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

U

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

UIFSplitPane - class com.jgoodies.uif_lite.component.UIFSplitPane.

A JSplitPane subclass that can try to remove the divider border.

UIFSplitPane() - Constructor for class com.jgoodies.uif_lite.component.UIFSplitPane

Constructs a UIFSplitPane configured to arrange the child components side-by-side horizontally with no continuous layout, using two buttons for the components.

UIFSplitPane(int) - Constructor for class com.jgoodies.uif_lite.component.UIFSplitPane

Constructs a UIFSplitPane configured with the specified orientation and no continuous layout.

UIFSplitPane(int, boolean) - Constructor for class com.jgoodies.uif_lite.component.UIFSplitPane

Constructs a UIFSplitPane with the specified orientation and redrawing style.

UIFSplitPane(int, Component, Component) - Constructor for class com.jgoodies.uif_lite.component.UIFSplitPane

Constructs a UIFSplitPane with the specified orientation and the given componenents.

UIFSplitPane(int, boolean, Component, Component) - Constructor for class com.jgoodies.uif_lite.component.UIFSplitPane

Constructs a UIFSplitPane with the specified orientation, redrawing style, and given components.

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

USE_ALL - Static variable in class edu.sdsc.sirius.dialogs.StructureAlignmentDialog

USE_DEFINED - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants

Sequence set option: use sequences from the database.

USE_LOADED - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants

Sequence set option: use sequences loaded in the SequenceViewer.

USE_SELECTION - Static variable in class edu.sdsc.sirius.dialogs.StructureAlignmentDialog

USE_SET - Static variable in class edu.sdsc.sirius.dialogs.StructureAlignmentDialog

UrlLoader - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlLoader.

UrlLoader is a loader class for generating a PdbWrapper that allows an application to access a network-based PDB file.

UrlLoader(URL) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlLoader

Create a new UrlLoader from the specified URL.

UrlPdbWrapper - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper.

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

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

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

undoDepth - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache

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

undoEnabled - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache

undoProcess - Static variable in class edu.sdsc.sirius.viewers.StructureViewer

unregisterEntry(Entry) - Method in class edu.sdsc.sirius.workbench.WBManager

Remove any references to the Entry object.

up - Variable in class edu.sdsc.sirius.export.ViewerParameters

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

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

updateAppearance() - Method in class Viewer

updateAppearance() - Method in interface edu.sdsc.sirius.util.Manager

Causes the main application to refresh all visual elements.

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

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

updateBondOrders(Structure) - Static method in class edu.sdsc.sirius.util.StructureMath

This method checks whether the structure is a protein or DNA and assigns correct bond orders in case they have not been assigned.

updateBoundWaters() - Method in class Viewer

updateBoundWaters() - Method in interface edu.sdsc.sirius.util.Manager

Update display of crystallographic waters

updateBoundWaters(boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

updateBoundWaters(Structure, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

updateBuilderDialog() - Method in class Viewer

updateBuilderDialog() - Method in interface edu.sdsc.sirius.util.Manager

This method is called when the builder dialog is updated, e.g.

updateChain(Chain, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles

This method determines whether the chain has any ribbon and whether its residues are selected.

updateContent(int, int, double) - Method in class edu.sdsc.sirius.ray.ImagePreviewPanel

updateContent() - Method in class edu.sdsc.sirius.workbench.WBListPanel

Updates the list of items by calling WBManager and rebuilds the tree.

updateCoordinates(Structure, double[], float[], boolean, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

updateFileSuffix(String) - Method in class edu.sdsc.sirius.dialogs.ImageExportDialog

updateList() - Method in class edu.sdsc.sirius.workbench.WBListDialog

Updates the displayed list of the content.

updateMonitorDialog() - Method in class Viewer

updateMonitorDialog() - Method in interface edu.sdsc.sirius.util.Manager

This method is called when any change has been made to the display markers and causes the dialog to redraw itself to reflect the change.

updateMouseResponse(int) - Method in class Viewer

updateMouseResponse(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

updateMouseResponse(int) - Method in interface edu.sdsc.sirius.util.Manager

Update variables that control speed of the structure motion response to the motion of the mouse pointer

updateMouseResponse(int) - Method in class edu.sdsc.sirius.viewers.StructureViewer

updateOptionsMenu() - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanelFrame

Updates Options menu in response to addition or removal of columns.

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

This method runs through records and adds or removes buttons as necessary

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

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

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

updatePanels() - Method in class edu.sdsc.sirius.builder.BuilderDialog

This method checks whether a custom panel is needed and adds or removes it, as necessary

updatePanels() - Method in class edu.sdsc.sirius.builder.BuilderPanel

updateParameters() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel

This method is called by SequenceViewer to set the dimenstions of the panel elements dependent on font size.

updateSequence(Sequence, String) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

This method runs through the symbols in the sequence display of the given Sequence object and inserts dashes wherever necessary

updateToolbar() - Method in class Viewer

updateToolbar() - Method in interface edu.sdsc.sirius.util.Manager

Update the toolbar in response to any change in its configuration.

updateTree() - Method in class edu.sdsc.sirius.monitors.MonitorDialog

updateTree() - Method in class edu.sdsc.sirius.monitors.MonitorPanel

updateUI() - Method in class com.jgoodies.uif_lite.component.UIFSplitPane

Updates the UI and sets an empty divider border.

updateUI() - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame

Updates the UI.

updateView() - Method in class Viewer

This method is different from updateAppearance, in that it doesn't mark all renderables as dirty, but only forces the geometry viewer to update the view by calling its display method.

updateView() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

updateView() - Method in interface edu.sdsc.sirius.util.Manager

Causes a display refresh without regenerating all renderables, as it happens in updateAppearance() method.

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

updateView(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel

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

updateVisibility(Residue) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser