Index (biojava-structure-gui 5.0.1 API)

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

A

AboutDialog - Class in org.biojava.nbio.structure.align.gui
AboutDialog() - Constructor for class org.biojava.nbio.structure.align.gui.AboutDialog
AbstractAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol: An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol.
AbstractAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.ChooseDirAction
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener: Invoked when the user presses the stop button.
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel: The user selected one of the Combo boxes...
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.JPrintPanel
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyDistMaxListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyExportListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.MySaveFileListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.align.gui.ShowPDBIDListener
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
actionPerformed(ActionEvent) - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryListener
adapter - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol
adapter - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
addAligPosListener(AlignmentPositionListener) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
addOneSystemProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
AFPChainCoordManager - Class in org.biojava.nbio.structure.align.gui.aligpanel
AFPChainCoordManager() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
AFPFromFasta - Class in demo: Demo displaying a structural alignment from a FASTA file using FastaAFPChainConverter.
AFPFromFasta() - Constructor for class demo.AFPFromFasta
AlignedPosition - Class in org.biojava.nbio.structure.gui.util
AlignedPosition() - Constructor for class org.biojava.nbio.structure.gui.util.AlignedPosition
ALIGNMENT_PANEL - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
AlignmentCalc - Class in org.biojava.nbio.structure.align.gui: A class that obtains two structures via DAS and aligns them This is done in a separate thread.
AlignmentCalc(AlignmentGui, Structure, Structure, String, String) - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentCalc: requests an alignment of pdb1 vs pdb 2.
AlignmentCalc - Class in org.biojava.nbio.structure.gui.util: A class that obtains two structures via DAS and aligns them This is done in a separate thread.
AlignmentCalc(AlignmentGui, Structure, Structure) - Constructor for class org.biojava.nbio.structure.gui.util.AlignmentCalc: requests an alignment of pdb1 vs pdb 2.
AlignmentCalcDB - Class in org.biojava.nbio.structure.align.gui
AlignmentCalcDB(AlignmentGui, Structure, String, UserConfiguration, String, Boolean) - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
AlignmentCalculationRunnable - Interface in org.biojava.nbio.structure.align.gui
alignmentEnded() - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
AlignmentGui - Class in org.biojava.nbio.structure.align.gui: A JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, or after manual upload.
AlignmentGui() - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentGui
AlignmentGuiDemo - Class in demo: Get an instance of the two alignment GUIs.
AlignmentGuiDemo() - Constructor for class demo.AlignmentGuiDemo
AlignmentPositionListener - Interface in org.biojava.nbio.structure.gui.events
alignmentStarted(String, String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
AlignmentTextPanel - Class in org.biojava.nbio.structure.align.gui
AlignmentTextPanel() - Constructor for class org.biojava.nbio.structure.align.gui.AlignmentTextPanel
AligPanel - Class in org.biojava.nbio.structure.align.gui.aligpanel: A JPanel that can display an AFPChain in a nice way and interact with Jmol.
AligPanel() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
AligPanelMouseMotionListener - Class in org.biojava.nbio.structure.align.gui.aligpanel
AligPanelMouseMotionListener(AligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
AligUIManager - Class in org.biojava.nbio.structure.align.webstart
AligUIManager() - Constructor for class org.biojava.nbio.structure.align.webstart.AligUIManager
AlternativeAlignmentFrame - Class in org.biojava.nbio.structure.gui.util: a frame showing the alternative alignments, which are the result of a structure superimposition
AlternativeAlignmentFrame(Structure, Structure) - Constructor for class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
applyValues() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
AtomInfo - Class in org.biojava.nbio.structure.align.gui.jmol: This class uniquely describes an atom
AtomInfo() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
AtomInfoParser - Class in org.biojava.nbio.structure.align.gui.jmol
AtomInfoParser() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
AutoSuggestProvider - Interface in org.biojava.nbio.structure.align.gui.autosuggest: A class that provides auto-completion suggestions for JAutoSuggest

B

BACKGROUND_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
BiojavaJmol - Class in org.biojava.nbio.structure.gui: A class that provides a simple GUI for Jmol
BiojavaJmol() - Constructor for class org.biojava.nbio.structure.gui.BiojavaJmol
BLACK_WHITE_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
BrowserOpener - Class in org.biojava.nbio.structure.align.webstart
BrowserOpener() - Constructor for class org.biojava.nbio.structure.align.webstart.BrowserOpener

C

calcScale(int) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay: 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
ceColumnNames - Static variable in class org.biojava.nbio.structure.align.gui.DBResultTable
ChooseDirAction - Class in org.biojava.nbio.structure.align.gui: Ask the user to provide a directory containting PDB files.
ChooseDirAction(JTextField, UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.gui.ChooseDirAction
cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
cleanup() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
cleanUp() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
cleanup() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
cleanUp() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
cleanup() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc
cleanup() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
cleanUp() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
clear() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider: reset all suggestions
clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
clear() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
clear() - Method in interface org.biojava.nbio.structure.gui.Selection
clear() - Method in class org.biojava.nbio.structure.gui.SelectionImpl
clear() - Method in interface org.biojava.nbio.structure.gui.StructureViewer: Clear the current display
clear() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper: Clears all finite endpoints
clearListeners() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
clearListeners() - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that colors subunits by their sequence cluster ids.
colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that colors subunits by their sequence cluster ids.
colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that colors the subunits of a structure by different colors
colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that colors the subunits of a structure by different colors
colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that colors subunits to highlight the symmetry within a structure
colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that colors subunits to highlight the symmetry within a structure Different subunits should have a consistent color scheme or different shade of the same colors
colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
ColorConverter - Class in org.biojava.nbio.structure.symmetry.jmolScript
ColorConverter() - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
coloring - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
ColorInterpolator - Interface in org.biojava.nbio.structure.gui.util.color
colorPalette - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
ColorUtils - Class in org.biojava.nbio.structure.gui.util.color
ColorUtils() - Constructor for class org.biojava.nbio.structure.gui.util.color.ColorUtils
colorWheel - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
COMMAND_LINE_HELP - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
ConfigPDBInstallPanel - Class in org.biojava.nbio.structure.align.gui
configureParameters() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
configureParameters() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
ConfigXMLHandler - Class in org.biojava.nbio.structure.align.webstart: XML content handler for serialisation of RegistryConfiguration class
ConfigXMLHandler() - Constructor for class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
containsKey(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
containsValue(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
ContinuousColorMapper - Interface in org.biojava.nbio.structure.gui.util.color: Provides a mapping between real numbers and Colors.
ContinuousColorMapperTransform - Class in org.biojava.nbio.structure.gui.util.color: Maps colors by performing a transform of the input data and then passing the transformed value to a ContinuousColorMapper for rendering.
ContinuousColorMapperTransform(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform: Creates a transform.
convertColor4f(Color) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
convertColor4f(Color[]) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
CookBook - Class in demo
CookBook() - Constructor for class demo.CookBook
CoordManager - Class in org.biojava.nbio.structure.gui.util: a class that manages the conversion of sequence coordinate system to JPanel drawing coordinates
CoordManager() - Constructor for class org.biojava.nbio.structure.gui.util.CoordManager
createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
createGradients() - Static method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
createImage(String, String, Object, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
createImageIcon(String) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator: Returns an ImageIcon, or null if the path was invalid.
CS_HSV - Static variable in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace: The HSV color space
cyan - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils

D

darker(Color, double) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils: Make a color darker.
DBResultTable - Class in org.biojava.nbio.structure.align.gui
DBResultTable() - Constructor for class org.biojava.nbio.structure.align.gui.DBResultTable
DBSearchGUI - Class in org.biojava.nbio.structure.align.gui
DBSearchGUI() - Constructor for class org.biojava.nbio.structure.align.gui.DBSearchGUI
debug(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
DEFAULT_CHAR_SIZE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: size per character
DEFAULT_CHAR_SIZE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Size per character
DEFAULT_HEIGHT - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
DEFAULT_LINE_LENGTH - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: number of chars per line
DEFAULT_LINE_LENGTH - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Number of chars per line
DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: separation of line 1 and 2 in alignment
DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Separation between sequences in the alignment
DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: Space on the right side between sequence and legend.
DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Space on the right side between sequence and legend.
DEFAULT_SCRIPT - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
DEFAULT_WIDTH - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
DEFAULT_X_RIGHT_BORDER - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DEFAULT_X_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: left boundary
DEFAULT_X_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Left boundary
DEFAULT_X_START - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DEFAULT_Y_BOTTOM - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DEFAULT_Y_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DEFAULT_Y_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: top boundary
DEFAULT_Y_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Top boundary
DEFAULT_Y_START - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DEFAULT_Y_STEP - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: size of space between rows
DEFAULT_Y_STEP - Variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Size of space between rows.
DEFAULT_Y_STEP - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
DefaultAutoSuggestProvider - Class in org.biojava.nbio.structure.align.gui.autosuggest
DefaultAutoSuggestProvider() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
DefaultMatrixMapper - Class in org.biojava.nbio.structure.gui.util.color: Color Mapper which mimics the default coloring of JMatrixPanel pixels.
DefaultMatrixMapper(double, float) - Constructor for class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
defaultProperties - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo
demo - package demo
DemoAlignmentFromFasta - Class in demo: Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file.
DemoAlignmentFromFasta() - Constructor for class demo.DemoAlignmentFromFasta
DemoCE - Class in demo
DemoCE() - Constructor for class demo.DemoCE
DemoCeSymm - Class in demo: Quick demo of how to call CE-Symm programmatically.
DemoCeSymm() - Constructor for class demo.DemoCeSymm
DemoFATCAT - Class in demo
DemoFATCAT() - Constructor for class demo.DemoFATCAT
DemoMultipleMC - Class in demo: Demo for running the CEMC Algorithm on a protein family and visualizing the results.
DemoMultipleMC() - Constructor for class demo.DemoMultipleMC
DemoNWALignment - Class in demo
DemoNWALignment() - Constructor for class demo.DemoNWALignment
DemoQuatSymmetryJmol - Class in demo: This demo shows how to display the QuatSymmetryResults of a structure.
DemoQuatSymmetryJmol() - Constructor for class demo.DemoQuatSymmetryJmol
DemoRotationAxis - Class in demo: A demo for how to use RotationAxis to display the rotation for an alignment.
DemoRotationAxis() - Constructor for class demo.DemoRotationAxis
DemoShowBiolAssembly - Class in demo
DemoShowBiolAssembly() - Constructor for class demo.DemoShowBiolAssembly
DemoShowCATHDomain - Class in demo
DemoShowCATHDomain() - Constructor for class demo.DemoShowCATHDomain
DemoShowLargeAssembly - Class in demo
DemoShowLargeAssembly() - Constructor for class demo.DemoShowLargeAssembly
DemoShowValidationResults - Class in demo
DemoShowValidationResults() - Constructor for class demo.DemoShowValidationResults
DemoStructureFromFasta - Class in demo: Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file.
DemoStructureFromFasta() - Constructor for class demo.DemoStructureFromFasta
DemoSW3DAligner - Class in demo
DemoSW3DAligner() - Constructor for class demo.DemoSW3DAligner
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Set all the member variables to null.
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel: Clean up this instance for garbage collection, to avoid memory leaks...
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
dialogAsk(String, String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
display(AFPChain, Group[], Atom[], Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
display(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay: Display a MultipleAlignment with a JmolPanel.
display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay: Display an AFPChain alignment
display(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Displays a single structure in a cartoon representation with each symmetric repeat colored differently.
DisplayAFP - Class in org.biojava.nbio.structure.align.gui: A utility class for visualistion of structure alignments
DisplayAFP() - Constructor for class org.biojava.nbio.structure.align.gui.DisplayAFP
displayFull(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Displays a multiple alignment of the whole structure transformations colored by blocks, corresponding to the symmetric protodomains.
displayRepeats(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Displays a multiple alignment of the symmetry repeats.
DIST_MATRICES - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
doInBackground() - Method in class org.biojava.nbio.structure.align.gui.StructureLoaderThread
DOT_PLOT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
DotPlotListener(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener
DotPlotPanel - Class in org.biojava.nbio.structure.align.gui: Displays the dot plot trace for an alignment.
DotPlotPanel(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.DotPlotPanel
downloadingStructures(String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that draws symmetry or inertia axes for a structure.
drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that draws symmetry or inertia axes for a structure.
drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
drawBoxes(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel: draw high scoring fragments that are used for the initial alignment seed selection
drawDistances(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel: For each element in matrix, draw it as a colored square or pixel.
drawIdx(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
drawPairs(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel: draw alternative alignments
drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that draws an invisible polyhedron around a structure.
drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that draws an invisible polyhedron around a structure.
drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
drawScale(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel: draw the Scale
drawSequence(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel: draw the Amino acid sequence

E

entrySet() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
EQR_COLOR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
EQUIVALENT - Static variable in class org.biojava.nbio.structure.gui.util.AlignedPosition: flag if this position is equivalent
error(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
errorEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
eval(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Execute a command String in the current Jmol panel.
evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
evalString(String) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
executeCmd(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel

F

f1Dot2(float) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
FASTA_FORMAT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
fatal(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
fatalEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
FATCAT_BLOCK - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
FATCAT_TEXT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
fatColumnNames - Static variable in class org.biojava.nbio.structure.align.gui.DBResultTable
fDot2(double) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
frame - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
fromCIEXYZ(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
fromRGB(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
fromString(String) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
functionXY(String, int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
functionXYZ(String, int, int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener

G

GAP_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
get(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
getAboutMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getAdapter() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
getAFPChain() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
getAfpChain() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
getAlgorithm() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
getAligMap() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
getAlignmentFromFasta() - Static method in class demo.DemoAlignmentFromFasta
getAlignmentPanelMenu(JFrame, ActionListener, AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator: Create the menu for the Alignment Panel representation of Structural Alignments.
getAlignmentTextMenu(JFrame, ActionListener, AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator: Create the menu for the Text representations of Structural Alignments.
getAligSeq(Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: returns the AligSeq (0 or 1) for a point returns -1 if not over an alig seq.
getAligSeq(Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Returns the index of the structure, for a given point in the Panel.
getAlnSequences() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
getAlternativeAligs() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getAlternativeAligs() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getAtomArray(Atom[], List<Group>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Returns the first atom for each group
getAtomArrays() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
getAtomForAligPos(AFPChain, int, int, Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Return the atom at alignment position aligPos.
getAtomName() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
getAutoSuggestProvider() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
getAxisTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getCa1() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
getCa1() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
getCa2() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
getCa2() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
getCellColor() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getCellColor() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getChain() - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
getChain1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
getChainId() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
getCloseMenuItem(JFrame) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getColor() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
getColor() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
getColor(double) - Method in interface org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper
getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform: Return the color corresponding to submapper.getColor(transform(value)).
getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
getColorPalette() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Return the color pattelete of the AlignmentJmol instance.
getComparator(int) - Method in class org.biojava.nbio.structure.align.gui.MyTableRowSorter
getConfig() - Method in class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
getCoordManager() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
getCoordManager() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
getDBResultMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getDBSearch() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
getDefaultConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script to set the default orientation for a structure
getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script to set the default orientation for a structure
getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getDefaultText() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
getDistanceMatrices() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Returns a List of internal Distance Matrices, one for each structure in the alignment.
getDistanceMatrices() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
getDistanceMatrices() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
getEndLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
getEndLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
getEQRAlignmentPos(AFPChain) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
getEquivalent() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
getExitMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getExportPDBMenuItem(AbstractAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getFarmJob() - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
getFileFormatSelect() - Static method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
getFilePath1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
getFragmentPairs() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getFragmentPairs() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getFrame() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
getFrame() - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
getFromFtp() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
getGradientMapper(int, double, double) - Static method in class org.biojava.nbio.structure.gui.util.color.GradientMapper: Constructs a gradientMapper to draw one of the pre-defined gradients For example, GradientMapper.getGradientMapper(GradientMapper.RAINBOW_GRADIENT, 0, 10)
getHelpMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getHSVColorSpace() - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
getIcon(ActionListener, String) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getIdx1() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay: get the identical position in the alignment
getIdx2() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay: get the identical position in the alignment
getInstance() - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
getInstance() - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
getInstance(int) - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
getInstance() - Static method in class org.biojava.nbio.structure.gui.util.ScopInstallationInstance
getInstance() - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
getInstance(AxisAligner, String) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns an instance of a JmolSymmetryScriptGenerator, based on the symmetry of a structure (factory method)
getInstanceNoVisibilityChange() - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
getInstanceNoVisibilityChange() - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
getInstanceNoVisibilityChange() - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
getInstantaneousOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that sets a specific orientation instantaneously
getIntermediate(Color, Color, int, int) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
getInterpolator() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
getJmolColor(Color4f) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
getJmolColorScript(Map<Color4f, List<String>>) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
getJmolLigandScript() - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
getJmolPanel() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Return the jmolPanel instance of the AlignmentJmol.
getJmolPoint(Tuple3d) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
getJmolScript4Block(AFPChain, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
getJmolString(MultipleAlignment, List<Atom[]>, ColorBrewer, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol: Generate a Jmol command String that colors the aligned residues of every structure.
getJmolString(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
getJSpecViewProperty(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
getLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: provide the coordinates for where to draw the legend for line X and if it is chain 1 or 2
getLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Provide the coordinates for where to draw the legend for line X given the structure index.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer
getLoadMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getLogLevel() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
getMapSeqToStruct() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
getMatrix() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getMatrix() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getMatrixPanel() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getMaxExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns the maximum extension (length) of structure
getMaxExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup: Returns the maximum extension (length) of structure
getMaximumSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
getMaxNrSuggestions() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider: Get the maximun nr of suggestions
getMaxNrSuggestions() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
getMaxNrSuggestions() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
getMeanExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup: Returns the mean extension (length) of structure
getMessage() - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
getMinimumSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
getModelNumber() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
getMultiBlockJmolString(MultipleAlignment, List<Atom[]>, ColorBrewer, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol: Colors every Block of the structures with a different color, following the palette.
getMultipleAlignment() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
getMultipleAlignment() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
getMultipleAlignmentMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getMultipleStructureAligner() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
getName1() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
getName2() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
getNames() - Method in class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
getOpenPDBMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that sets a specific orientation
getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns the number of orientations available for this structure
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns the name of a specific orientation
getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn: Returns the name of a specific orientation
getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn: Returns the name of a specific orientation
getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns the name of a specific orientation
getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedron
getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that sets a specific orientation and zoom to draw either axes or polyhedron
getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getOutFileLocation() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getPairwiseAlignmentMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getPairwiseStructureAligner() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
getPanelPos(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: get the position of the sequence position on the Panel
getPanelPos(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Get the X position on the Panel of a particular sequence position.
getPanelPos(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
getParameters() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
getPDBDirField() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
getPdbInfo(Atom) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools: get jmol style info: jmol style: [MET]508:A.CA/1 #3918 insertion code: [ASP]1^A:A.CA/1 #2
getPdbInfo(Atom, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
getPDBresnum(int, AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP: Return a list of pdb Strings corresponding to the aligned positions of the molecule.
getPDBresnum(int, MultipleAlignment, Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay: Utility method used in the MultipleAlignmentJmol Frame, when the aligned residues of a structure in the alignment have to be selected for formatting them (coloring and style).
getPDBUploadPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getPos(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
getPos1() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
getPos2() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
getPreferredHeight() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: Y coordinate size
getPreferredHeight() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Y coordinate size
getPreferredSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
getPreferredWidth() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: X coordinate size
getPreferredWidth() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: X coordinate size
getPrintMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getRegistryInfo() - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
getResidueName() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
getResidueNumber() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getSaturation() - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
getSaveAlignmentMenuItem(AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getScale() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getScale() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
getScale() - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
getScalevalue() - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
getSCOP() - Method in class org.biojava.nbio.structure.gui.util.ScopInstallationInstance
getScopSelectPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getSelectedAlignmentPos() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
getSelectedAlignmentPos() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
getSelection() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
getSelection() - Method in interface org.biojava.nbio.structure.gui.Selection
getSelection() - Method in class org.biojava.nbio.structure.gui.SelectionImpl
getSelection() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
getSelectPDBPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getSeqPos(int, Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: Convert from a X position in the JPanel to alignment position
getSeqPos(int, Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Convert from an X position in the JPanel to the position in the sequence alignment.
getSeqPos(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager: start counting at 0...
getShowPDBMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
getStatusListener() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
getStructure() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Return the current Structure in the AlignmentJmol instance.
getStructure1() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBDirPanel
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBServerPanel
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
getStructure1() - Method in class org.biojava.nbio.structure.gui.util.ScopSelectPanel
getStructure1() - Method in interface org.biojava.nbio.structure.gui.util.StructurePairSelector
getStructure2() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBDirPanel
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBServerPanel
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
getStructure2() - Method in class org.biojava.nbio.structure.gui.util.ScopSelectPanel
getStructure2() - Method in interface org.biojava.nbio.structure.gui.util.StructurePairSelector
getStructureAlignment() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
getStructureAlignment() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getStructureFromFasta() - Static method in class demo.DemoStructureFromFasta
getStructurePairAligner() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
getStructures() - Method in class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
getSuggestion(String) - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider: get a list of suggestions for a userInput
getSuggestion(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
getSuggestion(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
getSummaryPos() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
getSummaryPos() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
getSymmTitle(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Create a symmetry title for a display frame (Jmol, alignment, etc).
getTabPane() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
getTitle() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Return the title of the AlignmentJmol window.
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns transformation matrix to orient structure
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getViewer() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
getWebStartConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns the Jmol zoom to fit polyhedron and symmetry axes.
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorI
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorO
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorT
gold - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
GradientMapper - Class in org.biojava.nbio.structure.gui.util.color: Maps a set of real values onto a gradient.
GradientMapper() - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
GradientMapper(Color, Color) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
GradientMapper(Color, Color, ColorSpace) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
GradientPanel - Class in org.biojava.nbio.structure.gui.util.color
GradientPanel(ContinuousColorMapper, double, double) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientPanel
GradientRenderer() - Constructor for class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer
gradients - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
GUIAlignmentProgressListener - Class in org.biojava.nbio.structure.align.gui: a GUI that allows to watch progress as multiple alignments are being processed.
GUIAlignmentProgressListener() - Constructor for class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
GUIFarmJobRunnable - Class in org.biojava.nbio.structure.align.gui
GUIFarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.nbio.structure.align.gui.GUIFarmJobRunnable

H

handlePopupMenu(int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
HelpDialog - Class in org.biojava.nbio.structure.align.gui
HelpDialog() - Constructor for class org.biojava.nbio.structure.align.gui.HelpDialog
hexPropertyNames - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo
hideAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script to hide axes
hideAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script to hide axes
hideAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
hidePolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
hidePolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
hidePolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
hideSuggest() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest: Force the suggestions to be hidden (Useful for buttons, e.g.
HSVColorSpace - Class in org.biojava.nbio.structure.gui.util.color
HSVColorSpace() - Constructor for class org.biojava.nbio.structure.gui.util.color.HSVColorSpace

I

IDX_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
info(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
initAlignmentGUIMenu(JFrame) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
initCoords() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Display the structures after the variable initialization in the constructor.
initCoords() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
initCoords() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
initJmolMenu(JFrame, AbstractAlignmentJmol, AFPChain, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator: Provide a JMenuBar that can be added to a JFrame containing a JmolPanel.
initMenu() - Static method in class org.biojava.nbio.structure.gui.util.MenuCreator: provide a JMenuBar that can be added to a JFrame
interpolate(Color, Color, float) - Method in interface org.biojava.nbio.structure.gui.util.color.ColorInterpolator: Interpolates to a color between a and b
interpolate(Color, Color, float) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator: Interpolates to a color between a and b
interrupt() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc: stops what is currently happening and does not continue
interrupt() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB: stops what is currently happening and does not continue
interrupt() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
interrupt() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
interrupt() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc: stops what is currently happening and does not continue
interrupt() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
isDomainSplit() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
isEmpty() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
isHexProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
isInterrupted() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
isSuggestVisible() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
isURLProperty(String) - Method in class org.biojava.nbio.structure.align.gui.SystemInfo

J

JAutoSuggest - Class in org.biojava.nbio.structure.align.gui.autosuggest: A JTextField that can make suggestions for auto-complete.
JAutoSuggest() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
JAutoSuggest(int) - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
JAutoSuggest(Frame) - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
JMatrixPanel - Class in org.biojava.nbio.structure.gui: a JPanel that can display a difference of distance matrix and paths that have been taken for the alignment
JMatrixPanel() - Constructor for class org.biojava.nbio.structure.gui.JMatrixPanel
JmolAlignedPositionListener - Class in org.biojava.nbio.structure.gui.events
JmolAlignedPositionListener(BiojavaJmol, StructurePairAligner) - Constructor for class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
jmolColorByChain() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel: assign a custom color to the Jmol chains command.
jMolFloat(double) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a lower precision floating point number for Jmol
jmolInClassPath() - Static method in class org.biojava.nbio.structure.gui.BiojavaJmol: returns true if Jmol can be found in the classpath, otherwise false.
JmolLoggerAdapter(Logger) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
jmolPanel - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
JmolPanel - Class in org.biojava.nbio.structure.align.gui.jmol
JmolPanel() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
JmolPanel.JmolLoggerAdapter - Class in org.biojava.nbio.structure.align.gui.jmol
JmolSymmetryScriptGenerator - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGenerator() - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
JmolSymmetryScriptGeneratorC1 - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorC1(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
JmolSymmetryScriptGeneratorCn - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorCn(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
JmolSymmetryScriptGeneratorDn - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorDn(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
JmolSymmetryScriptGeneratorH - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorH(HelixAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
JmolSymmetryScriptGeneratorI - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorI(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorI
JmolSymmetryScriptGeneratorO - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorO(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorO
JmolSymmetryScriptGeneratorPointGroup - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorPointGroup(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
JmolSymmetryScriptGeneratorT - Class in org.biojava.nbio.structure.symmetry.jmolScript
JmolSymmetryScriptGeneratorT(RotationAxisAligner, String) - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorT
JmolTools - Class in org.biojava.nbio.structure.align.gui.jmol
JmolTools() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.JmolTools
JmolViewerImpl - Class in org.biojava.nbio.structure.gui
JmolViewerImpl() - Constructor for class org.biojava.nbio.structure.gui.JmolViewerImpl
JNLPProxy - Class in org.biojava.nbio.structure.align.webstart
JPrintPanel - Class in org.biojava.nbio.structure.align.gui
JPrintPanel() - Constructor for class org.biojava.nbio.structure.align.gui.JPrintPanel

K

keyMask - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
keyReleased(KeyEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener: takes care of the cursor up/down keys.
keySet() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper

L

lighter(Color, double) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils: Make a color lighter.
LINE_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
LinearColorInterpolator - Class in org.biojava.nbio.structure.gui.util.color
LinearColorInterpolator() - Constructor for class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
LinearColorInterpolator(ColorSpace) - Constructor for class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
LinearColorInterpolator.InterpolationDirection - Enum in org.biojava.nbio.structure.gui.util.color
LOAD_ALIGNMENT_XML - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
LOAD_DB_RESULTS - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
LogColorMapper - Class in org.biojava.nbio.structure.gui.util.color: Performs a log10 transform on input before passing the values off to another colorMapper.
LogColorMapper(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.LogColorMapper: Creates a new LogColorMapper with base 10.
LogColorMapper(ContinuousColorMapper, int) - Constructor for class org.biojava.nbio.structure.gui.util.color.LogColorMapper: If logspaceMapper maps values x1 to x2, this creates a mapper for values base^x1 to base^x2
logStatus(String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener

M

main(String[]) - Static method in class demo.AFPFromFasta
main(String[]) - Static method in class demo.AlignmentGuiDemo
main(String[]) - Static method in class demo.CookBook
main(String[]) - Static method in class demo.DemoAlignmentFromFasta
main(String[]) - Static method in class demo.DemoCE
main(String[]) - Static method in class demo.DemoCeSymm
main(String[]) - Static method in class demo.DemoFATCAT
main(String[]) - Static method in class demo.DemoMultipleMC
main(String[]) - Static method in class demo.DemoQuatSymmetryJmol
main(String[]) - Static method in class demo.DemoRotationAxis
main(String[]) - Static method in class demo.DemoShowBiolAssembly
main(String[]) - Static method in class demo.DemoShowCATHDomain
main(String[]) - Static method in class demo.DemoShowLargeAssembly
main(String[]) - Static method in class demo.DemoShowValidationResults
main(String[]) - Static method in class demo.DemoStructureFromFasta
main(String[]) - Static method in class demo.DemoSW3DAligner
main(String[]) - Static method in class demo.ShowStructureInJmol
main(String[]) - Static method in class demo.WebStartClientDemo
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.DBResultTable
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.DotPlotPanel
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.MemoryMonitor
main(String[]) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
main(String[]) - Static method in class org.biojava.nbio.structure.align.webstart.JNLPProxy
main(String[]) - Static method in class org.biojava.nbio.structure.align.webstart.WebStartDBSearch
main(String[]) - Static method in class org.biojava.nbio.structure.align.webstart.WebStartDBSearchResults
main(String[]) - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain: If no arguments, shows AlignmentGui for pairwise alignments.
main(String[]) - Static method in class org.biojava.nbio.structure.gui.BiojavaJmol
main(String[]) - Static method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
main(String[]) - Static method in class org.biojava.nbio.structure.gui.SequenceDisplay
main(String[]) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
main(String[]) - Static method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
main(String[]) - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
main(String[]) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
mapper - Variable in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform
MAX_SCALE - Static variable in class org.biojava.nbio.structure.gui.SequenceDisplay: the maximum value that the scale can get
MemoryMonitor - Class in org.biojava.nbio.structure.align.gui: Tracks Memory allocated & used, displayed in graph form.
MemoryMonitor() - Constructor for class org.biojava.nbio.structure.align.gui.MemoryMonitor
MemoryMonitor.Surface - Class in org.biojava.nbio.structure.align.gui
MenuCreator - Class in org.biojava.nbio.structure.align.gui: Create the menus for structure alignment GUI windows (JFrames).
MenuCreator() - Constructor for class org.biojava.nbio.structure.align.gui.MenuCreator
MenuCreator - Class in org.biojava.nbio.structure.gui.util: Create the menu for BiojavaJmol
MenuCreator() - Constructor for class org.biojava.nbio.structure.gui.util.MenuCreator
MenuCreator.DotPlotListener - Class in org.biojava.nbio.structure.align.gui: Creates a frame to display a DotPlotPanel.
MINIMUM_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
minimumLayoutSize(Container) - Method in class org.biojava.nbio.structure.gui.WrapLayout: Returns the minimum dimensions needed to layout the visible components contained in the specified target container.
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
mouseClicked(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseDragged(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
mouseEntered(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
mouseExited(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseMoved(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
mouseOverPosition(AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
mouseOverPosition(AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
mousePressed(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
mouseReleased(MouseEvent) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
mPanel - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
MULTIPLE_ALIGN - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
MultipleAlignmentCalc - Class in org.biojava.nbio.structure.align.gui: A class that obtains structures via DAS and aligns them.
MultipleAlignmentCalc(MultipleAlignmentGUI, List<Structure>, List<StructureIdentifier>) - Constructor for class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc: Requests an alignment of the pdbs.
MultipleAlignmentCoordManager - Class in org.biojava.nbio.structure.align.gui.aligpanel: Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.
MultipleAlignmentCoordManager(int, int) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Constructor.
MultipleAlignmentGUI - Class in org.biojava.nbio.structure.align.gui: A JFrame that allows to trigger a multiple structure alignment, either from files in a directory or after manual upload.
MultipleAlignmentGUI() - Constructor for class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
MultipleAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol: A class that provides a 3D visualization Frame in Jmol for MultipleAlignments.
MultipleAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol: Default constructor creates an empty JmolPanel window, from where alignments can be made through the align menu.
MultipleAlignmentJmol(MultipleAlignment, List<Atom[]>) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol: The constructor displays the Mutltiple Alignment in a new JmolPanel Frame.
MultipleAlignmentJmolDisplay - Class in org.biojava.nbio.structure.align.gui: Utility Class that provides helper methods for the visualization of MultipleAlignments.
MultipleAlignmentJmolDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
MultipleAligPanel - Class in org.biojava.nbio.structure.align.gui.aligpanel: A JPanel that can display the sequence alignment of a MultipleAlignment in a nice way and interact with Jmol by selecting the aligned atoms of the sequence selection.
MultipleAligPanel() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel: Default constructor.
MultipleAligPanel(AFPChain, Atom[], Atom[], AbstractAlignmentJmol) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel: Constructor using an afpChain and the atom arrays for pairwise alignments.
MultipleAligPanel(MultipleAlignment, AbstractAlignmentJmol) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel: Constructor using a MultipleAlignment.
MultipleAligPanelMouseMotionListener - Class in org.biojava.nbio.structure.align.gui.aligpanel: Mouse Motion Listener for the MultipleAligPanel, which provides methods to obtain positions of the mouse and connect them to the sequence alignment positions using the information in MultipleAlignmentCoordManager.
MultipleAligPanelMouseMotionListener(MultipleAligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
MultipleStatusDisplay - Class in org.biojava.nbio.structure.align.gui.aligpanel: This class provides information of the selected positions in the MultipleAligPanel.
MultipleStatusDisplay(MultipleAligPanel) - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay: Constructor using an alignment panel as a parent, where the information will be displayed.
MyAlignmentLoadListener - Class in org.biojava.nbio.structure.align.gui: Loads an alignment in an XML format and displays its content in a new Jmol panel.
MyAlignmentLoadListener() - Constructor for class org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener
MyDistMaxListener - Class in org.biojava.nbio.structure.align.gui: Shows the interatomic Distance Matrices of all the Structures aligned in different Frames.
MyDistMaxListener(AbstractAlignmentJmol) - Constructor for class org.biojava.nbio.structure.align.gui.MyDistMaxListener
MyExportListener - Class in org.biojava.nbio.structure.align.gui
MyJmolStatusListener - Class in org.biojava.nbio.structure.align.gui.jmol
MyJmolStatusListener() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
MyOpenPdbFileListener - Class in org.biojava.nbio.structure.align.gui
MyOpenPdbFileListener() - Constructor for class org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener
MySaveFileListener - Class in org.biojava.nbio.structure.align.gui: Save an alignment to a specified File by the user.
MySaveFileListener(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.MySaveFileListener
MySaveFileListener(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.gui.MySaveFileListener
MySaveFileListener(AFPChain, MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.gui.MySaveFileListener: Constructor to avoid checking which of the two is null before instantiating this class.
MyTableRowSorter - Class in org.biojava.nbio.structure.align.gui
MyTableRowSorter(TableModel) - Constructor for class org.biojava.nbio.structure.align.gui.MyTableRowSorter

N

NOT_ALIGNED - Static variable in class org.biojava.nbio.structure.gui.util.AlignedPosition: they can be shown in the same column (for a compact display) , but they are not structurally equivalent
notifyCalcFinished() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
notifyCalcFinished() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
notifyCalcFinished() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
notifyCalcFinished() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
notifyCallback(int, Object[]) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
notifyCallback(CBK, Object[]) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
notifyEnabled(int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
notifyEnabled(CBK) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
nrOpenWindows - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

O

openStringInline(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
orange - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
org.biojava.nbio.structure.align.gui - package org.biojava.nbio.structure.align.gui
org.biojava.nbio.structure.align.gui.aligpanel - package org.biojava.nbio.structure.align.gui.aligpanel
org.biojava.nbio.structure.align.gui.autosuggest - package org.biojava.nbio.structure.align.gui.autosuggest
org.biojava.nbio.structure.align.gui.jmol - package org.biojava.nbio.structure.align.gui.jmol: Utility methods for better interaction with Jmol.
org.biojava.nbio.structure.align.webstart - package org.biojava.nbio.structure.align.webstart: Classes related to Java Web Start
org.biojava.nbio.structure.gui - package org.biojava.nbio.structure.gui
org.biojava.nbio.structure.gui.events - package org.biojava.nbio.structure.gui.events
org.biojava.nbio.structure.gui.util - package org.biojava.nbio.structure.gui.util
org.biojava.nbio.structure.gui.util.color - package org.biojava.nbio.structure.gui.util.color
org.biojava.nbio.structure.symmetry.gui - package org.biojava.nbio.structure.symmetry.gui
org.biojava.nbio.structure.symmetry.jmolScript - package org.biojava.nbio.structure.symmetry.jmolScript

P

paint(Graphics) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
paint(Graphics) - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.gui.util.color.GradientPanel
paintComponent(Graphics) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
PAIRS_ONLY - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
PAIRWISE_ALIGN - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
ParameterGUI - Class in org.biojava.nbio.structure.align.gui: UI for ConfigStrucAligParams, for the AlignmentGUI.
ParameterGUI(ConfigStrucAligParams, String) - Constructor for class org.biojava.nbio.structure.align.gui.ParameterGUI: Constructor for a ParameterGUI.
parse(String) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser: parses e.g.
PDBDirPanel - Class in org.biojava.nbio.structure.gui.util: A class to define where a structure for the alignment is coming from
PDBDirPanel() - Constructor for class org.biojava.nbio.structure.gui.util.PDBDirPanel: load the PDB files from a local directory
PDBServerPanel - Class in org.biojava.nbio.structure.gui.util: A class to define where a structure for the alignment is coming from
PDBServerPanel() - Constructor for class org.biojava.nbio.structure.gui.util.PDBServerPanel: load the PDB files from a local directory
PDBUploadPanel - Class in org.biojava.nbio.structure.gui.util: A JPanel to upload 2 custom PDB files.
PDBUploadPanel() - Constructor for class org.biojava.nbio.structure.gui.util.PDBUploadPanel
PDBUploadPanel(boolean) - Constructor for class org.biojava.nbio.structure.gui.util.PDBUploadPanel
PHYLOGENETIC_TREE - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
playOrientations() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations
playOrientations() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script that displays a symmetry polyhedron and symmetry axes and then loop through different orientations
playOrientations() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
positionSelected(AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
positionSelected(AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
preferredLayoutSize(Container) - Method in class org.biojava.nbio.structure.gui.WrapLayout: Returns the preferred dimensions for this layout given the visible components in the specified target container.
print(Graphics, PageFormat, int) - Method in class org.biojava.nbio.structure.align.gui.JPrintPanel
PRINT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
printSymmetryAxes(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Generates a String that displays the symmetry axes of a structure.
printSymmetryAxes(CeSymmResult, boolean) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Generates a String that displays the symmetry axes of a structure.
printSymmetryGroup(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay: Given a symmetry alignment, it draws the symmetry group axes and the polyhedron box around the structure.
put(Double, Color) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper: Adds a gradient endpoint at the specified position.
putAll(Map<? extends Double, ? extends Color>) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper

Q

quickSort(String[], int, int) - Static method in class org.biojava.nbio.structure.align.gui.SystemInfo: Stripped-down QuickSort.

R

RAINBOW_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
RAINBOW_INTENSITY_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
rangeSelected(AlignedPosition, AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
RasmolCommandListener - Class in org.biojava.nbio.structure.align.gui.jmol: a utility class that listens to Ramsol script commands in the @link BiojavaJmol class
RasmolCommandListener(JmolPanel, JTextField) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener
readStructure(String, int) - Static method in class demo.DemoShowLargeAssembly: Load a specific biological assembly for a PDB entry
RED_BLUE_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
remove(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
RenderStyle - Enum in org.biojava.nbio.structure.gui
repaint() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
repaint() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
requestingAlignmentsFromServer(int) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
requestUserConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
resetDisplay() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Return to the initial state of the alignment visualization.
resetDisplay() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
resetDisplay() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
resizeInnerPanel(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
rotateHue(Color, float) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils: Rotate a color through HSB space
rotateJmol(Matrix) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
run() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
run() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
run() - Method in class org.biojava.nbio.structure.align.gui.GUIFarmJobRunnable
run() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
run() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
run() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc
run() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc

S

SAVE_ALIGNMENT_XML - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
SCALE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
ScaleableMatrixPanel - Class in org.biojava.nbio.structure.gui: A JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm.
ScaleableMatrixPanel() - Constructor for class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
ScaleableMatrixPanel.GradientRenderer - Class in org.biojava.nbio.structure.gui: A renderer for the the gradient dropdown menu at the top of scaleableMatrixPanes.
SCOP_VERSION - Static variable in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
SCOPAutoSuggestProvider - Class in org.biojava.nbio.structure.align.gui.autosuggest
SCOPAutoSuggestProvider() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
ScopInstallationInstance - Class in org.biojava.nbio.structure.gui.util
ScopSelectPanel - Class in org.biojava.nbio.structure.gui.util
ScopSelectPanel() - Constructor for class org.biojava.nbio.structure.gui.util.ScopSelectPanel
ScopSelectPanel(boolean) - Constructor for class org.biojava.nbio.structure.gui.util.ScopSelectPanel
scroll - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
SELECT_EQR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
Selection - Interface in org.biojava.nbio.structure.gui
SelectionImpl - Class in org.biojava.nbio.structure.gui
SelectionImpl() - Constructor for class org.biojava.nbio.structure.gui.SelectionImpl
selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
selectionLocked() - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
selectionLocked() - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
selectionUnlocked() - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
selectionUnlocked() - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
SelectMultiplePanel - Class in org.biojava.nbio.structure.gui.util: A Text Panel that allows the user to specify multiple structure identifiers, space separated.
SelectMultiplePanel() - Constructor for class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
SelectMultiplePanel(boolean) - Constructor for class org.biojava.nbio.structure.gui.util.SelectMultiplePanel
SelectPDBPanel - Class in org.biojava.nbio.structure.align.gui: A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
SelectPDBPanel() - Constructor for class org.biojava.nbio.structure.align.gui.SelectPDBPanel
SelectPDBPanel(boolean) - Constructor for class org.biojava.nbio.structure.align.gui.SelectPDBPanel
sentResultsToServer(int, String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
seqFont - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
SEQUENCE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
SequenceDisplay - Class in org.biojava.nbio.structure.gui: A sequence display that can show the results of a protein structure alignment.
SequenceDisplay(StructurePairAligner) - Constructor for class org.biojava.nbio.structure.gui.SequenceDisplay
SequenceMouseListener - Class in org.biojava.nbio.structure.gui.util: a mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriate SequenceListener and FeatureListener events
SequenceMouseListener(SequenceDisplay) - Constructor for class org.biojava.nbio.structure.gui.util.SequenceMouseListener
SequenceScalePanel - Class in org.biojava.nbio.structure.gui.util: A class that draws a Sequence as a rectangle, a scale display over it.
SequenceScalePanel(int) - Constructor for class org.biojava.nbio.structure.gui.util.SequenceScalePanel
serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.ChooseDirAction
serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor
serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
setAFPChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
setAFPChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
setAfpChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
setAlgorithm(StructureAlignment) - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
setAligMap(List<AlignedPosition>) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
setAlignmentJmol(AbstractAlignmentJmol) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
setAlternativeAlignment(AlternativeAlignment) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
setAlternativeAlignments(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
setAtomName(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
setAtoms(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Create and set a new structure from a given atom array.
setAutoSuggestProvider(AutoSuggestProvider) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
setAxisTransformation(RotationAxisAligner) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
setCa2(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
setCa2(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
setCallbackFunction(String, String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
setCellColor(ContinuousColorMapper) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
setCellColor(ContinuousColorMapper) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
setChain(Chain) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
setChain(Chain) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
setChainId(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
setColor(Color) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
setColor(Color) - Method in interface org.biojava.nbio.structure.gui.StructureViewer: Apply this color to the current Selection
setColorByBlocks(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
setColorSpace(ColorSpace, LinearColorInterpolator.InterpolationDirection[]) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator: Sets the ColorSpace to use for interpolation.
setColorSpace(ColorSpace) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
setDefault() - Method in class org.biojava.nbio.structure.align.gui.ParameterGUI
setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Sets a default Jmol script used for coloring.
setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
setDefaultText(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
setEquivalent(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
setFarmJob(FarmJob) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
setFromFtp(JCheckBox) - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
setInterpolationDirection(int, LinearColorInterpolator.InterpolationDirection) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
setInterpolator(ColorInterpolator) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
setJmolPanel(JmolPanel) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Set the jmolPanel of the AlignmentJmol instance.
setLength(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
setLookAndFeel() - Static method in class org.biojava.nbio.structure.align.webstart.AligUIManager
setMatrix(Matrix) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel: sets the distance matrix to be displayed
setMatrix(Matrix) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
setMaxNrSuggestions(int) - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider: set the maximum number of suggestions to return
setMaxNrSuggestions(int) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
setMaxNrSuggestions(int) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
setModelNumber(int) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
setNrCPUs(int) - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc: does not do anything here...
setNrCPUs(int) - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
setNrCPUs(int) - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
setNrCPUs(int) - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
setNrCPUs(int) - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Sets the type of bioassembly to be colored.
setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
setPaintDefaults(Graphics2D) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel: set some default rendering hints, like text antialiasing on
setPDBDirField(JTextField) - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
setPolyhedron(Polyhedron) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
setPos(int, int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
setPos1(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
setPos2(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
setPreferredSize() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
setResidueName(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo: Including insertion code
setResidueNumber(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
setRotationGroup(RotationGroup) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
setSaturation(float) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
setScale(float) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
setScale(float) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
setScale(float) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
setScalevalue(double) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
setSelectedAlignmentPos(int) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
setSelectedAlignmentPos(int) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
setSelection(Selection) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
setSelection(List<AtomInfo>) - Method in interface org.biojava.nbio.structure.gui.Selection
setSelection(List<AtomInfo>) - Method in class org.biojava.nbio.structure.gui.SelectionImpl
setSelection(Selection) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
setStructure(Structure) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Set a new Structure to visualize in the AlignmentJmol window.
setStructure(Structure) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
setStructure(Structure) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
setStructure(Structure) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
setStructure(Structure) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
setStructure1(Structure) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
setStructure1(Structure) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
setStructure2(Structure) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
setStructure2(Structure) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
setStructureAlignmentJmol(AbstractAlignmentJmol) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
setStyle(RenderStyle) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
setStyle(RenderStyle) - Method in interface org.biojava.nbio.structure.gui.StructureViewer: Apply this style to the current selection
setTabPane(JTabbedPane) - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
setText(String) - Method in class org.biojava.nbio.structure.align.gui.AlignmentTextPanel
setTextField(JTextField) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
setTextOutput(boolean) - Method in class org.biojava.nbio.structure.align.gui.MySaveFileListener: If true, the alignment format saved will be a text output (FASTA for MultipleAlignments and FatCat for pairwise alignments)
setTitle(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol: Set the title of the AlignmentJmol window.
setTitle(String) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
setTitle(String) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
setZoom(int) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
setZoom(int) - Method in interface org.biojava.nbio.structure.gui.StructureViewer: Set the Zoom level
show(BufferedReader, UserConfiguration) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable
show(File, UserConfiguration) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable
show(URL, UserConfiguration) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable
showAboutDialog() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator: Show some info about this GUI
showAlignmentImage(AFPChain, String) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
showAlignmentImage(MultipleAlignment, String) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay: Creates a new Frame with the String output representation of the MultipleAlignment.
showAlignmentPanel(AFPChain, Atom[], Atom[], AbstractAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
showAlternative(int) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator: Returns a Jmol script to show axes
showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH: Returns a Jmol script to show axes
showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
showConsole(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
showDialog() - Method in class org.biojava.nbio.structure.align.gui.AboutDialog
showDialog() - Static method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
showDialog() - Method in class org.biojava.nbio.structure.align.gui.HelpDialog
showDialog() - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
showDistanceMatrix(int) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
showDocument(URL) - Static method in class org.biojava.nbio.structure.align.webstart.BrowserOpener: open a URL in the browser that was used to launch SPICE
showDocument(String) - Static method in class org.biojava.nbio.structure.align.webstart.BrowserOpener: open a URL in the browser that was used to launch SPICE
showDocument(URL) - Static method in class org.biojava.nbio.structure.align.webstart.JNLPProxy
showMemoryMonitor() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
showMultipleAligmentPanel(MultipleAlignment, AbstractAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay: Creates a new Frame with the MultipleAlignment Sequence Panel.
ShowPDBIDListener - Class in org.biojava.nbio.structure.align.gui
ShowPDBIDListener() - Constructor for class org.biojava.nbio.structure.align.gui.ShowPDBIDListener
showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
showProgressBar() - Static method in class org.biojava.nbio.structure.align.gui.StructureLoaderThread
ShowStructureInJmol - Class in demo: Demo how to load and display a structure in Jmol
ShowStructureInJmol() - Constructor for class demo.ShowStructureInJmol
showSuggest() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest: Force the suggestions to be displayed (Useful for buttons e.g.
showSystemInfo() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
showUrl(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
SIMILARITY_COLOR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
size() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
SIZE - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
sleepAmount - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
slider - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
SLIDER_STEPS - Static variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
smartAdapter - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol
smartAdapter - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl
SqrtColorMapper - Class in org.biojava.nbio.structure.gui.util.color: Performs a sqrt transform on input before passing the values off to another colorMapper.
SqrtColorMapper(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.SqrtColorMapper: Creates a new SqrtColorMapper.
start() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
startElement(String, String, String, Attributes) - Method in class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
stateChanged(ChangeEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
stateChanged(ChangeEvent) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
stateChanged(ChangeEvent) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
status - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
StatusDisplay - Class in org.biojava.nbio.structure.align.gui.aligpanel
StatusDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
stop() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider: Interrupt searching for suggestions
stop() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
stop() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
stop() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
storeParameters() - Method in class org.biojava.nbio.structure.align.gui.ParameterGUI
structure - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
StructureAlignmentDisplay - Class in org.biojava.nbio.structure.align.gui
StructureAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
StructureAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol: A class that provides a simple GUI for Jmol
StructureAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
StructureAlignmentJmol(AFPChain, Atom[], Atom[]) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
StructureLoaderThread - Class in org.biojava.nbio.structure.align.gui
StructurePairSelector - Interface in org.biojava.nbio.structure.gui.util: To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.
StructureViewer - Interface in org.biojava.nbio.structure.gui
SUMMARY_POS - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager: Position at which the alignment summary is printed
SUMMARY_POS - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager: Position at which the alignment summary is printed
surf - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor
Surface() - Constructor for class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
SymmetryCalc - Class in org.biojava.nbio.structure.symmetry.gui: Calculates a symmetry analysis and displays the results.
SymmetryCalc(SymmetryGui, Structure) - Constructor for class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc: Requests for a structure to analyze.
SymmetryDisplay - Class in org.biojava.nbio.structure.symmetry.gui: Class that provides visualizations methods for symmetry alignments.
SymmetryDisplay() - Constructor for class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
SymmetryGui - Class in org.biojava.nbio.structure.symmetry.gui: A JFrame that allows to trigger a symmetry analysis, either from files in a directory or after manual upload Adapted from the AlignmentGui class in biojava.
SymmetryListener - Class in org.biojava.nbio.structure.symmetry.gui: Action Listener for the symmetry menu.
SymmetryListener(MultipleAlignmentJmol, CeSymmResult) - Constructor for class org.biojava.nbio.structure.symmetry.gui.SymmetryListener
SystemInfo - Class in org.biojava.nbio.structure.align.gui
SystemInfo() - Constructor for class org.biojava.nbio.structure.align.gui.SystemInfo

T

text - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
TEXT_ONLY - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
TEXT_SCALE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
thread - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
toCIEXYZ(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
toggleSelection(AlignedPosition) - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
toggleSelection(AlignedPosition) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
toHexColor(Color) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
toRGB(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
toString() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
toString() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
transform(double) - Method in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform: An arbitrary transform over reals
transform(double) - Method in class org.biojava.nbio.structure.gui.util.color.LogColorMapper: Apply log transform.
transform(double) - Method in class org.biojava.nbio.structure.gui.util.color.SqrtColorMapper: Return sqrt(value).
triggerMouseOverPosition(int, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
triggerSelectionLocked(boolean) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
triggerSelectionLocked(boolean) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener

U

updateDisplay() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
urlPropertyNames - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo

V

valueOf(String) - Static method in enum org.biojava.nbio.structure.gui.RenderStyle: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.biojava.nbio.structure.gui.RenderStyle: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
values() - Static method in enum org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection: Returns an array containing the constants of this enum type, in the order they are declared.
viewer - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol
viewer - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl

W

warn(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
warnEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
WebStartClientDemo - Class in demo
WebStartClientDemo() - Constructor for class demo.WebStartClientDemo
WebStartDBSearch - Class in org.biojava.nbio.structure.align.webstart: A Web Start wrapper for a FarmJobRunnable.
WebStartDBSearch() - Constructor for class org.biojava.nbio.structure.align.webstart.WebStartDBSearch
WebStartDBSearchResults - Class in org.biojava.nbio.structure.align.webstart
WebStartDBSearchResults() - Constructor for class org.biojava.nbio.structure.align.webstart.WebStartDBSearchResults
WebStartMain - Class in org.biojava.nbio.structure.align.webstart
WebStartMain() - Constructor for class org.biojava.nbio.structure.align.webstart.WebStartMain
WHITE_BLACK_GRADIENT - Static variable in class org.biojava.nbio.structure.gui.util.color.GradientMapper
windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
windowActivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
windowClosed(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
windowClosing(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
windowDeactivated(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
windowDeiconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
windowIconified(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
windowOpened(WindowEvent) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
WrapLayout - Class in org.biojava.nbio.structure.gui: FlowLayout subclass that fully supports wrapping of components.
WrapLayout() - Constructor for class org.biojava.nbio.structure.gui.WrapLayout: Constructs a new WrapLayout with a left alignment and a default 5-unit horizontal and vertical gap.
WrapLayout(int) - Constructor for class org.biojava.nbio.structure.gui.WrapLayout: Constructs a new FlowLayout with the specified alignment and a default 5-unit horizontal and vertical gap.
WrapLayout(int, int, int) - Constructor for class org.biojava.nbio.structure.gui.WrapLayout: Creates a new flow layout manager with the indicated alignment and the indicated horizontal and vertical gaps.

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