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

P

P - Static variable in class edu.sdsc.mbt.util.Element

PATTERN_TABLE - Static variable in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

PATTERN_TABLE - Static variable in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

PH_CUSTOM - Static variable in class edu.sdsc.sirius.dialogs.HydrogenDialog

PH_NEUTRAL - Static variable in class edu.sdsc.sirius.dialogs.HydrogenDialog

PICK_ATOMS - Static variable in class edu.sdsc.mbt.util.PickUtils

PICK_AUTO - Static variable in class edu.sdsc.mbt.util.PickUtils

PICK_CHAINS - Static variable in class edu.sdsc.mbt.util.PickUtils

PICK_FRAGMENTS - Static variable in class edu.sdsc.mbt.util.PickUtils

PICK_MOLECULES - Static variable in class edu.sdsc.mbt.util.PickUtils

PICK_RESIDUES - Static variable in class edu.sdsc.mbt.util.PickUtils

POINT - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle

Standard - Styles: Polyline

POSITION_LEFT - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

POSITION_TOP - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

PROPERTYNAME_DIVIDER_BORDER_VISIBLE - Static variable in class com.jgoodies.uif_lite.component.UIFSplitPane

Holds the name of the bound property that tries to show or hide the split pane's divider border.

PROPERTY_COLOR - Static variable in class edu.sdsc.mbt.viewables.StructureStyles

PROPERTY_COLOR - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

PROPERTY_RADIUS - Static variable in class edu.sdsc.mbt.viewables.StructureStyles

PROPERTY_RENDERING - Static variable in class edu.sdsc.mbt.viewables.StructureStyles

PROPERTY_RIBBON_COLOR - Static variable in class edu.sdsc.mbt.viewables.StructureStyles

PROPERTY_RIBBON_VISIBILITY - Static variable in class edu.sdsc.mbt.viewables.StructureStyles

PagePrintable - class edu.sdsc.sirius.util.PagePrintable.

Class that implements printing functions for the supplied images.

PagePrintable(Image, int, int, int, int) - Constructor for class edu.sdsc.sirius.util.PagePrintable

Constructor

Path - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path.

The Path class provides a lightweight pointer to an actual PDB entity, such as an edu.sdsc.sirius.viewers.StructureViewerImpl.pdb.Atom or edu.sdsc.sirius.viewers.StructureViewerImpl.pdb.Residue.

Path() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path

Path(String[]) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path

Creates a Path based on the given strings.

Path(String) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path

Creates a path based on the given string.

Pb - Static variable in class edu.sdsc.mbt.util.Element

Pd - Static variable in class edu.sdsc.mbt.util.Element

Pdb - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Pdb.

Pdb is a simple bag to hold Models.

Pdb() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Pdb

PdbDialog - class edu.sdsc.sirius.dialogs.PdbDialog.

PdbDialog(JFrame, Manager, Vector) - Constructor for class edu.sdsc.sirius.dialogs.PdbDialog

PdbEntryLoader - class edu.sdsc.sirius.io.PdbEntryLoader.

PdbEntryLoader() - Constructor for class edu.sdsc.sirius.io.PdbEntryLoader

PdbLoadDialog - class edu.sdsc.sirius.dialogs.PdbLoadDialog.

PdbLoadDialog(JFrame, Manager) - Constructor for class edu.sdsc.sirius.dialogs.PdbLoadDialog

PdbWrapper - interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper.

PeriodicTable - class edu.sdsc.mbt.util.PeriodicTable.

Provides a container object to hold chemical Element objects.

PeriodicTable() - Constructor for class edu.sdsc.mbt.util.PeriodicTable

PickUtils - class edu.sdsc.mbt.util.PickUtils.

This class provides a number of utility methods for handling picking and subsequent selection.

PickUtils() - Constructor for class edu.sdsc.mbt.util.PickUtils

Point3f - class edu.sdsc.mbt.viewers.GLViewerImpl.util.Point3f.

Point3f() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.util.Point3f

Point3f(float, float, float) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.util.Point3f

PreferencesCache - class edu.sdsc.sirius.dialogs.PreferencesCache.

This class serves as a temporary repository of all user selections in the preferences dialog.

PreferencesCache() - Constructor for class edu.sdsc.sirius.dialogs.PreferencesCache

PreferencesDialog - class edu.sdsc.sirius.dialogs.PreferencesDialog.

Implementation of the Preferences dialog used to set all user-adjustable parameters.

PreferencesDialog(JFrame, Manager) - Constructor for class edu.sdsc.sirius.dialogs.PreferencesDialog

Priestle - class edu.sdsc.mbt.viewers.GLViewerImpl.Priestle.

Priestle encapsulates a procedure used to smooth the coordinates passed to one of the geometry classes.

Priestle() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.Priestle

ProgressPanel - class edu.sdsc.sirius.viewers.ProgressPanel.

Provides a GUI component to display a simple progress meter.

ProgressPanel() - Constructor for class edu.sdsc.sirius.viewers.ProgressPanel

ProteinFragmentPanel - class edu.sdsc.sirius.builder.ProteinFragmentPanel.

ProteinFragmentPanel() - Constructor for class edu.sdsc.sirius.builder.ProteinFragmentPanel

ProteinProperties - class edu.sdsc.sirius.util.ProteinProperties.

This class stores information about bonding in standard amino acids and is used by the pdb loader to create bonds

ProteinProperties() - Constructor for class edu.sdsc.sirius.util.ProteinProperties

Pt - Static variable in class edu.sdsc.mbt.util.Element

PubmedLineData - class edu.sdsc.sirius.dialogs.TableImpl.PubmedLineData.

A container class for data displayed in one row of the table of ResultPanel.

PubmedLineData() - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.PubmedLineData

PubmedLineData(String, String, String, String) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.PubmedLineData

PubmedResultPanel - class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel.

This class implements a panel used to display sequence data retrieved from a database.

PubmedResultPanel(JPanel, DataSet) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel

Constructs the ResultPanel when created as in a frame typically storing search results.

pH - Variable in class edu.sdsc.sirius.dialogs.HydrogenEvent

paint(Graphics) - Method in class edu.sdsc.sirius.dialogs.ElementSelectionPanel.PtButton

paint(Graphics) - Method in class edu.sdsc.sirius.dialogs.ElementStylesEditor.PtButton

paint(Graphics) - Method in class edu.sdsc.sirius.util.TabListCellRenderer

paintComponent(Graphics) - Method in class edu.sdsc.sirius.dialogs.JFontPreviewPanel

paintImage() - Method in class edu.sdsc.sirius.dialogs.DistributionViewer

parent - Variable in class edu.sdsc.mbt.viewables.StructureDocument

parent_id - Variable in class edu.sdsc.sirius.util.StructureItem

parseDoubleList(String) - Static method in class edu.sdsc.sirius.util.DataService

parseResidueList(Structure, Chain, String) - Static method in class edu.sdsc.sirius.util.DataService

partialCharge - Variable in class edu.sdsc.mbt.Atom

Partial Charge (-1.0 - 3.0).

path - Variable in class edu.sdsc.mbt.util.Octree

pdbCode - Variable in class edu.sdsc.sirius.util.StructureItem

percent - Variable in class edu.sdsc.mbt.util.StatusEvent

The progress percentage (0.0-1.0).

period_number - Variable in class edu.sdsc.mbt.util.Element

phFlag - Variable in class edu.sdsc.sirius.dialogs.HydrogenDialog

phFlag - Variable in class edu.sdsc.sirius.dialogs.HydrogenEvent

pickLevel - Static variable in class edu.sdsc.mbt.util.PickUtils

pickLevelComponent(StructureComponent, double[]) - Static method in class edu.sdsc.mbt.util.PickUtils

Walk the data hierarchy (atom/bond-residue-fragment-chain-molecule) from the given structure component level toward the current pick level, and return the current pick level component.

point - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Point3f

pointOnUnitSphere(int, int, double[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.VirtualSphere2

Project a 2D point on a circle to a 3D point on the +z hemisphere of a unit sphere.

position - Variable in class edu.sdsc.sirius.util.Location

povrayInstallationDirectoryLinux - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

povrayInstallationDirectoryWin - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

preferredLayoutSize(Container) - Method in class edu.sdsc.sirius.util.DialogLayout

preferredLayoutSize(Container) - Method in class edu.sdsc.sirius.util.ExtensionLayout

print(Graphics, PageFormat, int) - Method in class edu.sdsc.sirius.util.PagePrintable

Printing method.

printChildNamingScheme() - Method in class edu.sdsc.mbt.util.Octree

???

printData() - Method in class edu.sdsc.sirius.dialogs.DistributionViewer

printData() - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

printData() - Method in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

printData() - Method in class edu.sdsc.sirius.viewers.TreeViewer.InfoViewer

printHandler(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

printImage() - Method in class edu.sdsc.sirius.dialogs.DistributionViewer

printSetupHandler() - Method in class edu.sdsc.sirius.dialogs.DistributionViewer

printSetupHandler() - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

printSetupHandler() - Method in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

printSetupHandler() - Method in class edu.sdsc.sirius.viewers.SequenceViewer

println(int, String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.util.Debug

Prints a line of debugging information if the specified level is greater than or equal to the current debugging level.

println(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.util.Debug

Outputs a line of debugging info, regardless of current debug level.

process() - Method in class edu.sdsc.sirius.dialogs.MotifDialog

process() - Method in class edu.sdsc.sirius.dialogs.PdbDialog

process() - Method in class edu.sdsc.sirius.dialogs.PreferencesDialog

processAlignment(String) - Method in class edu.sdsc.sirius.dialogs.StructureAlignmentDialog

processAlignmentOutput(String) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

processButtonClick(String) - Method in class edu.sdsc.sirius.builder.CustomFragmentPanel

processButtonClick(String) - Method in interface edu.sdsc.sirius.builder.FragmentGroupPanel

processButtonClick(String) - Method in class edu.sdsc.sirius.builder.GeneralFragmentPanel

processButtonClick(String) - Method in class edu.sdsc.sirius.builder.ProteinFragmentPanel

processClick(int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel

Method that handles mouse clicks depending on the row where they occurred.

processClick(int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel

Method that handles mouse clicks depending on the row where they occurred.

processClick(int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

Method that handles mouse clicks depending on the row where they occurred.

processClick(int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

processDisplayDialogEvent(DisplayDialogEvent) - Method in interface edu.sdsc.sirius.dialogs.DisplayDialogListener

processDisplayDialogEvent(DisplayDialogEvent) - Method in class edu.sdsc.sirius.viewers.StructureViewer

Processes a DisplayDialogEvent.

processMotif(String) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel

processMotifSearch(String) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

processMoveEvent(MoveEvent) - Method in interface edu.sdsc.mbt.viewers.GLViewerImpl.MoveEventListener

processMoveEvent(MoveEvent) - Method in class edu.sdsc.sirius.viewers.StructureViewer

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.builder.SaveFragmentDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.AlignmentSettingsDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.AngleDialog

This method is called by StructureViewer in response to a mouse click and sets the currently active text field to the String representation of the clicked StructureComponent.

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.AtomDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.AtomRenameDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.BondOrderDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.BreakBondDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.BumpDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.CenterDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.ChargeDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.ColorDialog

This method is called by StructureViewer in response to a mouse click and sets the currently active text field to the String representation of the clicked StructureComponent.

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.ComponentColorDialog

This method is called by StructureViewer in response to a mouse click and sets the currently active text field to the String representation of the clicked StructureComponent.

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.ComponentRenderingDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.ComponentRibbonDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.CreateBondDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.CreateSequenceDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.DataWBListerDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.DihedralDialog

processPick(String, StructureComponent) - Method in interface edu.sdsc.sirius.dialogs.DisplayDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.DistanceDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.FogDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.HBDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.HybridizationDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.HydrogenDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.ImageExportDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.LabelDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.MotionDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.PdbDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.PdbLoadDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.RayTracerDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.RenderingDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.ReplaceAtomDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.ReplaceResidueDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.ResidueLabelDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.ResidueRenameDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.RibbonColorDialog

This method is called by StructureViewer in response to a mouse click and sets the currently active text field to the String representation of the clicked StructureComponent.

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.RibbonDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.RotateBondDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.SelectListDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.SelectionAreaDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.SequenceRenameDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.StructureAlignmentDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.StructureEditDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.StructureRenameDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.StructureSelectionDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.StructureSetDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.StructureSuperpositionAlignDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.SuperimposeDialog

This method is called by StructureViewer in response to a mouse click and sets the currently active text field to the String representation of the clicked StructureComponent.

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.VisibilityDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.dialogs.WeightDialog

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.workbench.WBListDialog

This is a blank method included for compatibility with DisplayDialog tracking system (one modal dialog is displayed at a time, so we need to know what is open and what is closed).

processPick(String, StructureComponent) - Method in class edu.sdsc.sirius.workbench.WBSaveDialog

processPickEvent(GvPickEvent) - Method in interface edu.sdsc.mbt.viewers.GLViewerImpl.GvPickEventListener

processPickEvent(GvPickEvent) - Method in class edu.sdsc.sirius.viewers.StructureViewer

processSelection() - Method in class edu.sdsc.sirius.dialogs.EntryListerDialog

processSequenceStylesEvent(SequenceStylesEvent) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

In this viewer, coloring and selection are simplified and are handled directly through the Cell objects for performance reasons.

processSequenceStylesEvent(SequenceStylesEvent) - Method in interface edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEventListener

processSequenceStylesEvent(SequenceStylesEvent) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser

processStatusEvent(StatusEvent) - Method in interface edu.sdsc.mbt.util.StatusListener

processStatusEvent(StatusEvent) - Method in class edu.sdsc.sirius.viewers.StatusPanel

Gets called when the toolkit's Status class desides that there is a status message that the user should see (ie: on "output").

processStructureComponentEvent(StructureComponentEvent) - Method in interface edu.sdsc.mbt.StructureComponentEventListener

processStructureComponentEvent(StructureComponentEvent) - Method in class edu.sdsc.mbt.viewables.StructureStyles

Please complete the missing tags for main

processStructureComponentEvent(StructureComponentEvent) - Method in class edu.sdsc.sirius.viewers.RamachandranViewer

processStructureComponentEvent(StructureComponentEvent) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

processStructureComponentEvent(StructureComponentEvent) - Method in class edu.sdsc.sirius.viewers.StructureViewer

processStructureComponentEvent(StructureComponentEvent) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser

processStructureDocumentEvent(StructureDocumentEvent) - Method in class edu.sdsc.sirius.viewers.RamachandranViewer

processStructureDocumentEvent(StructureDocumentEvent) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

processStructureDocumentEvent(StructureDocumentEvent) - Method in class edu.sdsc.sirius.viewers.StructureViewer

Process a StructureDocumentEvent message.

processStructureDocumentEvent(StructureDocumentEvent) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser

processStructureDocumentEvent(StructureDocumentEvent) - Method in interface edu.sdsc.sirius.viewers.Viewer

Process a StructureDocumentEvent message.

processStructureStylesEvent(StructureStylesEvent) - Method in class edu.sdsc.mbt.viewables.StructureStyles

Informs all registered listeners that a style has changed.

processStructureStylesEvent(StructureStylesEvent) - Method in interface edu.sdsc.mbt.viewables.StructureStylesEventListener

processStructureStylesEvent(StructureStylesEvent) - Method in class edu.sdsc.sirius.viewers.RamachandranViewer

processStructureStylesEvent(StructureStylesEvent) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

processStructureStylesEvent(StructureStylesEvent) - Method in class edu.sdsc.sirius.viewers.StructureViewer

Process in incoming StructureStylesEvent.

processStructureStylesEvent(StructureStylesEvent) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser

progress(float, String) - Static method in class edu.sdsc.mbt.util.Status

Show a short progress message and a percentage completed.

property - Variable in class edu.sdsc.mbt.viewables.StructureStylesEvent

The specific property that was changed in the Style object (see each Style sub-classes for a list of valid states).

property - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEvent