) - Method in class apollo.dataadapter.chado.jdbc.JdbcChadoAdapter

DEFAULT - Static variable in class apollo.dataadapter.synteny.builder.Model

default_3prime - Static variable in class apollo.analysis.filter.AnalysisFilter

DEFAULT_COLOR - Static variable in class apollo.config.FeatureProperty

default_columns - Static variable in class apollo.config.FeatureProperty

DEFAULT_CONFIG_FILE - Static variable in class apollo.dataadapter.ensj19.EnsJAdapterGUI

DEFAULT_STYLE - Static variable in class apollo.config.FeatureProperty

DEFAULT_TIER - Static variable in class apollo.dataadapter.analysis.AnalysisPanel

DEFAULT_TYPE - Static variable in class apollo.dataadapter.analysis.AnalysisPanel

DefaultBaseRenderer - Class in apollo.gui.detailviewers.exonviewer

DefaultBaseRenderer(int, int) - Constructor for class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer

DefaultBaseRenderer - Class in apollo.gui.detailviewers.sequencealigner

DefaultBaseRenderer(int, int) - Constructor for class apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer

DefaultDisplayPrefs - Class in apollo.config

DefaultDisplayPrefs() - Constructor for class apollo.config.DefaultDisplayPrefs

DefaultNameAdapter - Class in apollo.config

If no name adapter is specified, and no or human gene def, then DefaultNameAdapter is used.

DefaultNameAdapter() - Constructor for class apollo.config.DefaultNameAdapter

defaultRowHeader - Variable in class apollo.gui.detailviewers.exonviewer.SeqAlignPanel

DELETE - Static variable in class apollo.dataadapter.chado.ChadoTransaction

DELETE - Static variable in class apollo.editor.FeatureChangeEvent

DELETE - Static variable in class apollo.editor.TransactionOperation

DELETE_BUTTON - Static variable in class apollo.dataadapter.synteny.builder.Controller

DELETE_SET_BUTTON - Static variable in class apollo.dataadapter.synteny.builder.Controller

deleteCDS(long) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

deleteComment(long, Comment) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

deleteComment(Comment) - Method in class apollo.datamodel.AnnotatedFeature

deleteComment(int) - Method in class apollo.datamodel.AnnotatedFeature

deleteComment(Comment) - Method in interface apollo.datamodel.AnnotatedFeatureI

deleteComment(int) - Method in interface apollo.datamodel.AnnotatedFeatureI

deleteDbXref(long, DbXref) - Method in class apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter

deleteDbXref(DbXref) - Method in class apollo.datamodel.Identifier

deleteDrawable(Drawable) - Method in interface apollo.gui.drawable.Drawable

If drawable contains child, deletes it

deleteDrawable(Drawable) - Method in class apollo.gui.drawable.DrawableFeatureSet

deleteDrawable(Drawable) - Method in class apollo.gui.drawable.DrawableSeqFeature

Default no-op implementation, DrawableSeqFeature doesnt have children, do nothing.

deleteDrawable(Drawable) - Method in interface apollo.gui.drawable.DrawableSetI

deleteEvidence(String) - Method in class apollo.datamodel.AnnotatedFeature

deleteEvidence(String) - M