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

A

AboutDialog - class org.biojava.spice.gui.AboutDialog.

A Dialog to show version and copyright information for SPICE.

AboutDialog(SPICEFrame) - Constructor for class org.biojava.spice.gui.AboutDialog

AbstractAlignmentManager - class org.biojava.spice.manypanel.managers.AbstractAlignmentManager.

AbstractAlignmentManager() - Constructor for class org.biojava.spice.manypanel.managers.AbstractAlignmentManager

AbstractChainManager - class org.biojava.spice.manypanel.managers.AbstractChainManager.

AbstractChainManager() - Constructor for class org.biojava.spice.manypanel.managers.AbstractChainManager

AbstractChainRenderer - class org.biojava.spice.manypanel.renderer.AbstractChainRenderer.

AbstractChainRenderer() - Constructor for class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

AbstractFeature - class org.biojava.spice.feature.AbstractFeature.

An Abstract class representing a Feature as being diplayed in the SeqFeaturePanel A feature corresponds to everything that is visible in a "line" and can contain one or multiple Segments.

AbstractFeature() - Constructor for class org.biojava.spice.feature.AbstractFeature

AbstractPopupFrame - class org.biojava.spice.gui.AbstractPopupFrame.

a class that provides a "floating" frame that follows the position of the cursor the "content" of the panel is provided by the content Container that has to be provided by a class that extends this abstract class

AbstractPopupFrame() - Constructor for class org.biojava.spice.gui.AbstractPopupFrame

AbstractSegment - class org.biojava.spice.feature.AbstractSegment.

AbstractSegment() - Constructor for class org.biojava.spice.feature.AbstractSegment

AligLabel - class org.biojava.spice.gui.aligchooser.AligLabel.

AligLabel(String, Annotation, String) - Constructor for class org.biojava.spice.gui.aligchooser.AligLabel

AligPanelListener - class org.biojava.spice.gui.alignmentchooser.AligPanelListener.

AligPanelListener(AlignmentChooser) - Constructor for class org.biojava.spice.gui.alignmentchooser.AligPanelListener

AlignmentCalc - class org.biojava.spice.gui.alignment.AlignmentCalc.

a class that obtains two structures via DAS and aligns them This is done in a separate thread.

AlignmentCalc(AlignmentGui, String, String, String, String, SpiceDasSource[]) - Constructor for class org.biojava.spice.gui.alignment.AlignmentCalc

requests an alignment of pdb1 vs pdb 2.

AlignmentChooser - class org.biojava.spice.gui.alignmentchooser.AlignmentChooser.

A class to choose bewteen differen sequence and structure alignments.

AlignmentChooser(DasCoordinateSystem, DasCoordinateSystem) - Constructor for class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

AlignmentCursorPanel - class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel.

AlignmentCursorPanel() - Constructor for class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

AlignmentFilterActionListener - class org.biojava.spice.gui.aligchooser.AlignmentFilterActionListener.

AlignmentFilterActionListener(StructureAlignmentChooser) - Constructor for class org.biojava.spice.gui.aligchooser.AlignmentFilterActionListener

AlignmentGui - class org.biojava.spice.gui.alignment.AlignmentGui.

AlignmentGui(RegistryConfiguration) - Constructor for class org.biojava.spice.gui.alignment.AlignmentGui

AlignmentItemListener - class org.biojava.spice.gui.aligchooser.AlignmentItemListener.

AlignmentItemListener(StructureAlignmentChooser) - Constructor for class org.biojava.spice.gui.aligchooser.AlignmentItemListener

AlignmentManager - class org.biojava.spice.manypanel.managers.AlignmentManager.

AlignmentManager(String, DasCoordinateSystem, DasCoordinateSystem) - Constructor for class org.biojava.spice.manypanel.managers.AlignmentManager

AlignmentPanel - class org.biojava.spice.manypanel.renderer.AlignmentPanel.

AlignmentPanel() - Constructor for class org.biojava.spice.manypanel.renderer.AlignmentPanel

AlignmentPanelMouseListener - class org.biojava.spice.manypanel.renderer.AlignmentPanelMouseListener.

AlignmentPanelMouseListener(AlignmentRenderer) - Constructor for class org.biojava.spice.manypanel.renderer.AlignmentPanelMouseListener

AlignmentRenderer - class org.biojava.spice.manypanel.renderer.AlignmentRenderer.

AlignmentRenderer() - Constructor for class org.biojava.spice.manypanel.renderer.AlignmentRenderer

AlignmentServerSwitcher - class org.biojava.spice.gui.AlignmentServerSwitcher.

AlignmentServerSwitcher(SpiceApplication) - Constructor for class org.biojava.spice.gui.AlignmentServerSwitcher

AlignmentSortPopup - class org.biojava.spice.gui.aligchooser.AlignmentSortPopup.

AlignmentSortPopup(StructureAlignment, StructureAlignmentChooser, boolean) - Constructor for class org.biojava.spice.gui.aligchooser.AlignmentSortPopup

AlignmentTool - class org.biojava.spice.manypanel.AlignmentTool.

AlignmentTool() - Constructor for class org.biojava.spice.manypanel.AlignmentTool

AlignmentTools - class org.biojava.spice.das.AlignmentTools.

AlignmentTools(RegistryConfiguration) - Constructor for class org.biojava.spice.das.AlignmentTools

AlignmentType - Static variable in class org.biojava.spice.config.SpiceDefaults

AlternativeAlignmentFrame - class org.biojava.spice.gui.alignment.AlternativeAlignmentFrame.

a frame showing the alternative alignments, which are the result of a structure superimposition

AlternativeAlignmentFrame(Structure, Structure) - Constructor for class org.biojava.spice.gui.alignment.AlternativeAlignmentFrame

ArrowPanel - class org.biojava.spice.manypanel.renderer.ArrowPanel.

a class to draw two arrows, that, if pressed will launch an alignmentChooser ...

ArrowPanel() - Constructor for class org.biojava.spice.manypanel.renderer.ArrowPanel

AtomInfo - class org.biojava.spice.jmol.AtomInfo.

AtomInfo() - Constructor for class org.biojava.spice.jmol.AtomInfo

AtomInfoParser - class org.biojava.spice.jmol.AtomInfoParser.

AtomInfoParser() - Constructor for class org.biojava.spice.jmol.AtomInfoParser

accessionCode - Variable in class org.biojava.spice.gui.msdkeyword.Deposition

actionPerformed(ActionEvent) - Method in class org.biojava.spice.gui.BrowseMenuListener

actionPerformed(ActionEvent) - Method in class org.biojava.spice.gui.SelectionLockMenuListener

actionPerformed(ActionEvent) - Method in class org.biojava.spice.gui.SpiceMenuListener

actionPerformed(ActionEvent) - Method in class org.biojava.spice.gui.StructureCommandListener

actionPerformed(ActionEvent) - Method in class org.biojava.spice.gui.aligchooser.AlignmentFilterActionListener

actionPerformed(ActionEvent) - Method in class org.biojava.spice.gui.aligchooser.AlignmentSortPopup

addAdjustmentListener(AdjustmentListener) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

add an adjustmentListener to the horizontal scrollbar

addAlignmentListener(AlignmentListener) - Method in class org.biojava.spice.alignment.StructureAlignmentBuilder

addAlignmentListener(AlignmentListener) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

addAlignmentRenderer(AlignmentRenderer) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

addConfigListener(ConfigurationListener) - Method in class org.biojava.spice.config.RegistryConfigIO

addDasSourceListener(DasSourceListener) - Method in class org.biojava.spice.das.SingleFeatureThread

addDasSourceListener(DasSourceListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addDasSourceListener(DasSourceListener) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

addDrawableDasSource(DrawableDasSource) - Method in class org.biojava.spice.manypanel.renderer.FeatureRenderer

addEnspListener(ObjectListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addEnspSequenceListener(SequenceListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addEnspSpiceFeatureListener(SpiceFeatureListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addFeatureListener(FeatureListener) - Method in class org.biojava.spice.das.SingleFeatureThread

addFeatureListener(FeatureListener) - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

addFeatureRenderer(FeatureRenderer) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

addJmolStatusListener(JmolStatusListener) - Method in class org.biojava.spice.jmol.StructurePanel

Add a JmolStatus listener to Jmol

addMatrix(Alignment, String, Matrix) - Static method in class org.biojava.spice.das.AlignmentTools

add a Matrix to an object

addObject(Alignment, String, String, String, String, String, String, String, List) - Static method in class org.biojava.spice.das.AlignmentTools

add a new object to an alignment

addObject1Listener(ObjectListener) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

addObject2Listener(ObjectListener) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

addObjectListener(ObjectListener) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

a panel to choose a seq-structure alignment

addPDBPositionListener(SequenceListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addPDBSequenceListener(SequenceListener) - Method in class org.biojava.spice.gui.SelectionPanel

addPDBSequenceListener(SequenceListener) - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

addPDBSequenceListener(SequenceListener) - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

addPDBSequenceListener(SequenceListener) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

addPDBSequenceListener(SequenceListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addPDBSpiceFeatureListener(SpiceFeatureListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addScaleChangeListener(ScaleListener) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

addSegment(int, int, String) - Method in class org.biojava.spice.feature.AbstractFeature

add a segment to this feature

addSegment(Segment) - Method in class org.biojava.spice.feature.AbstractFeature

addSegment(int, int, String) - Method in interface org.biojava.spice.feature.Feature

add a segment to this feature

addSegment(Segment) - Method in interface org.biojava.spice.feature.Feature

addSeq1FeatureListener(SpiceFeatureListener) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

addSeq2FeatureListener(SpiceFeatureListener) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

addSequence1Listener(SequenceListener) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

addSequence2Listener(SequenceListener) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

addSequenceListener(SequenceListener) - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

addSequenceListener(SequenceListener) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

addSequenceListener(SequenceListener) - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

addSequenceRenderer(SequenceRenderer) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

addServer(SpiceDasSource) - Method in class org.biojava.spice.config.RegistryConfiguration

add a new DAS server to the list of available ones.

addServerAtStart(SpiceDasSource) - Method in class org.biojava.spice.config.RegistryConfiguration

addSpice(SPICEFrame) - Method in class org.biojava.spice.gui.SpiceTabbedPane

addSpiceFeatureListener(SpiceFeatureListener) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

addSpiceFeatureListener(SpiceFeatureListener) - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

addSpiceFeatureListener(SpiceFeatureListener) - Method in class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener

addStructureAlignmentListener(StructureAlignmentListener) - Method in class org.biojava.spice.gui.alignment.AlignmentCalc

addStructureAlignmentListener(StructureAlignmentListener) - Method in class org.biojava.spice.gui.alignment.AlignmentGui

addStructureAlignmentListener(StructureAlignmentListener) - Method in class org.biojava.spice.gui.alignment.AlternativeAlignmentFrame

addStructureListener(StructureListener) - Method in class org.biojava.spice.alignment.StructureAlignmentBuilder

addStructureListener(StructureListener) - Method in class org.biojava.spice.gui.SelectionPanel

addStructureListener(StructureListener) - Method in class org.biojava.spice.gui.SpiceChainDisplay

addStructureListener(StructureListener) - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

addStructureListener(StructureListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addStructureListener(StructureListener) - Method in class org.biojava.spice.manypanel.managers.StructureManager

addStructureRenderer(StructureRenderer) - Method in class org.biojava.spice.manypanel.managers.StructureManager

addTab(String, Component, boolean) - Method in class org.biojava.spice.gui.CloseableTabbedPane

addTab(String, Component) - Method in class org.biojava.spice.gui.CloseableTabbedPane

addTabListener(TabListener) - Method in class org.biojava.spice.gui.CloseableTabbedPane

addUniProtListener(ObjectListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addUniProtSequenceListener(SequenceListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addUniProtSpiceFeatureListener(SpiceFeatureListener) - Method in class org.biojava.spice.manypanel.BrowserPane

addVector(Alignment, String, Atom) - Static method in class org.biojava.spice.das.AlignmentTools

add a shift vector to an alignment

argumentTypes - Static variable in class org.biojava.spice.config.SpiceDefaults

B

BACKGROUND_COLOR - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

BrowseMenuListener - class org.biojava.spice.gui.BrowseMenuListener.

BrowseMenuListener() - Constructor for class org.biojava.spice.gui.BrowseMenuListener

BrowseMenuListener(URL) - Constructor for class org.biojava.spice.gui.BrowseMenuListener

BrowserOpener - class org.biojava.spice.utils.BrowserOpener.

BrowserOpener() - Constructor for class org.biojava.spice.utils.BrowserOpener

BrowserPane - class org.biojava.spice.manypanel.BrowserPane.

The main Container for the different sequence and alignment panels

BrowserPane(String) - Constructor for class org.biojava.spice.manypanel.BrowserPane

create a BrowserPane that only has a structure Panel

BrowserPane(String, String, String) - Constructor for class org.biojava.spice.manypanel.BrowserPane

create a browserPane that has PDB, Uniprot and ENSP panels

C

CASPCOORDSYS - Static variable in class org.biojava.spice.config.SpiceDefaults

CLASS - Static variable in class org.biojava.spice.gui.logging.LoggingPanel

Constant for LoggingPanel.setColumnVisible(org.biojava.spice.gui.logging.LoggingPanel.Column, boolean).

COLOR_MATCH_ONE - Static variable in class org.biojava.spice.manypanel.renderer.AlignmentPanel

COLOR_MATCH_TWO - Static variable in class org.biojava.spice.manypanel.renderer.AlignmentPanel

COLOR_MISMATCH_ONE - Static variable in class org.biojava.spice.manypanel.renderer.AlignmentPanel

COLOR_MISMATCH_TWO - Static variable in class org.biojava.spice.manypanel.renderer.AlignmentPanel

ChainRendererMouseListener - class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener.

a mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriate SequenceListener and FeatureListener events

ChainRendererMouseListener(AbstractChainRenderer) - Constructor for class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

CliTools - class org.biojava.spice.utils.CliTools.

Utilities for autoconfiguring javabeans based on command line arguments.

CloseableTabbedPane - class org.biojava.spice.gui.CloseableTabbedPane.

CloseableTabbedPane(ImageIcon) - Constructor for class org.biojava.spice.gui.CloseableTabbedPane

CloseableTabbedPane() - Constructor for class org.biojava.spice.gui.CloseableTabbedPane

CloseableTabbedPane.ClosingIcon - class org.biojava.spice.gui.CloseableTabbedPane.ClosingIcon.

the idea for this class stems from limewire's CancelSearchIconProxy class, thanks for going open source guys.

CloseableTabbedPane.ClosingIcon(ImageIcon) - Constructor for class org.biojava.spice.gui.CloseableTabbedPane.ClosingIcon

CloseableTabbedPane.ClosingListener - class org.biojava.spice.gui.CloseableTabbedPane.ClosingListener.

CloseableTabbedPane.ClosingListener() - Constructor for class org.biojava.spice.gui.CloseableTabbedPane.ClosingListener

CollectTools - class org.biojava.spice.utils.CollectTools.

Utilities for working with collections.

CollectTools() - Constructor for class org.biojava.spice.utils.CollectTools

ColorTools - class org.biojava.spice.utils.ColorTools.

ColorTools() - Constructor for class org.biojava.spice.utils.ColorTools

ComponentResizedChainListener - class org.biojava.spice.manypanel.renderer.ComponentResizedChainListener.

ComponentResizedChainListener(AbstractChainRenderer) - Constructor for class org.biojava.spice.manypanel.renderer.ComponentResizedChainListener

ConfigGui - class org.biojava.spice.config.ConfigGui.

ConfigGui(SpiceApplication) - Constructor for class org.biojava.spice.config.ConfigGui

ConfigPanel - class org.biojava.spice.gui.ConfigPanel.

a Component that provides the GUI for configuring SPICE

ConfigPanel(SpiceApplication, RegistryConfiguration) - Constructor for class org.biojava.spice.gui.ConfigPanel

ConfigXMLHandler - class org.biojava.spice.config.ConfigXMLHandler.

XML content handler for serialisation of RegistryConfiguration class

ConfigXMLHandler() - Constructor for class org.biojava.spice.config.ConfigXMLHandler

ConfigurationException - class org.biojava.spice.config.ConfigurationException.

An exception during the parsing of a PDB file.

ConfigurationException(String) - Constructor for class org.biojava.spice.config.ConfigurationException

Constructs a StructureException object.

ConfigurationException(Throwable) - Constructor for class org.biojava.spice.config.ConfigurationException

Constructs a StructureException object.

ConfigurationListener - interface org.biojava.spice.config.ConfigurationListener.

An interface to define an even listener, if the DAS - registry has been contacted and a new Configuration retrieved

CoordManager - class org.biojava.spice.manypanel.renderer.CoordManager.

a class that manages the conversion of sequence coordinate system to JPanel drawing coordinates

CoordManager() - Constructor for class org.biojava.spice.manypanel.renderer.CoordManager

CursorPanel - class org.biojava.spice.manypanel.renderer.CursorPanel.

a class that paints the sequence position "cursor" and the selected region of a sequence

CursorPanel() - Constructor for class org.biojava.spice.manypanel.renderer.CursorPanel

calcScale(int) - Method in interface org.biojava.spice.manypanel.Scaleable

something between 0 and 100 - percent if 100 - the painting should fill the currently visible display 0 is zoomdepth as big as possible

calcScale(int) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

a value of 100 means that the whole sequence should be displayed in the current visible window a factor of 1 means that one amino acid shoud be drawn as big as possible

characters(char[], int, int) - Method in class org.biojava.spice.config.ConfigXMLHandler

characters(char[], int, int) - Method in class org.biojava.spice.gui.msdkeyword.MSDContentHandler

checkDrawSelectedFeature(Feature, int, Graphics, int) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

check if the feature is selected, if yes, color the background in SELECTED_FEATURE_COLOR

choose(SpiceServer) - Static method in class org.biojava.spice.server.UserChoosesSpiceDialog

classification - Variable in class org.biojava.spice.gui.msdkeyword.Deposition

cleanUp() - Method in class org.biojava.spice.gui.alignment.AlignmentGui

cleanUp() - Method in class org.biojava.spice.gui.alignment.AlternativeAlignmentFrame

cleanup() - Method in class org.biojava.spice.gui.alignment.AlignmentCalc

clear() - Method in class org.biojava.spice.SpiceApplication

clear the displayed data

clear() - Method in class org.biojava.spice.gui.BrowseMenuListener

clear() - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

clear() - Method in class org.biojava.spice.manypanel.managers.FeatureManager

clear() - Method in interface org.biojava.spice.manypanel.managers.ObjectManager

clear the current reference object

clear() - Method in class org.biojava.spice.manypanel.managers.StructureManager

clearAlignment() - Method in class org.biojava.spice.alignment.StructureAlignmentBuilder

clearAlignment() - Method in class org.biojava.spice.gui.aligchooser.MenuAlignmentListener

clearAlignment() - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

clearAlignment() - Method in class org.biojava.spice.manypanel.managers.AbstractAlignmentManager

clearAlignment() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

clearAlignment() - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

clearAlignment() - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanel

clearAlignment() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

clearAlignmentRenderers() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

clearDasSourceListeners() - Method in class org.biojava.spice.das.SingleFeatureThread

clearDasSources() - Method in class org.biojava.spice.manypanel.BrowserPane

clearDasSources() - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

clearDasSources() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

clearDasSources() - Method in class org.biojava.spice.manypanel.managers.FeatureManager

clearDasSources() - Method in class org.biojava.spice.manypanel.managers.SequenceManager

clearDasSources() - Method in class org.biojava.spice.manypanel.managers.StructureManager

clearDasSources() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

removes the DasSourcePanels from display

clearDasSources() - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

clearDasSources() - Method in class org.biojava.spice.manypanel.renderer.FeatureRenderer

clearDisplay() - Method in class org.biojava.spice.gui.SelectionPanel

clearDisplay() - Method in class org.biojava.spice.jmol.StructurePanel

clearDisplay() - Method in class org.biojava.spice.manypanel.BrowserPane

clearDisplay() - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

clearDisplay() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

clearDisplay() - Method in class org.biojava.spice.manypanel.renderer.SequenceRenderer

clearDisplay() - Method in class org.biojava.spice.manypanel.renderer.StructureRenderer

clearFeatureListeners() - Method in class org.biojava.spice.das.SingleFeatureThread

clearFeatureListeners() - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

clearListeners() - Method in class org.biojava.spice.SpiceApplication

unregister all event listeners and make the application ready for being garbage collected

clearListeners() - Method in class org.biojava.spice.alignment.StructureAlignmentBuilder

clearListeners() - Method in class org.biojava.spice.gui.SelectionPanel

clearListeners() - Method in class org.biojava.spice.gui.SpiceMenuListener

clearListeners() - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

clearListeners() - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

clearListeners() - Method in class org.biojava.spice.gui.alignment.AlignmentCalc

clearListeners() - Method in class org.biojava.spice.gui.alignment.AlignmentGui

clearListeners() - Method in class org.biojava.spice.gui.alignment.AlternativeAlignmentFrame

clearListeners() - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

clearListeners() - Method in class org.biojava.spice.jmol.StructurePanel

remove the listeners from Jmol again.

clearListeners() - Method in class org.biojava.spice.manypanel.BrowserPane

removes all listeners

clearListeners() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

clearObjectListeners() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

clearPanel() - Method in class org.biojava.spice.jmol.StructurePanelListener

clearSelection() - Method in class org.biojava.spice.gui.SpiceMenuListener

clearSelection() - Method in class org.biojava.spice.gui.StatusPanel

clearSelection() - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

clearSelection() - Method in class org.biojava.spice.jmol.StructurePanelListener

clearSelection() - Method in interface org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener

clearSelection() - Method in class org.biojava.spice.manypanel.managers.FeatureManager

clearSelection() - Method in class org.biojava.spice.manypanel.managers.SequenceManager

clearSelection() - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

clearSelection() - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

clearSelection() - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

clearSelection() - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

clearSelection() - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

clearSelection1() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

clearSelection2() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

clearSequenceListeners() - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

clearSequenceListeners() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

clearSequenceListeners() - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

clearSpiceFeatureListeners() - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

clearSpiceFeatureListeners() - Method in class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener

clearStructureListeners() - Method in class org.biojava.spice.gui.SpiceChainDisplay

clearStructureListeners() - Method in class org.biojava.spice.manypanel.managers.StructureManager

clone() - Method in class org.biojava.spice.feature.AbstractFeature

clone() - Method in class org.biojava.spice.feature.AbstractSegment

clone() - Method in interface org.biojava.spice.feature.Feature

clone() - Method in class org.biojava.spice.feature.FeatureImpl

clone() - Method in class org.biojava.spice.feature.HistogramFeature

clone() - Method in class org.biojava.spice.feature.HistogramSegment

clone() - Method in interface org.biojava.spice.feature.Segment

clone() - Method in class org.biojava.spice.feature.SegmentImpl

closingIcon - Variable in class org.biojava.spice.gui.CloseableTabbedPane

colNames - Static variable in class org.biojava.spice.config.DasSourceConfigPanel

colorToString(Color) - Static method in class org.biojava.spice.utils.ColorTools

convert a Color to a html style hexadecimal String representation e.g.

colour(int, int, String) - Method in class org.biojava.spice.jmol.StructurePanelListener

selects a single position and does spacefill on

colour(int, int, int, String) - Method in class org.biojava.spice.jmol.StructurePanelListener

comeBackLater(FeatureEvent) - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

comeBackLater(FeatureEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.FeatureListener

the server says that he is busy and we should try again in x seconds

comeBackLater(FeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

comeBackLater(FeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

compare(Object, Object) - Method in class org.biojava.spice.alignment.StructureAlignmentComparator

compare(Object, Object) - Method in class org.biojava.spice.feature.FeatureComparator

compare(Object, Object) - Method in class org.biojava.spice.feature.FeatureMapComparator

compare(Object, Object) - Method in class org.biojava.spice.feature.SegmentComparator

componentHidden(ComponentEvent) - Method in class org.biojava.spice.gui.alignmentchooser.AligPanelListener

componentHidden(ComponentEvent) - Method in class org.biojava.spice.manypanel.renderer.ComponentResizedChainListener

componentMoved(ComponentEvent) - Method in class org.biojava.spice.gui.alignmentchooser.AligPanelListener

componentMoved(ComponentEvent) - Method in class org.biojava.spice.manypanel.renderer.ComponentResizedChainListener

componentResized(ComponentEvent) - Method in class org.biojava.spice.gui.alignmentchooser.AligPanelListener

componentResized(ComponentEvent) - Method in class org.biojava.spice.manypanel.renderer.ComponentResizedChainListener

componentShown(ComponentEvent) - Method in class org.biojava.spice.gui.alignmentchooser.AligPanelListener

componentShown(ComponentEvent) - Method in class org.biojava.spice.manypanel.renderer.ComponentResizedChainListener

configureBean(Object, String[]) - Static method in class org.biojava.spice.utils.CliTools

Configure a JavaBean based on a set of command line arguments.

contains(int, int) - Method in class org.biojava.spice.gui.CloseableTabbedPane.ClosingIcon

Verifies if x and y are within the icon's borders.

containsKeyword(SpiceDasSource, String) - Static method in class org.biojava.spice.config.SearchDasSourceManager

check if a das source contains a keyword

coordinatesAreFractional(Object) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

createAlignmentMenu(SpiceMenuListener) - Static method in class org.biojava.spice.gui.MenuCreator

createAlignmentTable(Alignment, String) - Static method in class org.biojava.spice.manypanel.AlignmentTool

returns a list of maps relative to one accession code that has the length of the alignment (can include gaps).

createArtificalStructure() - Method in class org.biojava.spice.alignment.StructureAlignment

create a single structure, that joins all the actively selected chains together for proper display in the 3D panel currently: each structure is a new model.

createArtificalStructure(int) - Method in class org.biojava.spice.alignment.StructureAlignment

create a single structure, that joins all the actively selected chains together for proper display in the 3D panel currently: each structure is a new model.

createChain(Alignment, String) - Method in class org.biojava.spice.StructureBuilder

create a chain that corrresponds to a sequence

createChain(Alignment, String, String, String) - Static method in class org.biojava.spice.manypanel.AlignmentTool

creates a chaing that represents the alignment relative to the query.

createContent(Feature) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

createContent(Segment) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

createDisplayMenu(ActionListener) - Static method in class org.biojava.spice.gui.MenuCreator

create a JMenu to be used for interacting with the structure Panel.

createFileMenu(SpiceMenuListener) - Static method in class org.biojava.spice.gui.MenuCreator

createFrame() - Method in class org.biojava.spice.gui.AbstractPopupFrame

createHelpMenu(SpiceMenuListener) - Static method in class org.biojava.spice.gui.MenuCreator

createImage(String, String, int) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

createImageIcon(String) - Static method in class org.biojava.spice.SpiceApplication

Returns an ImageIcon, or null if the path was invalid.

createImageIcon(String) - Static method in class org.biojava.spice.gui.MenuCreator

createSpiceStructure(Alignment, Structure, String) - Method in class org.biojava.spice.StructureBuilder

create a structure to be displayed in SPICE

D

DASTYLINK - Static variable in class org.biojava.spice.gui.BrowseMenuListener

DEFAULT_CAPABILITY - Static variable in class org.biojava.spice.das.SpiceDasSource

DEFAULT_NICKNAME - Static variable in class org.biojava.spice.das.SpiceDasSource

DEFAULT_X_RIGHT_BORDER - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

DEFAULT_X_START - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

DEFAULT_Y_BOTTOM - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

DEFAULT_Y_HEIGHT - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

DEFAULT_Y_START - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

DEFAULT_Y_STEP - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

DIST - Static variable in class org.biojava.spice.gui.AbstractPopupFrame

DISULFID_TYPE - Static variable in class org.biojava.spice.config.SpiceDefaults

DasScrollPaneColumnHeader - class org.biojava.spice.manypanel.renderer.DasScrollPaneColumnHeader.

DasScrollPaneColumnHeader(SequenceScalePanel, CursorPanel) - Constructor for class org.biojava.spice.manypanel.renderer.DasScrollPaneColumnHeader

DasScrollPaneRowHeader - class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader.

DasScrollPaneRowHeader(JScrollPane) - Constructor for class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

DasSourceConfigPanel - class org.biojava.spice.config.DasSourceConfigPanel.

DasSourceConfigPanel(ConfigPanel, RegistryConfiguration) - Constructor for class org.biojava.spice.config.DasSourceConfigPanel

DasSourceDialog - class org.biojava.spice.gui.DasSourceDialog.

A Dialog that displays some information about a DAS source

DasSourceDialog(SpiceDasSource) - Constructor for class org.biojava.spice.gui.DasSourceDialog

DasSourceEvent - class org.biojava.spice.manypanel.eventmodel.DasSourceEvent.

something is happening with a DAS source

DasSourceEvent(DrawableDasSource) - Constructor for class org.biojava.spice.manypanel.eventmodel.DasSourceEvent

DasSourceListener - interface org.biojava.spice.manypanel.eventmodel.DasSourceListener.

some things that can happen with DAS sources

DasSourcePanel - class org.biojava.spice.manypanel.renderer.DasSourcePanel.

a class that draws the content of a das source

DasSourcePanel(DrawableDasSource) - Constructor for class org.biojava.spice.manypanel.renderer.DasSourcePanel

DasSourcePanelHeader - class org.biojava.spice.manypanel.renderer.DasSourcePanelHeader.

a class that takes care of rendering the head of a DrawableDassource (the header part of the scrollPane)

DasSourcePanelHeader(DrawableDasSource) - Constructor for class org.biojava.spice.manypanel.renderer.DasSourcePanelHeader

DasSourcePanelTableModel - class org.biojava.spice.config.DasSourcePanelTableModel.

DasSourcePanelTableModel(DasSourceConfigPanel, Object[][], String[], SpiceDasSource[]) - Constructor for class org.biojava.spice.config.DasSourcePanelTableModel

Deposition - class org.biojava.spice.gui.msdkeyword.Deposition.

thanks to Adel Golovin for providing most of this code.

Deposition() - Constructor for class org.biojava.spice.gui.msdkeyword.Deposition

Deposition(String, String, float, float, Date, String, String, String, String) - Constructor for class org.biojava.spice.gui.msdkeyword.Deposition

DrawUtils - class org.biojava.spice.manypanel.renderer.DrawUtils.

DrawUtils() - Constructor for class org.biojava.spice.manypanel.renderer.DrawUtils

Drawable - interface org.biojava.spice.manypanel.drawable.Drawable.

the interface for something that can be drawn

DrawableDasSource - class org.biojava.spice.manypanel.drawable.DrawableDasSource.

all the data about a particular DAS source and the Features associated with if ( and a particular accession code)

DrawableDasSource(SpiceDasSource) - Constructor for class org.biojava.spice.manypanel.drawable.DrawableDasSource

DrawableSequence - class org.biojava.spice.manypanel.drawable.DrawableSequence.

at its core a DraawableSequence is also a Structure obbject - but without coordinates

DrawableSequence(String) - Constructor for class org.biojava.spice.manypanel.drawable.DrawableSequence

DrawableSequence(String, Chain) - Constructor for class org.biojava.spice.manypanel.drawable.DrawableSequence

DrawableStructure - class org.biojava.spice.manypanel.drawable.DrawableStructure.

DrawableStructure(String) - Constructor for class org.biojava.spice.manypanel.drawable.DrawableStructure

dateFormat - Variable in class org.biojava.spice.gui.logging.LogPopupFrame

deduceElementSymbol(String) - Static method in class org.biojava.spice.jmol.JmolUtils

degreesPerRadian - Static variable in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

deleteServer(SpiceDasSource) - Method in class org.biojava.spice.config.DasSourceConfigPanel

deleteServer(int) - Method in class org.biojava.spice.config.RegistryConfiguration

delete server.

deselect(int) - Method in class org.biojava.spice.alignment.StructureAlignment

destroy() - Method in class org.biojava.spice.server.SpiceServer

stop listening at SPICEPORT for incoming connections ...

disableDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.BrowserPane

disableDasSource(DasSourceEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.DasSourceListener

a DAS source has been disabled

disableDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

disableDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

dispatchFrame() - Method in class org.biojava.spice.gui.AbstractPopupFrame

displayType - Variable in class org.biojava.spice.das.SpiceDasSource

dispose() - Method in class org.biojava.spice.gui.logging.LoggingPanel

Free any resources used by this LoggingPanel.

disposeFrame() - Method in class org.biojava.spice.gui.AbstractPopupFrame

usually the frame is not dispsosed, but just set to invisible!

doLayout() - Method in class org.biojava.spice.gui.logging.LoggingPanel

Layout this component.

drawHistogramFeature(HistogramFeature, int, int, Graphics, int, Color, Color, String) - Method in class org.biojava.spice.manypanel.renderer.HistogramPainter

drawScale(Graphics2D, int) - Method in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

draw the Scale

drawSequence(Graphics2D, int) - Method in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

draw the sequence

E

EMPTY_TAB_TXT - Static variable in class org.biojava.spice.gui.SpiceTabbedPane

ENSEMBLLINK - Static variable in class org.biojava.spice.gui.BrowseMenuListener

ENSPCOORDSYS - Static variable in class org.biojava.spice.config.SpiceDefaults

ENSPCOORDSYS - Static variable in class org.biojava.spice.manypanel.SpiceLayeredPanel

EnspType - Static variable in class org.biojava.spice.config.SpiceDefaults

enableDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.BrowserPane

enableDasSource(DasSourceEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.DasSourceListener

a DAS source has been enabled

enableDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

enableDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

endElement(String, String, String) - Method in class org.biojava.spice.config.ConfigXMLHandler

endElement(String, String, String) - Method in class org.biojava.spice.gui.msdkeyword.MSDContentHandler

endStringBuffer(StringBuffer) - Method in class org.biojava.spice.gui.logging.LogPopupFrame

entColors - Static variable in class org.biojava.spice.manypanel.drawable.DrawableDasSource

equals(Feature) - Method in class org.biojava.spice.feature.AbstractFeature

test if two features are equivalent important: only comares type,method and source.

equals(Feature) - Method in interface org.biojava.spice.feature.Feature

test if two features are equivalent

equals(Segment) - Method in class org.biojava.spice.feature.SegmentImpl

equals(DrawableDasSource) - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

if the url of two das sources is the same this will return true;

eval(String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

executeCmd(String) - Method in interface org.biojava.spice.jmol.JmolCommander

executeCmd(String) - Method in class org.biojava.spice.jmol.StructurePanel

Send a RASMOL like command to Jmol

executeCmd(String) - Method in class org.biojava.spice.jmol.StructurePanelListener

send a RASMOL like command to Jmol

expData - Variable in class org.biojava.spice.gui.msdkeyword.Deposition

extractId(Alignment, String) - Static method in class org.biojava.spice.manypanel.AlignmentTool

F

FEATURE_PANEL_HEIGHT - Static variable in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

FRAME_PREF_HEIGHT - Static variable in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

FRAME_WIDTH - Static variable in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

Feature - interface org.biojava.spice.feature.Feature.

FeatureComparator - class org.biojava.spice.feature.FeatureComparator.

a comparator to sort Features byt type

FeatureComparator() - Constructor for class org.biojava.spice.feature.FeatureComparator

FeatureImpl - class org.biojava.spice.feature.FeatureImpl.

a class to store FeatureData and to visualize them coordinate system of features is always UniProt ! PDBresnum features served by DAS need to be converted into UniProt coord sys first.

FeatureImpl() - Constructor for class org.biojava.spice.feature.FeatureImpl

FeatureListener - interface org.biojava.spice.manypanel.eventmodel.FeatureListener.

a feature listener that returns the raw features as returned by a DAS source.

FeatureManager - class org.biojava.spice.manypanel.managers.FeatureManager.

takes care of dealing with Features - requests them from DAS and converts them into Drawables

FeatureManager() - Constructor for class org.biojava.spice.manypanel.managers.FeatureManager

FeatureMapComparator - class org.biojava.spice.feature.FeatureMapComparator.

a comparator to sort Features if they are still in a Map ( sorts by type )

FeatureMapComparator() - Constructor for class org.biojava.spice.feature.FeatureMapComparator

FeatureRenderer - class org.biojava.spice.manypanel.renderer.FeatureRenderer.

FeatureRenderer() - Constructor for class org.biojava.spice.manypanel.renderer.FeatureRenderer

feature2XML(Feature, XMLWriter) - Method in class org.biojava.spice.gui.SaveLoadSession

featureSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.gui.StatusPanel

featureSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.jmol.StructurePanelListener

featureSelected(SpiceFeatureEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener

featureSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

featureSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

featureSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

featureSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

filterProperty - Static variable in class org.biojava.spice.gui.aligchooser.MenuAlignmentListener

filterSources(SpiceDasSource[]) - Method in class org.biojava.spice.StartParameterFilter

fromChain(String, Chain) - Static method in class org.biojava.spice.manypanel.drawable.DrawableSequence

fromDasSource(DasSource) - Static method in class org.biojava.spice.das.SpiceDasSource

convert DasSource to SpiceDasSource

fromDasSource(SpiceDasSource) - Static method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

fromString(String, String) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

fromXML(File) - Method in class org.biojava.spice.gui.SaveLoadSession

parse the serialized session.spice file

functionXY(String, int, int) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

G

GENCODECOORDSYS - Static variable in class org.biojava.spice.config.SpiceDefaults

GENCODEType - Static variable in class org.biojava.spice.config.SpiceDefaults

get3DStylesheet() - Method in class org.biojava.spice.das.SpiceDasSource

get the stylesheet containing the instructions how to paint in 3D.

getAccessionCode() - Method in class org.biojava.spice.gui.msdkeyword.Deposition

getAccessionCode() - Method in class org.biojava.spice.manypanel.drawable.DrawableSequence

getAccessionCode() - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

getAccessionCodes() - Method in class org.biojava.spice.alignment.StructureAlignment

getActiveChainFromName(String) - Method in class org.biojava.spice.manypanel.managers.StructureManager

getAddLocalPanel() - Method in class org.biojava.spice.gui.ConfigPanel

getAdjust1() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getAdjust2() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getAlignment() - Method in class org.biojava.spice.alignment.StructureAlignment

getAlignmentChooser() - Method in class org.biojava.spice.gui.SelectionPanel

getAlignmentListeners() - Method in class org.biojava.spice.alignment.StructureAlignmentBuilder

getAlignmentObject(Alignment, DasCoordinateSystem) - Method in class org.biojava.spice.StructureBuilder

retrieve the HashMap for the sequence

getAlignmentServers(List, DasCoordinateSystem, DasCoordinateSystem) - Method in class org.biojava.spice.manypanel.BrowserPane

test if a server is a UniProt vs PDBresnum alignment server

getAlignmentServers() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getAlignments(String) - Method in class org.biojava.spice.das.AlignmentTools

get alignments for a particular uniprot or pdb code

getAllDasSources() - Static method in class org.biojava.spice.manypanel.SpiceLayeredPanel

getAllServers() - Method in class org.biojava.spice.config.RegistryConfiguration

getAlphaGradient(Color, double) - Static method in class org.biojava.spice.manypanel.renderer.DrawUtils

getArrowPanel() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getArrowPanel() - Method in class org.biojava.spice.manypanel.renderer.StatusPanel

getAtomIterator(Object) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getAtomName() - Method in class org.biojava.spice.jmol.AtomInfo

getAtomSetAuxiliaryInfo(Object, int) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getAtomSetCollectionName(Object) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getAtomSetCollectionProperties(Object) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getAtomSetCount(Object) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

return the number of models (each model is an AtomSet)

getAtomSetName(Object, int) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getAtomSetNumber(Object, int) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getAtomSetProperties(Object, int) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getAvailablePanel() - Method in class org.biojava.spice.gui.ConfigPanel

getBackground(LogRecord) - Method in class org.biojava.spice.gui.logging.LoggingPanel

Returns the background color for the specified log record.

getBackupRegistry() - Method in class org.biojava.spice.SpiceStartParameters

getBottomAlignmentManager() - Method in class org.biojava.spice.manypanel.BrowserPane

getBrowserPane() - Method in interface org.biojava.spice.SPICEFrame

get the BrowserPane that is doing the 2D display

getBrowserPane() - Method in class org.biojava.spice.SpiceApplication

getBrowsermenu() - Method in class org.biojava.spice.gui.BrowseMenuListener

getCapabilities() - Method in class org.biojava.spice.config.RegistryConfiguration

getCapacity() - Method in class org.biojava.spice.gui.logging.LoggingPanel

Returns the capacity.

getChain(int) - Method in interface org.biojava.spice.SPICEFrame

retreive info regarding structure

getChain(int) - Method in class org.biojava.spice.SpiceApplication

get Chain number X from structure

getChain(int) - Method in class org.biojava.spice.gui.SelectionPanel

getChain(int) - Method in class org.biojava.spice.gui.SpiceChainDisplay

getChain() - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

getChainDisplay() - Method in class org.biojava.spice.gui.SelectionPanel

getChainFromSequence(String) - Method in class org.biojava.spice.StructureBuilder

getChainFromString(String) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

getChainId() - Method in class org.biojava.spice.jmol.AtomInfo

getChainLength() - Method in class org.biojava.spice.manypanel.renderer.HistogramPainter

getChainPosByPDB(String) - Method in class org.biojava.spice.SpiceApplication

retreive the chainNumber by PDB character

getChainRendererMouseListener() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getCheck() - Method in class org.biojava.spice.gui.aligchooser.AligLabel

getCheckBoxListener() - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

getCigar(Alignment, String) - Static method in class org.biojava.spice.manypanel.AlignmentTool

getClassification() - Method in class org.biojava.spice.gui.msdkeyword.Deposition

getCode() - Method in class org.biojava.spice.SpiceStartParameters

get the accession code

getCodetype() - Method in class org.biojava.spice.SpiceStartParameters

returns the type of the accession code that is displayed.

getColor(int) - Method in class org.biojava.spice.alignment.StructureAlignment

re turns the color for a particular PDB file

getColor() - Method in class org.biojava.spice.feature.AbstractSegment

getColor() - Method in interface org.biojava.spice.feature.Segment

getColor() - Method in interface org.biojava.spice.manypanel.drawable.Drawable

get the color of the object

getColor() - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

getColor() - Method in class org.biojava.spice.manypanel.drawable.DrawableSequence

getColorGradient(Color, Color, double) - Static method in class org.biojava.spice.manypanel.renderer.DrawUtils

getColumnClass(int) - Method in class org.biojava.spice.config.DasSourcePanelTableModel

getColumnCount() - Method in class org.biojava.spice.config.DasSourcePanelTableModel

getColumnName(int) - Method in class org.biojava.spice.config.DasSourcePanelTableModel

getComponent() - Method in class org.biojava.spice.gui.TabEvent

getConfig() - Method in class org.biojava.spice.config.ConfigXMLHandler

getConfiguration() - Method in interface org.biojava.spice.SPICEFrame

retrieve configuration for DAS servers to use

getConfiguration() - Method in class org.biojava.spice.SpiceApplication

getConfiguration() - Method in class org.biojava.spice.config.DasSourceConfigPanel

getConfiguration() - Method in class org.biojava.spice.gui.ConfigPanel

getContactDate() - Method in class org.biojava.spice.config.RegistryConfiguration

getContent() - Method in class org.biojava.spice.gui.AbstractPopupFrame

this class needs to be provided by implementing sub-classes.

getContent() - Method in class org.biojava.spice.gui.logging.LogPopupFrame

getContent() - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

getContentPane() - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

getCoordSys1() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getCoordSys2() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getCoordinateSystem() - Method in class org.biojava.spice.alignment.StructureAlignment

getCoordinateSystem() - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

getCoordinateSystem() - Method in class org.biojava.spice.manypanel.managers.FeatureManager

getCoordinateSystem() - Method in interface org.biojava.spice.manypanel.managers.ObjectManager

getCurrentChainNumber() - Method in class org.biojava.spice.SpiceApplication

getCurrentChainNumber() - Method in class org.biojava.spice.gui.SelectionPanel

getCurrentChainNumber() - Method in class org.biojava.spice.gui.SpiceChainDisplay

getCurrentChainNumber() - Method in class org.biojava.spice.manypanel.drawable.DrawableStructure

getCursorPanel() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getCursorPanels() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getDasSource() - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

getDasSource() - Method in class org.biojava.spice.manypanel.eventmodel.DasSourceEvent

getDasSource() - Method in class org.biojava.spice.manypanel.eventmodel.SpiceFeatureEvent

getDasSource() - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanelHeader

getDasSourcePanels() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getDasSources() - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

getDasSources() - Method in class org.biojava.spice.manypanel.managers.FeatureManager

getDasSources() - Method in interface org.biojava.spice.manypanel.managers.ObjectManager

get the list of available Reference DAS servers

getDasSources() - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

getDeleteIcon() - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

getDepositions() - Method in class org.biojava.spice.gui.msdkeyword.MSDContentHandler

getDisplay() - Method in class org.biojava.spice.SpiceStartParameters

getDisplayHeight() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getDisplayHeight() - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

getDisplayHeight() - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

getDisplayLabel() - Method in class org.biojava.spice.SpiceStartParameters

getDisplayMessage() - Method in class org.biojava.spice.SpiceStartParameters

getDisplayType() - Method in class org.biojava.spice.das.SpiceDasSource

getDisplayWidth() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getDrawableDasSource() - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

returns a DrawableDasSource - i.e.

getDrawableDasSources() - Method in class org.biojava.spice.manypanel.renderer.FeatureRenderer

getDrawableSequence(String, String) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

getENSPCode() - Method in interface org.biojava.spice.SPICEFrame

getENSPCode() - Method in class org.biojava.spice.SpiceApplication

getENSPManager() - Method in class org.biojava.spice.manypanel.BrowserPane

getEnd() - Method in class org.biojava.spice.feature.AbstractSegment

getEnd() - Method in interface org.biojava.spice.feature.Segment

getEnspListener() - Method in class org.biojava.spice.gui.BrowseMenuListener

getEnspcoordsys() - Method in class org.biojava.spice.SpiceStartParameters

getEstimatedAtomCount(Object) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getExpData() - Method in class org.biojava.spice.gui.msdkeyword.Deposition

getFeature() - Method in class org.biojava.spice.manypanel.eventmodel.SpiceFeatureEvent

getFeaturePanel() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getFeatureTranslator1() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getFeatureTranslator2() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getFeatures() - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

getFilterBy() - Method in class org.biojava.spice.alignment.StructureAlignment

getFilterMenuFromAlignment(Alignment, ActionListener) - Static method in class org.biojava.spice.gui.aligchooser.MenuAlignmentListener

get the "filter by" menu

getFirstSelectedPos() - Method in class org.biojava.spice.alignment.StructureAlignment

get the position of the first selected structure or -1 if none selected.

getForeground(LogRecord) - Method in class org.biojava.spice.gui.logging.LoggingPanel

Returns the foreground color for the specified log record.

getFrom() - Method in class org.biojava.spice.gui.SendEmailGui

getGeneralConfigPanel() - Method in class org.biojava.spice.gui.ConfigPanel

getHandler() - Method in class org.biojava.spice.gui.logging.LoggingPanel

Returns the logging handler.

getHeteroList() - Method in class org.biojava.spice.gui.msdkeyword.Deposition

getIconHeight() - Method in class org.biojava.spice.gui.CloseableTabbedPane.ClosingIcon

getIconWidth() - Method in class org.biojava.spice.gui.CloseableTabbedPane.ClosingIcon

getId() - Method in class org.biojava.spice.gui.msdkeyword.Deposition

getId1() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getId2() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getIds() - Method in class org.biojava.spice.alignment.StructureAlignment

getInstance(int) - Method in class org.biojava.spice.server.SpiceServer

getIntObjectIds() - Method in class org.biojava.spice.alignment.StructureAlignment

getJmolRotation() - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

get the rotation out of Jmol

getJmolRotation() - Method in class org.biojava.spice.jmol.StructurePanel

get the rotation out of Jmol

getKnownDasSource(SpiceDasSource) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

getKnownSource(SpiceDasSource) - Method in class org.biojava.spice.config.RegistryConfiguration

getLabel1() - Method in class org.biojava.spice.manypanel.renderer.ArrowPanel

getLabel2() - Method in class org.biojava.spice.manypanel.renderer.ArrowPanel

getLabels() - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

getLabels() - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

getLastModified() - Method in class org.biojava.spice.gui.msdkeyword.Deposition

getLastSelectedPos() - Method in class org.biojava.spice.alignment.StructureAlignment

get the position of the first selected structure or -1 if none selected.

getLastSelectedPosition() - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

getLayeredPane() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getLink() - Method in class org.biojava.spice.feature.AbstractFeature

getLink() - Method in interface org.biojava.spice.feature.Feature

getLoaded() - Method in class org.biojava.spice.alignment.StructureAlignment

getLoading() - Method in interface org.biojava.spice.manypanel.drawable.Drawable

is the Drawable currently being loaded?

getLoading() - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

getLoading() - Method in class org.biojava.spice.manypanel.drawable.DrawableSequence

getLocalPDBPanel() - Method in class org.biojava.spice.gui.ConfigPanel

getLocalServerCapability() - Method in class org.biojava.spice.SpiceStartParameters

getLocalServerCoordSys() - Method in class org.biojava.spice.SpiceStartParameters

getLocalServerDisplayType() - Method in class org.biojava.spice.SpiceStartParameters

getLocalServerName() - Method in class org.biojava.spice.SpiceStartParameters

getLocalServerURL() - Method in class org.biojava.spice.SpiceStartParameters

getLocalServers() - Method in class org.biojava.spice.config.RegistryConfiguration

returns a list of local SpiceDasSources

getLogger() - Method in class org.biojava.spice.SpiceApplication

getLowerAlignmentManager() - Method in class org.biojava.spice.manypanel.renderer.ArrowPanel

getLowerObjectListener() - Method in class org.biojava.spice.manypanel.renderer.ArrowPanel

getMainFrame() - Method in class org.biojava.spice.gui.SpiceTabbedPane

getMatrices() - Method in class org.biojava.spice.alignment.StructureAlignment

getMax() - Method in class org.biojava.spice.feature.HistogramFeature

getMaxNrFeatures() - Method in class org.biojava.spice.das.SingleFeatureThread

getMaximumSize() - Method in class org.biojava.spice.gui.MemoryMonitor.Surface

getMenu() - Method in class org.biojava.spice.SpiceApplication

getMessage() - Method in class org.biojava.spice.gui.SendEmailGui

getMessageHeight() - Method in class org.biojava.spice.SpiceStartParameters

getMessageWidth() - Method in class org.biojava.spice.SpiceStartParameters

getMethod() - Method in class org.biojava.spice.feature.AbstractFeature

getMethod() - Method in interface org.biojava.spice.feature.Feature

getMin() - Method in class org.biojava.spice.feature.HistogramFeature

getMinimumSize() - Method in class org.biojava.spice.gui.MemoryMonitor.Surface

getModelNumber() - Method in class org.biojava.spice.jmol.AtomInfo

getName() - Method in class org.biojava.spice.feature.AbstractFeature

getName() - Method in class org.biojava.spice.feature.AbstractSegment

getName() - Method in interface org.biojava.spice.feature.Feature

getName() - Method in interface org.biojava.spice.feature.Segment

getNextPosition1(int, int, int) - Method in class org.biojava.spice.manypanel.managers.AbstractAlignmentManager

find the position in the other sequence closest to pos2

getNextPosition2(int, int, int) - Method in class org.biojava.spice.manypanel.managers.AbstractAlignmentManager

find the position in the other sequence closest to pos1

getNote() - Method in class org.biojava.spice.feature.AbstractFeature

getNote() - Method in class org.biojava.spice.feature.AbstractSegment

getNote() - Method in interface org.biojava.spice.feature.Feature

getNote() - Method in interface org.biojava.spice.feature.Segment

getNrStructures() - Method in class org.biojava.spice.alignment.StructureAlignment

getNumberSpices() - Method in class org.biojava.spice.gui.SpiceTabbedPane

getObject(String, Alignment) - Static method in class org.biojava.spice.das.AlignmentTools

getOpenDialogCoords() - Method in class org.biojava.spice.SpiceStartParameters

getPDBCode() - Method in interface org.biojava.spice.SPICEFrame

returns currently displayed PDB code; null if none

getPDBCode() - Method in class org.biojava.spice.SpiceApplication

send a command to Jmol * public void executeCmd(String cmd) { //logger.finest("executing Command "+ cmd); structurePanel.executeCmd(cmd); }

getPDBCodeFromAlignment(Alignment) - Static method in class org.biojava.spice.das.AlignmentTools

getPDBFileExtensions() - Method in class org.biojava.spice.config.RegistryConfiguration

getPDBHeader() - Method in class org.biojava.spice.gui.StatusPanel

getPDBListener() - Method in class org.biojava.spice.gui.BrowseMenuListener

getPDBPos(int, int) - Method in class org.biojava.spice.gui.StatusPanel

getPDBSequenceListener() - Method in class org.biojava.spice.manypanel.BrowserPane

getPanel() - Method in class org.biojava.spice.config.DasSourceConfigPanel

getPanelPos(int) - Method in class org.biojava.spice.manypanel.renderer.CoordManager

getParent() - Method in interface org.biojava.spice.SPICEFrame

returns the java.awt.Container of the spice object

getParent() - Method in class org.biojava.spice.feature.AbstractSegment

getParent() - Method in interface org.biojava.spice.feature.Segment

getParent() - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

getPdbSelectEnd() - Method in class org.biojava.spice.SpiceStartParameters

getPdbSelectStart() - Method in class org.biojava.spice.SpiceStartParameters

getPdbcoordsys() - Method in class org.biojava.spice.SpiceStartParameters

getPopupFrame() - Static method in class org.biojava.spice.SpiceApplication

getPosition1(int) - Method in class org.biojava.spice.manypanel.managers.AbstractAlignmentManager

getPosition2(int) - Method in class org.biojava.spice.manypanel.managers.AbstractAlignmentManager

getPreferredSize() - Method in class org.biojava.spice.gui.MemoryMonitor.Surface

getPreferredStructureAlignmentServerName() - Method in interface org.biojava.spice.SPICEFrame

getPreferredStructureAlignmentServerName() - Method in class org.biojava.spice.SpiceApplication

getRadio() - Method in class org.biojava.spice.gui.aligchooser.AligLabel

getRadioButtonListener() - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

getRasmolScript() - Method in class org.biojava.spice.SpiceStartParameters

getRasmolScript() - Method in class org.biojava.spice.alignment.StructureAlignment

getRasmolScript(int) - Method in class org.biojava.spice.alignment.StructureAlignment

getRasmolScripts() - Method in class org.biojava.spice.alignment.StructureAlignment

getRecipients() - Method in class org.biojava.spice.gui.SendEmailGui

getReferenceStructure() - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

the structure at that position is the first one

getRegistered() - Method in class org.biojava.spice.das.SpiceDasSource

getRegistry() - Method in class org.biojava.spice.SpiceStartParameters

getRegistryUrl() - Method in class org.biojava.spice.config.RegistryConfiguration

getRegistryurls() - Method in class org.biojava.spice.SpiceStartParameters

getResidueName() - Method in class org.biojava.spice.jmol.AtomInfo

getResidueNumber() - Method in class org.biojava.spice.jmol.AtomInfo

getResolution() - Method in class org.biojava.spice.gui.msdkeyword.Deposition

getRfactor() - Method in class org.biojava.spice.gui.msdkeyword.Deposition

getRowCount() - Method in class org.biojava.spice.config.DasSourcePanelTableModel

getRowHeaderListener() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getScale() - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

getScale() - Method in class org.biojava.spice.manypanel.eventmodel.ScaleEvent

getScale() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getScale() - Method in class org.biojava.spice.manypanel.renderer.HistogramPainter

getScale() - Method in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

getScale1() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getScale2() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getScore() - Method in class org.biojava.spice.feature.AbstractFeature

getScore() - Method in interface org.biojava.spice.feature.Feature

getScore() - Method in class org.biojava.spice.feature.HistogramSegment

getScrollPane() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getScrolled1() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getScrolled2() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getSearchBox() - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

getSegment() - Method in class org.biojava.spice.manypanel.eventmodel.SpiceFeatureEvent

getSegments() - Method in class org.biojava.spice.feature.AbstractFeature

getSegments() - Method in interface org.biojava.spice.feature.Feature

getSelection() - Method in class org.biojava.spice.alignment.StructureAlignment

getSelection() - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

getSelectionPanel() - Method in class org.biojava.spice.SpiceApplication

return the chain / alignment selection panel in the middle

getSeq1FeatureListeners() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getSeq1Listener() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getSeq1ScaleListener() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getSeq2FeatureListeners() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getSeq2Listener() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getSeq2ScaleListener() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getSeqPos(int) - Method in class org.biojava.spice.manypanel.renderer.CoordManager

start counting at 0...

getSeqPosByPDB(String) - Method in class org.biojava.spice.SpiceApplication

retreive the sequence position for a residue by it's PDB code.

getSeqSelectEnd() - Method in class org.biojava.spice.SpiceStartParameters

getSeqSelectStart() - Method in class org.biojava.spice.SpiceStartParameters

getSequence() - Method in class org.biojava.spice.manypanel.drawable.DrawableSequence

getSequence1() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getSequence2() - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

getSequenceListener1() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getSequenceListener2() - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

getServer(int) - Method in class org.biojava.spice.config.RegistryConfiguration

getServerAt(int) - Method in class org.biojava.spice.config.DasSourcePanelTableModel

getServers() - Method in class org.biojava.spice.config.DasSourcePanelTableModel

getServers() - Method in class org.biojava.spice.config.RegistryConfiguration

getServers(String, String) - Method in class org.biojava.spice.config.RegistryConfiguration

returns all DAS sources with a particular capability and coordinate system.

getServers(String) - Method in class org.biojava.spice.config.RegistryConfiguration

returns all servers with a particular capaibility.

getShiftVectors() - Method in class org.biojava.spice.alignment.StructureAlignment

getSortMenuFromAlignment(Alignment, ActionListener) - Static method in class org.biojava.spice.gui.aligchooser.MenuAlignmentListener

getSource() - Method in class org.biojava.spice.feature.AbstractFeature

getSource() - Method in interface org.biojava.spice.feature.Feature

getSpiceServer() - Method in interface org.biojava.spice.SPICEFrame

getSpiceServer() - Method in class org.biojava.spice.SpiceApplication

getSpiceStartParameters() - Method in interface org.biojava.spice.SPICEFrame

get the parameters that are used while loading the next molecule

getSpiceStartParameters() - Method in class org.biojava.spice.SpiceApplication

getSpiceTabbedPane() - Method in interface org.biojava.spice.SPICEFrame

getSpiceTabbedPane() - Method in class org.biojava.spice.SpiceApplication

getSpiceText(SPICEFrame) - Method in class org.biojava.spice.gui.SpiceTabbedPane

getStart() - Method in class org.biojava.spice.feature.AbstractSegment

getStart() - Method in interface org.biojava.spice.feature.Segment

getStatus(int) - Method in class org.biojava.spice.config.RegistryConfiguration

getStatus() - Method in class org.biojava.spice.das.SpiceDasSource

getStatusPanel() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getString(String) - Static method in class org.biojava.spice.ResourceManager

getStructure() - Method in interface org.biojava.spice.SPICEFrame

retreive the internal Structure object

getStructure() - Method in class org.biojava.spice.SpiceApplication

getStructure(int) - Method in class org.biojava.spice.alignment.StructureAlignment

getStructure() - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getStructure() - Method in class org.biojava.spice.jmol.StructurePanel

return the currently displayed structure object

getStructure() - Method in class org.biojava.spice.manypanel.drawable.DrawableStructure

getStructure() - Method in class org.biojava.spice.manypanel.managers.StructureManager

getStructureAlignment() - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

getStructureAlignment() - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

getStructureAlignmentListener() - Method in class org.biojava.spice.gui.SelectionPanel

getStructureAlignmentListeners() - Method in class org.biojava.spice.SpiceApplication

return all StructurteAlignmentListeners

getStructureAlignmentListeners() - Method in class org.biojava.spice.gui.alignment.AlternativeAlignmentFrame

getStructureAlignmentMode() - Method in class org.biojava.spice.SpiceStartParameters

getStructureColor() - Method in class org.biojava.spice.manypanel.renderer.StructureScalePanel

get the color do draw the structure region

getStructureFeature() - Method in class org.biojava.spice.manypanel.renderer.StructureScalePanel

getStructureIterator(Object) - Method in class org.biojava.spice.jmol.SpiceJmolAdapter

getStructureListener() - Method in class org.biojava.spice.manypanel.BrowserPane

getStructureListener() - Method in class org.biojava.spice.manypanel.managers.StructureManager

getStructureListeners() - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

getStructureManager() - Method in class org.biojava.spice.manypanel.BrowserPane

getStructureRenderer() - Method in class org.biojava.spice.manypanel.BrowserPane

getStructureServers() - Method in class org.biojava.spice.alignment.StructureAlignment

getStructures() - Method in class org.biojava.spice.alignment.StructureAlignment

getStylesheet() - Method in class org.biojava.spice.das.SpiceDasSource

returns the Stylesheet that is provided by a DAS source.

getStylesheet() - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

getSubject() - Method in class org.biojava.spice.gui.SendEmailGui

getSuggestions() - Method in class org.biojava.spice.gui.msdkeyword.MSDContentHandler

getSuggestions() - Method in class org.biojava.spice.gui.msdkeyword.MSDKeywordSearch

getTabData() - Method in class org.biojava.spice.config.DasSourceConfigPanel

getTabData(SpiceDasSource[]) - Method in class org.biojava.spice.config.DasSourceConfigPanel

getTabForSpice(SPICEFrame) - Method in class org.biojava.spice.gui.SpiceTabbedPane

getTabListener() - Method in class org.biojava.spice.gui.CloseableTabbedPane

getTabNumber() - Method in class org.biojava.spice.gui.TabEvent

getTableByCigar(String) - Static method in class org.biojava.spice.manypanel.AlignmentTool

returns a list of maps

getTableModel() - Method in class org.biojava.spice.config.DasSourceConfigPanel

getTitle() - Method in class org.biojava.spice.gui.msdkeyword.Deposition

getToolTipListener() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

getTopAlignmentManager() - Method in class org.biojava.spice.manypanel.BrowserPane

getTxtColor() - Method in class org.biojava.spice.feature.AbstractSegment

getTxtColor() - Method in interface org.biojava.spice.feature.Segment

getType() - Method in class org.biojava.spice.feature.AbstractFeature

getType() - Method in interface org.biojava.spice.feature.Feature

getType() - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

getTypeCoordMapping(String, SpiceStartParameters) - Method in class org.biojava.spice.gui.OpenDialog

getUPManager() - Method in class org.biojava.spice.manypanel.BrowserPane

getUniProtCode() - Method in interface org.biojava.spice.SPICEFrame

returns currently displayed UniProt code; null if none

getUniProtCode() - Method in class org.biojava.spice.SpiceApplication

getUniProtCodeFromAlignment(Alignment) - Static method in class org.biojava.spice.das.AlignmentTools

getUniProtListener() - Method in class org.biojava.spice.gui.BrowseMenuListener

getUniprotcoordsys() - Method in class org.biojava.spice.SpiceStartParameters

getUpdateBehave() - Method in class org.biojava.spice.config.RegistryConfiguration

getUpperAlignmentManager() - Method in class org.biojava.spice.manypanel.renderer.ArrowPanel

getUpperObjectListener() - Method in class org.biojava.spice.manypanel.renderer.ArrowPanel

getValueAt(int, int) - Method in class org.biojava.spice.config.DasSourcePanelTableModel

getVersion() - Static method in class org.biojava.spice.gui.AboutDialog

getViewer() - Method in interface org.biojava.spice.SPICEFrame

get the Jmol viewer

getViewer() - Method in class org.biojava.spice.SpiceApplication

getViewer() - Method in class org.biojava.spice.jmol.StructurePanel

returns the JmolViewer

H

HELIX_COLOR - Static variable in class org.biojava.spice.config.SpiceDefaults

HistogramFeature - class org.biojava.spice.feature.HistogramFeature.

a class that represents Histogram Style features in addition to normal features they know about Max and Minimum scores for the whole line Histogram feautes have only one (Histogram) Segment, which contains the scores for each position

HistogramFeature() - Constructor for class org.biojava.spice.feature.HistogramFeature

HistogramPainter - class org.biojava.spice.manypanel.renderer.HistogramPainter.

HistogramPainter(CoordManager, float, int) - Constructor for class org.biojava.spice.manypanel.renderer.HistogramPainter

HistogramSegment - class org.biojava.spice.feature.HistogramSegment.

a Histogram segment is an extension of the standard Segment with a score

HistogramSegment() - Constructor for class org.biojava.spice.feature.HistogramSegment

handlePopupMenu(int, int) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

hasUnlimitedFeatures() - Method in class org.biojava.spice.das.SpiceDasSource

headFont - Static variable in class org.biojava.spice.manypanel.renderer.DasSourcePanel

heteroList - Variable in class org.biojava.spice.gui.msdkeyword.Deposition

hideFrame() - Method in class org.biojava.spice.gui.AbstractPopupFrame

I

INFO_ICON_SIZE - Static variable in class org.biojava.spice.manypanel.renderer.DasSourcePanelHeader

INIT_SELECT - Static variable in class org.biojava.spice.jmol.StructurePanelListener

id - Variable in class org.biojava.spice.gui.msdkeyword.Deposition

initJmolDisplay() - Method in class org.biojava.spice.jmol.StructurePanel

call this upon startup.

initPanels() - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

initPanels() - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

interrupt() - Method in class org.biojava.spice.gui.alignment.AlignmentCalc

stops what is currently happening and does not continue

interruptTimer() - Method in class org.biojava.spice.gui.AbstractPopupFrame

isCellEditable(int, int) - Method in class org.biojava.spice.config.DasSourcePanelTableModel

isColumnVisible(LoggingPanel.Column) - Method in class org.biojava.spice.gui.logging.LoggingPanel

Returns true if the given column is visible.

isEntryName(String) - Static method in class org.biojava.spice.utils.UniProtAccessionCodeTools

test if a code is a uniprot entry name e.g.

isLoaded(int) - Method in class org.biojava.spice.alignment.StructureAlignment

isLocalUnlimitedFeatures() - Method in class org.biojava.spice.SpiceStartParameters

isNewTab() - Method in class org.biojava.spice.SpiceStartParameters

a new spice instance should be created as a new tab (isNewTab == true) or as a new SPICE window (isNewTab == false)

isNoRegistryContact() - Method in class org.biojava.spice.SpiceStartParameters

isSecstruc(String) - Method in class org.biojava.spice.feature.FeatureMapComparator

isSelected(int) - Method in class org.biojava.spice.alignment.StructureAlignment

isSeqStrucAlignmentServer(SpiceDasSource) - Method in class org.biojava.spice.config.RegistryConfiguration

test if a server is a UniProt vs PDBresnum alignment server

isShown() - Method in class org.biojava.spice.gui.AbstractPopupFrame

return a flag if the frame is currently shown

isZeroMatrix(Matrix) - Method in class org.biojava.spice.alignment.StructureAlignment

J

JNLPProxy - class org.biojava.spice.utils.JNLPProxy.

JScrollPaneCorner - class org.biojava.spice.manypanel.renderer.JScrollPaneCorner.

JScrollPaneCorner() - Constructor for class org.biojava.spice.manypanel.renderer.JScrollPaneCorner

JmolCommander - interface org.biojava.spice.jmol.JmolCommander.

JmolSpiceTranslator - class org.biojava.spice.jmol.JmolSpiceTranslator.

JmolSpiceTranslator() - Constructor for class org.biojava.spice.jmol.JmolSpiceTranslator

JmolUtils - class org.biojava.spice.jmol.JmolUtils.

some methods taken from Jmol, needed here to provide a good interface

JmolUtils() - Constructor for class org.biojava.spice.jmol.JmolUtils

joinStructures(Structure, Structure) - Method in class org.biojava.spice.StructureBuilder

joins the empty (= no 3D information) structure created from the uniprot sequences with the structure retrieved from PDB

K

keyReleased(KeyEvent) - Method in class org.biojava.spice.gui.StructureCommandListener

takes care of the cursur up/down keys.

L

LEVEL - Static variable in class org.biojava.spice.gui.logging.LoggingPanel

Constant for LoggingPanel.setColumnVisible(org.biojava.spice.gui.logging.LoggingPanel.Column, boolean).

LINE_HEIGHT - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

LINK_ICON_SIZE - Static variable in class org.biojava.spice.manypanel.renderer.DasSourcePanelHeader

LOGGER - Static variable in class org.biojava.spice.config.SpiceDefaults

LOGGER - Static variable in class org.biojava.spice.gui.logging.LoggingPanel

Constant for LoggingPanel.setColumnVisible(org.biojava.spice.gui.logging.LoggingPanel.Column, boolean).

LOG_LEVEL - Static variable in class org.biojava.spice.config.SpiceDefaults

LogPopupFrame - class org.biojava.spice.gui.logging.LogPopupFrame.

LogPopupFrame() - Constructor for class org.biojava.spice.gui.logging.LogPopupFrame

LogPopupFrame(LogRecord) - Constructor for class org.biojava.spice.gui.logging.LogPopupFrame

LoggingPanel - class org.biojava.spice.gui.logging.LoggingPanel.

THis class is taken from the LGPL package Geotools.

LoggingPanel() - Constructor for class org.biojava.spice.gui.logging.LoggingPanel

Constructs a new logging panel.

LoggingPanel(Logger) - Constructor for class org.biojava.spice.gui.logging.LoggingPanel

Constructs a new logging panel and register it to the specified logger.

LoggingPanel(String) - Constructor for class org.biojava.spice.gui.logging.LoggingPanel

Construct a logging panel and register it to the specified logger.

LoggingPanel.Column - class org.biojava.spice.gui.logging.LoggingPanel.Column.

Enumeration class for columns to be shown in a LoggingPanel.

LoggingPanelManager - class org.biojava.spice.gui.LoggingPanelManager.

LoggingPanelManager() - Constructor for class org.biojava.spice.gui.LoggingPanelManager

lastModified - Variable in class org.biojava.spice.gui.msdkeyword.Deposition

load(String, String) - Method in interface org.biojava.spice.SPICEFrame

starts a new thread and loads a new biological object into spice

load(String, String) - Method in class org.biojava.spice.SpiceApplication

load() - Method in class org.biojava.spice.config.PersistentConfig

loads Config from PersistenceService returns null if no PErsistenceService has been created ...

load() - Method in class org.biojava.spice.gui.SaveLoadSession

load a previously saved session into SPICE

loadAlignment(String, DasCoordinateSystem) - Method in class org.biojava.spice.SpiceApplication

load an alignment from an alignment server

loadAlignments(String) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

loadEnsp(String) - Method in class org.biojava.spice.SpiceApplication

start a new thead that retrieves uniprot sequence, and if available protein structure

loadEnsp(String, String) - Method in class org.biojava.spice.SpiceApplication

loadStructure(String) - Method in class org.biojava.spice.SpiceApplication

starts a new thread that retreives protein structure using the DAS structure command from some other server this thread will call the setStructure method to set the protein structure.

loadStylesheet() - Method in class org.biojava.spice.das.SpiceDasSource

loadUniprot(String) - Method in class org.biojava.spice.SpiceApplication

start a new thead that retrieves uniprot sequence, and if available protein structure

loadingFinished(DasSourceEvent) - Method in class org.biojava.spice.manypanel.BrowserPane

loadingFinished(DasSourceEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.DasSourceListener

the loading of the features of this das source has finished

loadingFinished(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

set that loading has been finised and remap the coordinates for protein structure codes...

loadingFinished(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

loadingStarted(DasSourceEvent) - Method in class org.biojava.spice.manypanel.BrowserPane

loadingStarted(DasSourceEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.DasSourceListener

the features of this das source are being loaded

loadingStarted(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

loadingStarted(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

logger - Static variable in class org.biojava.spice.ResourceManager

logger - Static variable in class org.biojava.spice.SpiceApplication

logger - Static variable in class org.biojava.spice.StartParameterFilter

logger - Static variable in class org.biojava.spice.alignment.StructureAlignment

logger - Static variable in class org.biojava.spice.alignment.StructureAlignmentBuilder

logger - Static variable in class org.biojava.spice.gui.AlignmentServerSwitcher

logger - Static variable in class org.biojava.spice.gui.BrowseMenuListener

logger - Static variable in class org.biojava.spice.gui.DasSourceDialog

logger - Static variable in class org.biojava.spice.gui.LoggingPanelManager

logger - Static variable in class org.biojava.spice.gui.OpenDialog

logger - Static variable in class org.biojava.spice.gui.SelectionPanel

logger - Static variable in class org.biojava.spice.gui.SpiceMenuListener

logger - Static variable in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

logger - Static variable in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

logger - Static variable in class org.biojava.spice.gui.alignment.AlignmentCalc

logger - Static variable in class org.biojava.spice.gui.alignment.AlignmentGui

logger - Static variable in class org.biojava.spice.gui.alignment.AlternativeAlignmentFrame

logger - Static variable in class org.biojava.spice.jmol.SpiceJmolAdapter

logger - Static variable in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

logger - Static variable in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

logger - Static variable in class org.biojava.spice.manypanel.renderer.StatusPanel

logger - Static variable in class org.biojava.spice.server.SpiceClient

logger - Static variable in class org.biojava.spice.server.SpiceServer

logger - Static variable in class org.biojava.spice.utils.BrowserOpener

loggingPanel - Static variable in class org.biojava.spice.gui.LoggingPanelManager

M

MAX_COME_BACK_ITERATIONS - Static variable in class org.biojava.spice.das.SingleFeatureThread

number of times the client tries to reconnect to the server if a "come back later" is returned.

MAX_SCALE - Static variable in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

MESSAGE - Static variable in class org.biojava.spice.gui.logging.LoggingPanel

Constant for LoggingPanel.setColumnVisible(org.biojava.spice.gui.logging.LoggingPanel.Column, boolean).

METAL_TYPE - Static variable in class org.biojava.spice.config.SpiceDefaults

METHOD - Static variable in class org.biojava.spice.gui.logging.LoggingPanel

Constant for LoggingPanel.setColumnVisible(org.biojava.spice.gui.logging.LoggingPanel.Column, boolean).

MINIMUM_HEIGHT - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

MSDContentHandler - class org.biojava.spice.gui.msdkeyword.MSDContentHandler.

MSDContentHandler() - Constructor for class org.biojava.spice.gui.msdkeyword.MSDContentHandler

MSDKeywordSearch - class org.biojava.spice.gui.msdkeyword.MSDKeywordSearch.

request all PDB accession codes that match to a particular keyword.

MSDKeywordSearch() - Constructor for class org.biojava.spice.gui.msdkeyword.MSDKeywordSearch

MSDLOCATION - Static variable in class org.biojava.spice.gui.msdkeyword.MSDKeywordSearch

MSDWindow - class org.biojava.spice.gui.msdkeyword.MSDWindow.

a dialog that lists the results of a keword search and allows to load matching PDBs in spice.

MSDWindow(SPICEFrame, String) - Constructor for class org.biojava.spice.gui.msdkeyword.MSDWindow

MSD_SITE_TYPE - Static variable in class org.biojava.spice.config.SpiceDefaults

MemoryMonitor - class org.biojava.spice.gui.MemoryMonitor.

Tracks Memory allocated & used, displayed in graph form.

MemoryMonitor() - Constructor for class org.biojava.spice.gui.MemoryMonitor

MemoryMonitor.Surface - class org.biojava.spice.gui.MemoryMonitor.Surface.

MemoryMonitor.Surface() - Constructor for class org.biojava.spice.gui.MemoryMonitor.Surface

MenuAlignmentListener - class org.biojava.spice.gui.aligchooser.MenuAlignmentListener.

MenuAlignmentListener(JMenu, StructureAlignmentChooser) - Constructor for class org.biojava.spice.gui.aligchooser.MenuAlignmentListener

MenuCreator - class org.biojava.spice.gui.MenuCreator.

MenuCreator() - Constructor for class org.biojava.spice.gui.MenuCreator

main(String[]) - Static method in class org.biojava.spice.Spice

the main call of the SPICE.

main(String[]) - Static method in class org.biojava.spice.gui.MemoryMonitor

main(String[]) - Static method in class org.biojava.spice.jmol.AtomInfoParser

main(String[]) - Static method in class org.biojava.spice.manypanel.SpiceLayeredPanel

main(String[]) - Static method in class org.biojava.spice.utils.JNLPProxy

main(String[]) - Static method in class org.biojava.spice.utils.UniProtAccessionCodeTools

makeTextPanel(String) - Method in class org.biojava.spice.gui.ConfigPanel

mapPDBFeature2Seq(Feature, Chain) - Static method in class org.biojava.spice.manypanel.renderer.PDB2SeqPositionMapper

markForHide() - Method in class org.biojava.spice.gui.AbstractPopupFrame

set a flag that this frame will be disposed in X seconds, unless updateFramePosition is called again

mouseClicked(MouseEvent) - Method in class org.biojava.spice.gui.AbstractPopupFrame

mouseClicked(MouseEvent) - Method in class org.biojava.spice.gui.StructureCommandListener

mouseClicked(MouseEvent) - Method in class org.biojava.spice.gui.aligchooser.AlignmentSortPopup

mouseClicked(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanelMouseListener

mouseClicked(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

mouseClicked(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener

mouseDragged(MouseEvent) - Method in class org.biojava.spice.gui.AbstractPopupFrame

when the mouse is dragged the frame stays at the same location and is not disposed

mouseDragged(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanelMouseListener

mouseDragged(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

mouseDragged(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener

mouseEntered(MouseEvent) - Method in class org.biojava.spice.gui.AbstractPopupFrame

mouseEntered(MouseEvent) - Method in class org.biojava.spice.gui.StructureCommandListener

mouseEntered(MouseEvent) - Method in class org.biojava.spice.gui.aligchooser.AlignmentSortPopup

mouseEntered(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanelMouseListener

mouseEntered(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

mouseEntered(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener

mouseExited(MouseEvent) - Method in class org.biojava.spice.gui.AbstractPopupFrame

mouseExited(MouseEvent) - Method in class org.biojava.spice.gui.StructureCommandListener

mouseExited(MouseEvent) - Method in class org.biojava.spice.gui.aligchooser.AlignmentSortPopup

mouseExited(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanelMouseListener

mouseExited(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

mouseExited(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener

mouseMoved(MouseEvent) - Method in class org.biojava.spice.gui.AbstractPopupFrame

mouseMoved(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanelMouseListener

mouseMoved(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

mouseMoved(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener

mouseOverFeature(SpiceFeatureEvent) - Method in class org.biojava.spice.gui.StatusPanel

mouseOverFeature(SpiceFeatureEvent) - Method in class org.biojava.spice.jmol.StructurePanelListener

mouseOverFeature(SpiceFeatureEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener

mouseOverFeature(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

mouseOverFeature(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

mouseOverFeature(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

mouseOverFeature(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

mouseOverSegment(SpiceFeatureEvent) - Method in class org.biojava.spice.gui.StatusPanel

mouseOverSegment(SpiceFeatureEvent) - Method in class org.biojava.spice.jmol.StructurePanelListener

mouseOverSegment(SpiceFeatureEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener

mouseOverSegment(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

mouseOverSegment(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

mouseOverSegment(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

mouseOverSegment(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

mousePressed(MouseEvent) - Method in class org.biojava.spice.gui.AbstractPopupFrame

mousePressed(MouseEvent) - Method in class org.biojava.spice.gui.SelectionLockPopupListener

mousePressed(MouseEvent) - Method in class org.biojava.spice.gui.StructureCommandListener

mousePressed(MouseEvent) - Method in class org.biojava.spice.gui.aligchooser.AlignmentSortPopup

mousePressed(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanelMouseListener

mousePressed(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

mousePressed(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener

mouseReleased(MouseEvent) - Method in class org.biojava.spice.gui.AbstractPopupFrame

mouseReleased(MouseEvent) - Method in class org.biojava.spice.gui.CloseableTabbedPane.ClosingListener

mouseReleased(MouseEvent) - Method in class org.biojava.spice.gui.SelectionLockPopupListener

mouseReleased(MouseEvent) - Method in class org.biojava.spice.gui.StructureCommandListener

mouseReleased(MouseEvent) - Method in class org.biojava.spice.gui.aligchooser.AlignmentSortPopup

mouseReleased(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanelMouseListener

mouseReleased(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

mouseReleased(MouseEvent) - Method in class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener

moveServer(int, int) - Method in class org.biojava.spice.config.RegistryConfiguration

move a server in the list of servers ...

moveToPosition(String, int) - Method in class org.biojava.spice.config.RegistryConfiguration

move the server with the url to position note: all positions relative to all servers

N

NO_RUNNING_SPICE - Static variable in class org.biojava.spice.server.SpiceProtocol

NO_SPICE_FOUND - Static variable in class org.biojava.spice.server.SpiceClient

newAlignment(AlignmentEvent) - Method in class org.biojava.spice.alignment.StructureAlignmentBuilder

newAlignment(AlignmentEvent) - Method in class org.biojava.spice.gui.aligchooser.MenuAlignmentListener

newAlignment(AlignmentEvent) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

convert the biojava alignment class into biojava feature objects

newAlignment(AlignmentEvent) - Method in class org.biojava.spice.manypanel.managers.AbstractAlignmentManager

newAlignment(AlignmentEvent) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

newConfigRetrieved(RegistryConfiguration) - Method in class org.biojava.spice.SpiceApplication

newConfigRetrieved(RegistryConfiguration) - Method in interface org.biojava.spice.config.ConfigurationListener

newConfigRetrieved(RegistryConfiguration) - Method in class org.biojava.spice.config.RegistryConfigIO

waiting for the thread that contacts the DAS registry to finish

newConfigRetrieved(RegistryConfiguration) - Method in class org.biojava.spice.gui.ConfigPanel

newDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.BrowserPane

newDasSource(DasSourceEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.DasSourceListener

a new DAS source to be added

newDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

add DasSourcePanels

newDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

newFeatures(FeatureEvent) - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

newFeatures(FeatureEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.FeatureListener

new features have been returned from the Annotation server

newFeatures(FeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

when new features are loaded the panel positions need to be recalculated.

newFeatures(FeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

newObject(Object) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

a new object has been returned

newObject(Object) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

newObject(Object) - Method in class org.biojava.spice.manypanel.managers.StructureManager

newObject1(Object) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

newObject2(Object) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

newObjectRequested(String) - Method in class org.biojava.spice.gui.SelectionPanel

newObjectRequested(String) - Method in class org.biojava.spice.gui.SpiceChainDisplay

newObjectRequested(String) - Method in class org.biojava.spice.gui.SpiceMenuListener

newObjectRequested(String) - Method in class org.biojava.spice.gui.StatusPanel

newObjectRequested(String) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

newObjectRequested(String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

newObjectRequested(String) - Method in class org.biojava.spice.jmol.StructurePanelListener

newObjectRequested(String) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

newObjectRequested(String) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

a new object has been requested.

newObjectRequested(String) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

trigger DAS Sequence request

newObjectRequested(String) - Method in class org.biojava.spice.manypanel.managers.StructureManager

a new structure should be loaded trigger the loading threads.

newObjectRequested(String) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

newObjectRequested(String) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

newObjectRequested(String) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

newObjectRequested1(String) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

newObjectRequested2(String) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

newSequence(SequenceEvent) - Method in class org.biojava.spice.gui.SpiceMenuListener

newSequence(SequenceEvent) - Method in class org.biojava.spice.gui.StatusPanel

newSequence(SequenceEvent) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

newSequence(SequenceEvent) - Method in class org.biojava.spice.jmol.StructurePanelListener

newSequence(SequenceEvent) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

newSequence(SequenceEvent) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

newSequence(SequenceEvent) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

newSequence(SequenceEvent) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

newSequence(SequenceEvent) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

newSequence1(SequenceEvent) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

newSequence1(SequenceEvent) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

newSequence2(SequenceEvent) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

newSequence2(SequenceEvent) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

newStructure(StructureEvent) - Method in class org.biojava.spice.gui.SelectionPanel

newStructure(StructureEvent) - Method in class org.biojava.spice.gui.SpiceChainDisplay

newStructure(StructureEvent) - Method in class org.biojava.spice.gui.StatusPanel

newStructure(StructureEvent) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

newStructure(StructureEvent) - Method in class org.biojava.spice.jmol.StructurePanelListener

newStructure(StructureEvent) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

newStructure(StructureEvent) - Method in class org.biojava.spice.manypanel.managers.StructureManager

a new Structure has been retrieved

newline - Static variable in class org.biojava.spice.config.SpiceDefaults

noAlignmentFound(AlignmentEvent) - Method in class org.biojava.spice.alignment.StructureAlignmentBuilder

noAlignmentFound(AlignmentEvent) - Method in class org.biojava.spice.gui.aligchooser.MenuAlignmentListener

noAlignmentFound(AlignmentEvent) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

noAlignmentFound(AlignmentEvent) - Method in class org.biojava.spice.manypanel.managers.AbstractAlignmentManager

noAlignmentFound(AlignmentEvent) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

no alignment could be found for this object ...

noObjectFound(String) - Method in class org.biojava.spice.gui.SelectionPanel

noObjectFound(String) - Method in class org.biojava.spice.gui.SpiceChainDisplay

noObjectFound(String) - Method in class org.biojava.spice.gui.SpiceMenuListener

noObjectFound(String) - Method in class org.biojava.spice.gui.StatusPanel

noObjectFound(String) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

noObjectFound(String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

noObjectFound(String) - Method in class org.biojava.spice.jmol.StructurePanelListener

noObjectFound(String) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

noObjectFound(String) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

noObjectFound(String) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

noObjectFound(String) - Method in class org.biojava.spice.manypanel.managers.StructureManager

noObjectFound(String) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

noObjectFound(String) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

noObjectFound(String) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

noObjectFound1(String) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

noObjectFound2(String) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

notifyAtomHovered(int, String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyAtomPicked(int, String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyCalcFinished() - Method in class org.biojava.spice.gui.alignment.AlignmentGui

notifyFileLoaded(String, String, String, Object, String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyFileNotLoaded(String, String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyFrameChanged(int) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyFrameChanged(int, int, int, int, int) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyMeasurementsChanged() - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyNewDefaultModeMeasurement(int, String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyNewPickingModeMeasurement(int, String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyResized(int, int) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyScriptStart(String, String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

notifyScriptTermination(String, int) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

nrInstances() - Method in class org.biojava.spice.server.SpiceServer

O

ObjectManager - interface org.biojava.spice.manypanel.managers.ObjectManager.

ObjectRenderer - interface org.biojava.spice.manypanel.renderer.ObjectRenderer.

OpenDialog - class org.biojava.spice.gui.OpenDialog.

Enter a new PDB, UniProt, or ENSP code to be loaded in SPICE.

OpenDialog(SpiceApplication) - Constructor for class org.biojava.spice.gui.OpenDialog

a dialog responsible for opening new entries.

org.biojava.spice - package org.biojava.spice

The main directory of SPICE.

org.biojava.spice.alignment - package org.biojava.spice.alignment

org.biojava.spice.config - package org.biojava.spice.config

the config section of SPICE.

org.biojava.spice.das - package org.biojava.spice.das

Everything related to DAS communication and data retreival.

org.biojava.spice.feature - package org.biojava.spice.feature

Everything related to Features.

org.biojava.spice.gui - package org.biojava.spice.gui

A collection of classes related to the GUI.

org.biojava.spice.gui.aligchooser - package org.biojava.spice.gui.aligchooser

org.biojava.spice.gui.alignment - package org.biojava.spice.gui.alignment

org.biojava.spice.gui.alignmentchooser - package org.biojava.spice.gui.alignmentchooser

The chooser of alternative UniProt to PDB alignments.

org.biojava.spice.gui.logging - package org.biojava.spice.gui.logging

org.biojava.spice.gui.msdkeyword - package org.biojava.spice.gui.msdkeyword

org.biojava.spice.jmol - package org.biojava.spice.jmol

org.biojava.spice.manypanel - package org.biojava.spice.manypanel

org.biojava.spice.manypanel.drawable - package org.biojava.spice.manypanel.drawable

org.biojava.spice.manypanel.eventmodel - package org.biojava.spice.manypanel.eventmodel

org.biojava.spice.manypanel.managers - package org.biojava.spice.manypanel.managers

org.biojava.spice.manypanel.renderer - package org.biojava.spice.manypanel.renderer

org.biojava.spice.server - package org.biojava.spice.server

org.biojava.spice.utils - package org.biojava.spice.utils

overlaps(int) - Method in class org.biojava.spice.feature.AbstractFeature

returns true if the specified sequence position is within the range of this Feature

overlaps(int) - Method in class org.biojava.spice.feature.AbstractSegment

overlaps(Segment) - Method in class org.biojava.spice.feature.AbstractSegment

overlaps(int) - Method in interface org.biojava.spice.feature.Feature

returns true if the specified sequence position is within the range of this Feature

overlaps(int) - Method in interface org.biojava.spice.feature.Segment

returns true if the specified sequence position is within the range of this Segment

overlaps(Segment) - Method in interface org.biojava.spice.feature.Segment

tests if two segments are overlapping

P

PDB2SeqPositionMapper - class org.biojava.spice.manypanel.renderer.PDB2SeqPositionMapper.

PDB2SeqPositionMapper() - Constructor for class org.biojava.spice.manypanel.renderer.PDB2SeqPositionMapper

PDBCOORDSYS - Static variable in class org.biojava.spice.config.SpiceDefaults

PDBCOORDSYS - Static variable in class org.biojava.spice.manypanel.SpiceLayeredPanel

PDBLINK - Static variable in class org.biojava.spice.gui.BrowseMenuListener

PDBLINK - Static variable in class org.biojava.spice.gui.StatusPanel

PDBLINK - Static variable in class org.biojava.spice.manypanel.renderer.StatusPanel

PDBType - Static variable in class org.biojava.spice.config.SpiceDefaults

PROVIEWLINK - Static variable in class org.biojava.spice.gui.BrowseMenuListener

PersistentConfig - class org.biojava.spice.config.PersistentConfig.

a class to store the config using the Java Web Start PersistenService.

PersistentConfig() - Constructor for class org.biojava.spice.config.PersistentConfig

paint(Graphics) - Method in class org.biojava.spice.gui.MemoryMonitor.Surface

paint(Graphics) - Method in class org.biojava.spice.jmol.StructurePanel

paint Jmol

paint(Graphics) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanel

paintComponent(Graphics) - Method in class org.biojava.spice.gui.alignmentchooser.ShowAligPanel

paintComponent(Graphics) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

paintComponent(Graphics) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

paintComponent(Graphics) - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

paintComponent(Graphics) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

paintComponent(Graphics) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanelHeader

paintComponent(Graphics, int) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanelHeader

paintComponent(Graphics) - Method in class org.biojava.spice.manypanel.renderer.JScrollPaneCorner

paintComponent(Graphics) - Method in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

paintComponent(Graphics) - Method in class org.biojava.spice.manypanel.renderer.StructureScalePanel

paintIcon(Component, Graphics, int, int) - Method in class org.biojava.spice.gui.CloseableTabbedPane.ClosingIcon

Overwrites paintIcon to get hold of the coordinates of the icon, this is a rather rude approach just to find out if the closingIcon was pressed.

parse(String) - Static method in class org.biojava.spice.jmol.AtomInfoParser

parses e.g.

plainFont - Static variable in class org.biojava.spice.manypanel.renderer.DasSourcePanel

postMail(String, String, String) - Method in class org.biojava.spice.utils.SendEmail

postMailFromGui(String[], String, String, String) - Method in class org.biojava.spice.gui.SendEmailGui

create a simple user interface to post emails

processInput(String, SpiceServer) - Method in class org.biojava.spice.server.SpiceProtocol

The input should look like: SPICE: test check if SPICE is there.

R

REGISTRY - Static variable in class org.biojava.spice.config.SpiceDefaults

RainbowPainter - class org.biojava.spice.gui.RainbowPainter.

gets the selection or the whole structure from spice and colors it by rainbow ...

RainbowPainter(JmolCommander, Group[]) - Constructor for class org.biojava.spice.gui.RainbowPainter

RegistryConfigIO - class org.biojava.spice.config.RegistryConfigIO.

a class to contact and retreive the configuration from a DAS registry server.

RegistryConfigIO(URL[]) - Constructor for class org.biojava.spice.config.RegistryConfigIO

RegistryConfiguration - class org.biojava.spice.config.RegistryConfiguration.

Container class for configuration

RegistryConfiguration() - Constructor for class org.biojava.spice.config.RegistryConfiguration

ResourceManager - class org.biojava.spice.ResourceManager.

A class that manages the Strings that are defined in the spice.properties file.

RowHeaderMouseListener - class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener.

a mouse listener that listens on mouse events of the scroll panel's row header

RowHeaderMouseListener(DasScrollPaneRowHeader) - Constructor for class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener

radiansPerDegree - Static variable in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

randomPick(Collection) - Static method in class org.biojava.spice.utils.CollectTools

recalcAlignmentDisplay() - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

recalculate the displayed alignment.

record2HTML(LogRecord) - Method in class org.biojava.spice.gui.logging.LogPopupFrame

record2HTMLBody(LogRecord, StringBuffer) - Method in class org.biojava.spice.gui.logging.LogPopupFrame

registerInstance(SPICEFrame) - Method in class org.biojava.spice.server.SpiceServer

registry - Static variable in class org.biojava.spice.manypanel.SpiceLayeredPanel

reload() - Method in interface org.biojava.spice.SPICEFrame

reload the currently displayed data

reload() - Method in class org.biojava.spice.SpiceApplication

force a re-load of all the currently displayed data

removeDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.BrowserPane

removeDasSource(DasSourceEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.DasSourceListener

remove a DAS source

removeDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

removeDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

removeDrawableDasSource(DrawableDasSource) - Method in class org.biojava.spice.manypanel.renderer.FeatureRenderer

removeEnspSequenceListener(SequenceListener) - Method in class org.biojava.spice.manypanel.BrowserPane

removeInstance(SPICEFrame) - Method in class org.biojava.spice.server.SpiceServer

removeSPICE(SPICEFrame) - Method in class org.biojava.spice.gui.SpiceTabbedPane

removeSequenceListener(SequenceListener) - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

removeStructureListener(StructureListener) - Method in class org.biojava.spice.manypanel.BrowserPane

removeStructureListener(StructureListener) - Method in class org.biojava.spice.manypanel.managers.StructureManager

removeUniProtSequenceListener(SequenceListener) - Method in class org.biojava.spice.manypanel.BrowserPane

repaint() - Method in class org.biojava.spice.gui.AbstractPopupFrame

repaint() - Method in class org.biojava.spice.gui.SelectionPanel

repaint() - Method in class org.biojava.spice.gui.aligchooser.AligLabel

repaint() - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

repaintBox(AligLabel, int, Color) - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

request(String) - Method in class org.biojava.spice.alignment.StructureAlignmentBuilder

requestedObject1(String) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

requestedObject2(String) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

reset() - Method in class org.biojava.spice.jmol.StructurePanel

reset the Jmol display

resetDisplay() - Method in interface org.biojava.spice.SPICEFrame

reset the display, but do not change data

resetDisplay() - Method in class org.biojava.spice.SpiceApplication

reset the Jmol panel

resetDisplay() - Method in class org.biojava.spice.jmol.StructurePanelListener

reset the Jmol panel

resetTimer() - Method in class org.biojava.spice.gui.AbstractPopupFrame

resolution - Variable in class org.biojava.spice.gui.msdkeyword.Deposition

rfactor - Variable in class org.biojava.spice.gui.msdkeyword.Deposition

rotateJmol(Matrix) - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

rotateJmol(Matrix) - Method in class org.biojava.spice.jmol.StructurePanel

send a rotation to Jmol

run() - Method in class org.biojava.spice.config.RegistryConfigIO

run() - Method in class org.biojava.spice.das.SingleFeatureThread

start thread

run() - Method in class org.biojava.spice.gui.MemoryMonitor.Surface

run() - Method in class org.biojava.spice.gui.alignment.AlignmentCalc

launch the calculation

run() - Method in class org.biojava.spice.server.SpiceMultiServerThread

S

SCALE_COLOR - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

SEARCH_DIRECTION_DECREASE - Static variable in class org.biojava.spice.manypanel.managers.AbstractAlignmentManager

SEARCH_DIRECTION_INCREASE - Static variable in class org.biojava.spice.manypanel.managers.AbstractAlignmentManager

SECSTRUC_TYPE - Static variable in class org.biojava.spice.config.SpiceDefaults

SELECTED_FEATURE_COLOR - Static variable in class org.biojava.spice.manypanel.renderer.DasSourcePanel

SEQUENCE_COLOR - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

SIZE - Static variable in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

SIZE - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

SORT_BY_NAME - Static variable in class org.biojava.spice.gui.aligchooser.MenuAlignmentListener

SPICEFrame - interface org.biojava.spice.SPICEFrame.

an interface that defines methods provided by the master application.

SPICEPORT - Static variable in class org.biojava.spice.server.SpiceServer

SPICE_ERROR - Static variable in class org.biojava.spice.server.SpiceProtocol

SPICE_OK - Static variable in class org.biojava.spice.server.SpiceProtocol

SPICE_SUBMITTED - Static variable in class org.biojava.spice.server.SpiceClient

SPICE_WHAT - Static variable in class org.biojava.spice.server.SpiceProtocol

STATUS_PANEL_HEIGHT - Static variable in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

STRAND_COLOR - Static variable in class org.biojava.spice.config.SpiceDefaults

STRUCTURE_BACKGROUND_COLOR - Static variable in class org.biojava.spice.gui.alignmentchooser.ShowAligPanel

STRUCTURE_BACKGROUND_COLOR - Static variable in class org.biojava.spice.manypanel.renderer.StructureScalePanel

STRUCTURE_CATEGORY - Static variable in class org.biojava.spice.gui.AlignmentServerSwitcher

STRUCTURE_COLOR - Static variable in class org.biojava.spice.gui.alignmentchooser.ShowAligPanel

STRUCTURE_DEFAULT_COLOR - Static variable in class org.biojava.spice.manypanel.renderer.StructureScalePanel

SaveLoadSession - class org.biojava.spice.gui.SaveLoadSession.

SaveLoadSession(SpiceApplication) - Constructor for class org.biojava.spice.gui.SaveLoadSession

ScaleEvent - class org.biojava.spice.manypanel.eventmodel.ScaleEvent.

ScaleEvent(float) - Constructor for class org.biojava.spice.manypanel.eventmodel.ScaleEvent

ScaleListener - interface org.biojava.spice.manypanel.eventmodel.ScaleListener.

Scaleable - interface org.biojava.spice.manypanel.Scaleable.

Interface for objects that can be scaled in an out

SearchDasSourceManager - class org.biojava.spice.config.SearchDasSourceManager.

a class that searches all DasSources for a particular keyword and returns a list of DasSources that match it

SearchDasSourceManager() - Constructor for class org.biojava.spice.config.SearchDasSourceManager

Segment - interface org.biojava.spice.feature.Segment.

a class to keep track of location information for a feature

SegmentComparator - class org.biojava.spice.feature.SegmentComparator.

SegmentComparator() - Constructor for class org.biojava.spice.feature.SegmentComparator

SegmentImpl - class org.biojava.spice.feature.SegmentImpl.

SegmentImpl() - Constructor for class org.biojava.spice.feature.SegmentImpl

SegmentPopupFrame - class org.biojava.spice.manypanel.renderer.SegmentPopupFrame.

provides the actual implementation of the AbstractPopupFrame This class takes care of the actual behaviour of when the popup appears, as well as provides the content

SegmentPopupFrame() - Constructor for class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

SelectionLockMenuListener - class org.biojava.spice.gui.SelectionLockMenuListener.

SelectionLockMenuListener(SPICEFrame, URL) - Constructor for class org.biojava.spice.gui.SelectionLockMenuListener

SelectionLockPopupListener - class org.biojava.spice.gui.SelectionLockPopupListener.

SelectionLockPopupListener(JPopupMenu) - Constructor for class org.biojava.spice.gui.SelectionLockPopupListener

SelectionPanel - class org.biojava.spice.gui.SelectionPanel.

a class that eithe provides a JList or a JCheckbox, depending if spice is running in structure alignment mode or in single protein mode

SelectionPanel(JMenu) - Constructor for class org.biojava.spice.gui.SelectionPanel

SendEmail - class org.biojava.spice.utils.SendEmail.

SendEmail() - Constructor for class org.biojava.spice.utils.SendEmail

SendEmailGui - class org.biojava.spice.gui.SendEmailGui.

SendEmailGui() - Constructor for class org.biojava.spice.gui.SendEmailGui

SeqToolTipListener - class org.biojava.spice.manypanel.renderer.SeqToolTipListener.

a class that displays a tooltip if mouse over a feature.

SeqToolTipListener(JComponent) - Constructor for class org.biojava.spice.manypanel.renderer.SeqToolTipListener

SequenceManager - class org.biojava.spice.manypanel.managers.SequenceManager.

SequenceManager() - Constructor for class org.biojava.spice.manypanel.managers.SequenceManager

SequenceRenderer - class org.biojava.spice.manypanel.renderer.SequenceRenderer.

SequenceRenderer() - Constructor for class org.biojava.spice.manypanel.renderer.SequenceRenderer

SequenceScalePanel - class org.biojava.spice.manypanel.renderer.SequenceScalePanel.

a class that draws a Sequence as a rectange, a scale display over it

SequenceScalePanel() - Constructor for class org.biojava.spice.manypanel.renderer.SequenceScalePanel

ShowAligPanel - class org.biojava.spice.gui.alignmentchooser.ShowAligPanel.

ShowAligPanel(Alignment) - Constructor for class org.biojava.spice.gui.alignmentchooser.ShowAligPanel

SingleFeatureThread - class org.biojava.spice.das.SingleFeatureThread.

a thread that connects to a DAS - Feature service and gets the features

SingleFeatureThread(String, SpiceDasSource) - Constructor for class org.biojava.spice.das.SingleFeatureThread

contact a single DAS feature server and retreive features

Spice - class org.biojava.spice.Spice.

SPICE is a browser for protein structure and sequence annotations built on the Distributed Annotation System.

Spice() - Constructor for class org.biojava.spice.Spice

SpiceApplication - class org.biojava.spice.SpiceApplication.

the main application layer of SPICE do not interact with this class directly, but interact with SPICEFrame interface.

SpiceApplication(SpiceStartParameters) - Constructor for class org.biojava.spice.SpiceApplication

start the spice appplication

SpiceChainDisplay - class org.biojava.spice.gui.SpiceChainDisplay.

SpiceChainDisplay(JList) - Constructor for class org.biojava.spice.gui.SpiceChainDisplay

SpiceClient - class org.biojava.spice.server.SpiceClient.

SpiceClient() - Constructor for class org.biojava.spice.server.SpiceClient

SpiceDasSource - class org.biojava.spice.das.SpiceDasSource.

Manages all data about a DAS source that SPICE requires

SpiceDasSource() - Constructor for class org.biojava.spice.das.SpiceDasSource

SpiceDefaults - class org.biojava.spice.config.SpiceDefaults.

SpiceDefaults() - Constructor for class org.biojava.spice.config.SpiceDefaults

SpiceFeatureEvent - class org.biojava.spice.manypanel.eventmodel.SpiceFeatureEvent.

SpiceFeatureEvent(SpiceDasSource, Feature) - Constructor for class org.biojava.spice.manypanel.eventmodel.SpiceFeatureEvent

SpiceFeatureEvent(SpiceDasSource, Feature, Segment) - Constructor for class org.biojava.spice.manypanel.eventmodel.SpiceFeatureEvent

SpiceFeatureListener - interface org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener.

SpiceJmolAdapter - class org.biojava.spice.jmol.SpiceJmolAdapter.

SpiceJmolAdapter() - Constructor for class org.biojava.spice.jmol.SpiceJmolAdapter

SpiceLayeredPanel - class org.biojava.spice.manypanel.SpiceLayeredPanel.

SpiceLayeredPanel() - Constructor for class org.biojava.spice.manypanel.SpiceLayeredPanel

SpiceMenuListener - class org.biojava.spice.gui.SpiceMenuListener.

This class takes care of the events that are triggered if a MenuItem is choosen from the main spice menu.

SpiceMenuListener(SPICEFrame, StructurePanelListener) - Constructor for class org.biojava.spice.gui.SpiceMenuListener

SpiceMultiServerThread - class org.biojava.spice.server.SpiceMultiServerThread.

A thread that listens to a port and a sends incomming messages to the SpiceProtocol

SpiceMultiServerThread(Socket, SpiceServer) - Constructor for class org.biojava.spice.server.SpiceMultiServerThread

SpiceProtocol - class org.biojava.spice.server.SpiceProtocol.

a class that defines the protocol how two instances of spice can communicate with each other.

SpiceProtocol() - Constructor for class org.biojava.spice.server.SpiceProtocol

SpiceServer - class org.biojava.spice.server.SpiceServer.

SpiceServer() - Constructor for class org.biojava.spice.server.SpiceServer

SpiceStartParameters - class org.biojava.spice.SpiceStartParameters.

a class to manage the SPICE statup parameters.

SpiceStartParameters() - Constructor for class org.biojava.spice.SpiceStartParameters

SpiceTabbedPane - class org.biojava.spice.gui.SpiceTabbedPane.

SpiceTabbedPane(SpiceServer) - Constructor for class org.biojava.spice.gui.SpiceTabbedPane

SpiceTabbedPane(SpiceServer, SpiceApplication) - Constructor for class org.biojava.spice.gui.SpiceTabbedPane

StartParameterFilter - class org.biojava.spice.StartParameterFilter.

a class that filters SpiceDasSources based on the SpiceStartParameters

StartParameterFilter() - Constructor for class org.biojava.spice.StartParameterFilter

StatusPanel - class org.biojava.spice.gui.StatusPanel.

a class to display status information contains a status display to display arbitraty text the PDB code of the currently displayed PDB file the UniProt code of the currently displayed UniProt sequence a progressBar to display ongoing progress

StatusPanel(SPICEFrame) - Constructor for class org.biojava.spice.gui.StatusPanel

StatusPanel - class org.biojava.spice.manypanel.renderer.StatusPanel.

StatusPanel() - Constructor for class org.biojava.spice.manypanel.renderer.StatusPanel

StructureAlignment - class org.biojava.spice.alignment.StructureAlignment.

StructureAlignment(DasCoordinateSystem) - Constructor for class org.biojava.spice.alignment.StructureAlignment

StructureAlignmentBuilder - class org.biojava.spice.alignment.StructureAlignmentBuilder.

a class that builds up a structure alignment and creates a StructureAlignment object

StructureAlignmentBuilder(DasCoordinateSystem) - Constructor for class org.biojava.spice.alignment.StructureAlignmentBuilder

StructureAlignmentChooser - class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser.

a JPanel that contains radio buttons to choose, which structures to show superimposed

StructureAlignmentChooser(JMenu) - Constructor for class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

StructureAlignmentComparator - class org.biojava.spice.alignment.StructureAlignmentComparator.

StructureAlignmentComparator(String) - Constructor for class org.biojava.spice.alignment.StructureAlignmentComparator

StructureAlignmentListener - interface org.biojava.spice.manypanel.eventmodel.StructureAlignmentListener.

StructureBuilder - class org.biojava.spice.StructureBuilder.

StructureBuilder(DasCoordinateSystem, DasCoordinateSystem) - Constructor for class org.biojava.spice.StructureBuilder

StructureCommandListener - class org.biojava.spice.gui.StructureCommandListener.

A class that listens to various events on the StructureCommand line ( where it is possible to enter RASMOL like commands) and takes care of clearing the selection upon startup tracking the history of entered commands sending the command to the structure panel, once Enter is being pressed.

StructureCommandListener(JmolCommander, JTextField) - Constructor for class org.biojava.spice.gui.StructureCommandListener

StructureCommandPanel - class org.biojava.spice.gui.StructureCommandPanel.

Provides an TextField that can be used to enter new RASMOL like commands that are sent to JMol.

StructureCommandPanel(JmolCommander) - Constructor for class org.biojava.spice.gui.StructureCommandPanel

StructureManager - class org.biojava.spice.manypanel.managers.StructureManager.

a manager class to manage to load structure data and convert them into a Drawable

StructureManager() - Constructor for class org.biojava.spice.manypanel.managers.StructureManager

StructurePanel - class org.biojava.spice.jmol.StructurePanel.

A panel that provides a wrapper around the Jmol viewer.

StructurePanel() - Constructor for class org.biojava.spice.jmol.StructurePanel

StructurePanelListener - class org.biojava.spice.jmol.StructurePanelListener.

A class that listens to SPICE events (like sequence position selected) and triggers the corresponding rasmol script in the Jmol display (the structurePanel)

StructurePanelListener(StructurePanel) - Constructor for class org.biojava.spice.jmol.StructurePanelListener

listens to spice events and creates the Rasmol scripts to be sent to Jmol

StructureRenderer - class org.biojava.spice.manypanel.renderer.StructureRenderer.

StructureRenderer() - Constructor for class org.biojava.spice.manypanel.renderer.StructureRenderer

StructureScalePanel - class org.biojava.spice.manypanel.renderer.StructureScalePanel.

StructureScalePanel() - Constructor for class org.biojava.spice.manypanel.renderer.StructureScalePanel

save(RegistryConfiguration) - Method in class org.biojava.spice.config.PersistentConfig

writes the configuration

save() - Method in class org.biojava.spice.gui.SaveLoadSession

save current SPICE session

saveConfiguration() - Method in class org.biojava.spice.config.RegistryConfigIO

write back the config to the SPICE application

saveConfiguration() - Method in class org.biojava.spice.gui.ConfigPanel

scaleChanged(ScaleEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.ScaleListener

scriptEcho(String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

scriptStatus(String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

search(String) - Method in class org.biojava.spice.gui.msdkeyword.MSDKeywordSearch

searchForKeyword(SpiceDasSource[], String) - Static method in class org.biojava.spice.config.SearchDasSourceManager

search all sources for a particular keyword and return matching das sources

segmentSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.gui.StatusPanel

segmentSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.jmol.StructurePanelListener

segmentSelected(SpiceFeatureEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener

segmentSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

segmentSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

segmentSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

segmentSelected(SpiceFeatureEvent) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

select(int) - Method in class org.biojava.spice.alignment.StructureAlignment

selectAllSources() - Method in class org.biojava.spice.config.DasSourceConfigPanel

selectedChain(StructureEvent) - Method in class org.biojava.spice.gui.SelectionPanel

selectedChain(StructureEvent) - Method in class org.biojava.spice.gui.SpiceChainDisplay

selectedChain(StructureEvent) - Method in class org.biojava.spice.gui.StatusPanel

selectedChain(StructureEvent) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

selectedChain(StructureEvent) - Method in class org.biojava.spice.jmol.StructurePanelListener

selectedChain(StructureEvent) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

selectedChain(StructureEvent) - Method in class org.biojava.spice.manypanel.managers.StructureManager

selectedDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.BrowserPane

selectedDasSource(DasSourceEvent) - Method in interface org.biojava.spice.manypanel.eventmodel.DasSourceListener

a DAS source has been selected (in the GUI)

selectedDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

selectedDasSource(DasSourceEvent) - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

selectedSeqPosition(int) - Method in class org.biojava.spice.gui.SpiceMenuListener

selectedSeqPosition(int) - Method in class org.biojava.spice.gui.StatusPanel

selectedSeqPosition(int) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

selectedSeqPosition(int) - Method in class org.biojava.spice.jmol.StructurePanelListener

selectedSeqPosition(int) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

selectedSeqPosition(int) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

selectedSeqPosition(int) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

selectedSeqPosition(int) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

selectedSeqPosition(int) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

selectedSeqPosition1(int) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

selectedSeqPosition1(int) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

selectedSeqPosition2(int) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

selectedSeqPosition2(int) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

selectedSeqRange(int, int) - Method in class org.biojava.spice.gui.SpiceMenuListener

selectedSeqRange(int, int) - Method in class org.biojava.spice.gui.StatusPanel

selectedSeqRange(int, int) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

selectedSeqRange(int, int) - Method in class org.biojava.spice.jmol.StructurePanelListener

select a range of sequence.

selectedSeqRange(int, int) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

selectedSeqRange(int, int) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

selectedSeqRange(int, int) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

selectedSeqRange(int, int) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

selectedSeqRange(int, int) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

stores the text in the clipboard

selectedSeqRange1(int, int) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

selectedSeqRange1(int, int) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

selectedSeqRange2(int, int) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

selectedSeqRange2(int, int) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

selectionLocked(boolean) - Method in class org.biojava.spice.gui.SpiceMenuListener

selectionLocked(boolean) - Method in class org.biojava.spice.gui.StatusPanel

selectionLocked(boolean) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

selectionLocked(boolean) - Method in class org.biojava.spice.jmol.StructurePanelListener

selectionLocked(boolean) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

selectionLocked(boolean) - Method in class org.biojava.spice.manypanel.managers.SequenceManager

selectionLocked(boolean) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

selectionLocked(boolean) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

selectionLocked(boolean) - Method in class org.biojava.spice.manypanel.renderer.SegmentPopupFrame

selectionLocked(boolean) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

selectionLocked1(boolean) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

selectionLocked2(boolean) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

send(SpiceStartParameters) - Method in class org.biojava.spice.server.SpiceClient

try to connect to SPICEPORT and see if already an instance of SPICE is running there

sendConsoleEcho(String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

sendConsoleMessage(String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

sendSyncScript(String, String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

seqFont - Static variable in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

serialVersionUID - Static variable in class org.biojava.spice.gui.MemoryMonitor.Surface

serialVersionUID - Static variable in class org.biojava.spice.gui.MemoryMonitor

serialVersionUID - Static variable in class org.biojava.spice.gui.alignmentchooser.ShowAligPanel

serialVersionUID - Static variable in class org.biojava.spice.manypanel.renderer.DasScrollPaneColumnHeader

serialVersionUID - Static variable in class org.biojava.spice.manypanel.renderer.SequenceRenderer

serialVersionUID - Static variable in class org.biojava.spice.manypanel.renderer.StatusPanel

serialVersionUID - Static variable in class org.biojava.spice.manypanel.renderer.StructureScalePanel

setAccessionCode(String) - Method in class org.biojava.spice.gui.msdkeyword.Deposition

setAccessionCode(String) - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

setAccessionCode(String) - Method in class org.biojava.spice.manypanel.renderer.StatusPanel

setAccessionCodes(String[]) - Method in class org.biojava.spice.alignment.StructureAlignment

setAlignment(Alignment) - Method in class org.biojava.spice.alignment.StructureAlignment

setAlignmentMap1(Map) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanel

setAlignmentMap1(Map) - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

setAlignmentMap2(Map) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanel

setAlignmentMap2(Map) - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

setAlignmentServers(SpiceDasSource[]) - Method in class org.biojava.spice.alignment.StructureAlignmentBuilder

setAlignmentServers(SpiceDasSource[]) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

setAlternativeAlignments(AlternativeAlignment[]) - Method in class org.biojava.spice.gui.alignment.AlternativeAlignmentFrame

setAtomName(String) - Method in class org.biojava.spice.jmol.AtomInfo

setBackground(Color) - Method in class org.biojava.spice.gui.aligchooser.AligLabel

setBackupRegistry(String[]) - Method in class org.biojava.spice.SpiceStartParameters

set backup registry servers.

setBorder(Border) - Method in class org.biojava.spice.gui.aligchooser.AligLabel

setBorderPainted(boolean) - Method in class org.biojava.spice.gui.aligchooser.AligLabel

setCallbackFunction(String, String) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

setCapabilities(String[]) - Method in class org.biojava.spice.config.RegistryConfiguration

setCapacity(int) - Method in class org.biojava.spice.gui.logging.LoggingPanel

Set the capacity.

setChain(Chain, int) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

setChain(Chain) - Method in class org.biojava.spice.gui.alignmentchooser.ShowAligPanel

setChain(Chain) - Method in class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener

setChain(Chain) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

setChain(Chain) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

setChain(Chain) - Method in class org.biojava.spice.manypanel.renderer.SeqToolTipListener

setChain(Chain) - Method in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

setChain(Chain) - Method in class org.biojava.spice.manypanel.renderer.StructureScalePanel

setChain1(Chain) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

setChain2(Chain) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

setChainId(String) - Method in class org.biojava.spice.jmol.AtomInfo

setChainLength(int) - Method in class org.biojava.spice.manypanel.renderer.HistogramPainter

setCheck(JCheckBox) - Method in class org.biojava.spice.gui.aligchooser.AligLabel

setClassification(String) - Method in class org.biojava.spice.gui.msdkeyword.Deposition

setCode(String) - Method in class org.biojava.spice.SpiceStartParameters

set the accession code to be displayed in SPICE.

setCodetype(String) - Method in class org.biojava.spice.SpiceStartParameters

sets the type of the accession code being displayed.

setColor(Color) - Method in class org.biojava.spice.feature.AbstractSegment

setColor(Color) - Method in interface org.biojava.spice.feature.Segment

setColor(Color) - Method in interface org.biojava.spice.manypanel.drawable.Drawable

set the color of the object

setColor(Color) - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

setColor(Color) - Method in class org.biojava.spice.manypanel.drawable.DrawableSequence

setColumnVisible(LoggingPanel.Column, boolean) - Method in class org.biojava.spice.gui.logging.LoggingPanel

Show or hide the given column.

setComponent(Component) - Method in class org.biojava.spice.gui.TabEvent

setComponentWidth(int) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

setConfiguration(RegistryConfiguration) - Method in class org.biojava.spice.config.RegistryConfigIO

set config fromoutside

setContactDate(Date) - Method in class org.biojava.spice.config.RegistryConfiguration

setCoordSys1(DasCoordinateSystem) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

setCoordSys2(DasCoordinateSystem) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

setCoordinateSystem(DasCoordinateSystem) - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

setCoordinateSystem(DasCoordinateSystem) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

setCoordinateSystem(DasCoordinateSystem) - Method in interface org.biojava.spice.manypanel.managers.ObjectManager

setCurrentChain(Chain, int) - Method in class org.biojava.spice.SpiceApplication

setCurrentChainNumber(int) - Method in class org.biojava.spice.gui.StatusPanel

setCurrentChainNumber(int) - Method in class org.biojava.spice.manypanel.drawable.DrawableStructure

setDasSource(SpiceDasSource) - Method in class org.biojava.spice.manypanel.eventmodel.SpiceFeatureEvent

setDasSources(SpiceDasSource[]) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

setDasSources(SpiceDasSource[]) - Method in class org.biojava.spice.manypanel.BrowserPane

set all das sources at once

setDasSources(SpiceDasSource[]) - Method in class org.biojava.spice.manypanel.managers.AbstractChainManager

add reference DAS source

setDasSources(SpiceDasSource[]) - Method in class org.biojava.spice.manypanel.managers.FeatureManager

setDasSources(SpiceDasSource[]) - Method in interface org.biojava.spice.manypanel.managers.ObjectManager

list of available Reference DAS servers

setDeleteIcon(ImageIcon) - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

setDescription(String) - Method in class org.biojava.spice.manypanel.renderer.StatusPanel

setDisplay(String) - Method in class org.biojava.spice.SpiceStartParameters

set a list of DAS - sources (by their unique Id from registry) to be highlited

setDisplayLabel(String) - Method in class org.biojava.spice.SpiceStartParameters

choose all das source belonging to a particular label to be highlited.

setDisplayLabels(String) - Method in class org.biojava.spice.StartParameterFilter

setDisplayMessage(String) - Method in class org.biojava.spice.SpiceStartParameters

setDisplayServers(String) - Method in class org.biojava.spice.StartParameterFilter

convert a ";" separated list of DAS source ids e.g.

setDisplayType(String) - Method in class org.biojava.spice.das.SpiceDasSource

setDrawableDasSource(DrawableDasSource) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

setDrawableSequence(DrawableSequence) - Method in class org.biojava.spice.manypanel.renderer.SequenceRenderer

setDrawableStructure(DrawableStructure) - Method in class org.biojava.spice.manypanel.renderer.StructureRenderer

setEnd(int) - Method in class org.biojava.spice.feature.AbstractSegment

setEnd(int) - Method in interface org.biojava.spice.feature.Segment

setEnspcoordsys(String) - Method in class org.biojava.spice.SpiceStartParameters

setExpData(String) - Method in class org.biojava.spice.gui.msdkeyword.Deposition

setFeature(Feature) - Method in class org.biojava.spice.manypanel.eventmodel.SpiceFeatureEvent

setFeatures(Feature[]) - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

a way to set Features from the outside

setFilterBy(String) - Method in class org.biojava.spice.alignment.StructureAlignment

setForceUpdate(boolean) - Method in class org.biojava.spice.config.RegistryConfigIO

enforce connecting to the registry, default: false

setFrameTitle(String) - Method in class org.biojava.spice.gui.SpiceTabbedPane

setFrameTitle(SPICEFrame) - Method in class org.biojava.spice.gui.SpiceTabbedPane

setHeteroList(String) - Method in class org.biojava.spice.gui.msdkeyword.Deposition

setId(String) - Method in class org.biojava.spice.gui.msdkeyword.Deposition

setIntObjectIds(String[]) - Method in class org.biojava.spice.alignment.StructureAlignment

setJmolPopup(JmolPopup) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

setJmolViewer(JmolViewer) - Method in class org.biojava.spice.jmol.JmolSpiceTranslator

setLabels(List) - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

setLastModified(Date) - Method in class org.biojava.spice.gui.msdkeyword.Deposition

setLastSelectedPosition(int) - Method in class org.biojava.spice.gui.aligchooser.AlignmentItemListener

setLength(int) - Method in class org.biojava.spice.manypanel.renderer.CoordManager

setLevelColor(Level, Color, Color) - Method in class org.biojava.spice.gui.logging.LoggingPanel

Set the foreground and background colors for messages of the specified level.

setLink(String) - Method in class org.biojava.spice.feature.AbstractFeature

setLink(String) - Method in interface org.biojava.spice.feature.Feature

setLoaded(boolean[]) - Method in class org.biojava.spice.alignment.StructureAlignment

setLoaded(int, boolean) - Method in class org.biojava.spice.alignment.StructureAlignment

setLoading(boolean) - Method in interface org.biojava.spice.manypanel.drawable.Drawable

the data for this drawable is currently being loaded

setLoading(boolean) - Method in class org.biojava.spice.manypanel.drawable.DrawableDasSource

setLoading(boolean) - Method in class org.biojava.spice.manypanel.drawable.DrawableSequence

setLoading(boolean) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

setLoading(boolean) - Method in class org.biojava.spice.manypanel.renderer.StatusPanel

setLocalServerCapability(String) - Method in class org.biojava.spice.SpiceStartParameters

setLocalServerCoordSys(String) - Method in class org.biojava.spice.SpiceStartParameters

setLocalServerDisplayType(String) - Method in class org.biojava.spice.SpiceStartParameters

setLocalServerName(String) - Method in class org.biojava.spice.SpiceStartParameters

setLocalServerURL(String) - Method in class org.biojava.spice.SpiceStartParameters

setLocalUnlimitedFeatures(boolean) - Method in class org.biojava.spice.SpiceStartParameters

setLogLevel(Level) - Static method in class org.biojava.spice.gui.LoggingPanelManager

setLowerAlignmentManager(AlignmentManager) - Method in class org.biojava.spice.manypanel.renderer.ArrowPanel

setLowerObjectListener(ObjectListener) - Method in class org.biojava.spice.manypanel.renderer.ArrowPanel

setMatrices(Matrix[]) - Method in class org.biojava.spice.alignment.StructureAlignment

setMax(double) - Method in class org.biojava.spice.feature.HistogramFeature

setMaxNrFeatures(int) - Method in class org.biojava.spice.das.SingleFeatureThread

set the maximum number of features that should be loaded by this thread.

setMenu(JMenuBar) - Method in class org.biojava.spice.SpiceApplication

setMessageHeight(Integer) - Method in class org.biojava.spice.SpiceStartParameters

setMessageWidth(Integer) - Method in class org.biojava.spice.SpiceStartParameters

setMethod(String) - Method in class org.biojava.spice.feature.AbstractFeature

setMethod(String) - Method in interface org.biojava.spice.feature.Feature

setMin(double) - Method in class org.biojava.spice.feature.HistogramFeature

setModelNumber(int) - Method in class org.biojava.spice.jmol.AtomInfo

setName(String) - Method in class org.biojava.spice.feature.AbstractFeature

setName(String) - Method in class org.biojava.spice.feature.AbstractSegment

setName(String) - Method in interface org.biojava.spice.feature.Feature

setName(String) - Method in interface org.biojava.spice.feature.Segment

setName(String) - Method in class org.biojava.spice.manypanel.renderer.StatusPanel

setNewTab(boolean) - Method in class org.biojava.spice.SpiceStartParameters

setNoRegistryContact(boolean) - Method in class org.biojava.spice.SpiceStartParameters

if set to true, the registry will notbe contacted

setNoUpdate(boolean) - Method in class org.biojava.spice.config.RegistryConfigIO

set flag if contaction should not be performed forceUpdate is stronger

setNote(String) - Method in class org.biojava.spice.feature.AbstractFeature

setNote(String) - Method in class org.biojava.spice.feature.AbstractSegment

setNote(String) - Method in interface org.biojava.spice.feature.Feature

setNote(String) - Method in interface org.biojava.spice.feature.Segment

setOpenDialogCoords(String) - Method in class org.biojava.spice.SpiceStartParameters

setPDBFileExtensions(String[]) - Method in class org.biojava.spice.config.RegistryConfiguration

setPDBHeader(Map) - Method in class org.biojava.spice.gui.StatusPanel

setPDBSelectEnd(String) - Method in class org.biojava.spice.jmol.StructurePanelListener

setPDBSelectStart(String) - Method in class org.biojava.spice.jmol.StructurePanelListener

setPaintDefaults(Graphics2D) - Method in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

set some default rendering hints, like text antialiasing on

setParent(Feature) - Method in class org.biojava.spice.feature.AbstractSegment

setParent(Feature) - Method in interface org.biojava.spice.feature.Segment

setPdbSelectEnd(String) - Method in class org.biojava.spice.SpiceStartParameters

setPdbSelectStart(String) - Method in class org.biojava.spice.SpiceStartParameters

setPdbcoordsys(String) - Method in class org.biojava.spice.SpiceStartParameters

setPrefSize() - Method in class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader

setPreferredStructureAlignmentServerName(String) - Method in interface org.biojava.spice.SPICEFrame

setPreferredStructureAlignmentServerName(String) - Method in class org.biojava.spice.SpiceApplication

setRadio(JRadioButton) - Method in class org.biojava.spice.gui.aligchooser.AligLabel

setRasmolScript(String) - Method in class org.biojava.spice.SpiceStartParameters

setRasmolScript(String) - Method in class org.biojava.spice.jmol.StructurePanelListener

setRasmolScripts(String[]) - Method in class org.biojava.spice.alignment.StructureAlignment

setReferenceServers1(DasSource[]) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

setReferenceServers2(DasSource[]) - Method in class org.biojava.spice.manypanel.managers.AlignmentManager

setReferenceStructure(int) - Method in class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser

the structure at that position is the first one

setRegistered(boolean) - Method in class org.biojava.spice.das.SpiceDasSource

setRegistry(String) - Method in class org.biojava.spice.SpiceStartParameters

set the primary registry.

setRegistryUrl(URL) - Method in class org.biojava.spice.config.RegistryConfiguration

setRegistryurls(URL[]) - Method in class org.biojava.spice.SpiceStartParameters

setResidueName(String) - Method in class org.biojava.spice.jmol.AtomInfo

setResidueNumber(String) - Method in class org.biojava.spice.jmol.AtomInfo

setResolution(float) - Method in class org.biojava.spice.gui.msdkeyword.Deposition

setRfactor(float) - Method in class org.biojava.spice.gui.msdkeyword.Deposition

setScale(float) - Method in class org.biojava.spice.gui.alignmentchooser.AlignmentChooser

setScale(float) - Method in class org.biojava.spice.gui.alignmentchooser.ShowAligPanel

setScale(float) - Method in class org.biojava.spice.manypanel.renderer.AbstractChainRenderer

setScale(float) - Method in class org.biojava.spice.manypanel.renderer.CoordManager

setScale(float) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

setScale(float) - Method in class org.biojava.spice.manypanel.renderer.DasSourcePanel

setScale(float) - Method in class org.biojava.spice.manypanel.renderer.HistogramPainter

setScale(float) - Method in class org.biojava.spice.manypanel.renderer.SequenceScalePanel

setScale1(float) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

setScale1(float) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanel

setScale1(float) - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

setScale2(float) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

setScale2(float) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanel

setScale2(float) - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

setScore(String) - Method in class org.biojava.spice.feature.AbstractFeature

setScore(String) - Method in interface org.biojava.spice.feature.Feature

setScore(double) - Method in class org.biojava.spice.feature.HistogramSegment

setScrolled1(int) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

setScrolled1(int) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanel

setScrolled1(Adjustable, int) - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

setScrolled2(int) - Method in class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel

setScrolled2(int) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanel

setScrolled2(Adjustable, int) - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

setSegment(Segment) - Method in class org.biojava.spice.manypanel.eventmodel.SpiceFeatureEvent

setSelected(int, boolean) - Method in class org.biojava.spice.alignment.StructureAlignment

setSelected(boolean) - Method in class org.biojava.spice.gui.aligchooser.AligLabel

setSelection(boolean[]) - Method in class org.biojava.spice.alignment.StructureAlignment

setSelectionPanel(SelectionPanel) - Method in class org.biojava.spice.alignment.StructureAlignmentBuilder

setSeqSelectEnd(int) - Method in class org.biojava.spice.SpiceStartParameters

setSeqSelectEnd(String) - Method in class org.biojava.spice.SpiceStartParameters

setSeqSelectStart(int) - Method in class org.biojava.spice.SpiceStartParameters

setSeqSelectStart(String) - Method in class org.biojava.spice.SpiceStartParameters

setSeqSelection(int, int) - Method in class org.biojava.spice.manypanel.BrowserPane

setSeqSelection(int, int) - Method in class org.biojava.spice.manypanel.renderer.CursorPanel

this selection will be auto-selected when the next sequence is loaded

setSequence(Chain) - Method in class org.biojava.spice.manypanel.drawable.DrawableSequence

setSequence1(Chain) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanel

setSequence1(Chain) - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

setSequence2(Chain) - Method in class org.biojava.spice.manypanel.renderer.AlignmentPanel

setSequence2(Chain) - Method in class org.biojava.spice.manypanel.renderer.AlignmentRenderer

setServerStatus(String, Boolean) - Method in class org.biojava.spice.config.ConfigGui

set status of server

setServerStatus(String, Boolean) - Method in class org.biojava.spice.config.DasSourceConfigPanel