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Classes | Public Member Functions | Protected Member Functions | Protected Attributes | Package Functions | Package Attributes | Private Member Functions | Private Attributes

jalview::gui::AppJmol Class Reference

Inheritance diagram for jalview::gui::AppJmol:
Inheritance graph
Collaboration diagram for jalview::gui::AppJmol:
Collaboration graph

List of all members.


class  RenderPanel

Public Member Functions

void addAlignmentPanel (AlignmentPanel nap)
 AppJmol (String file, String id, SequenceI[] seq, AlignmentPanel ap, String loadStatus, Rectangle bounds, String viewid)
 AppJmol (PDBEntry pdbentry, SequenceI[] seq, String[] chains, final AlignmentPanel ap)
 AppJmol (AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
 AppJmol (String file, String id, SequenceI[] seq, AlignmentPanel ap, String loadStatus, Rectangle bounds)
 AppJmol (String[] files, String[] ids, SequenceI[][] seqs, AlignmentPanel ap, boolean usetoColour, boolean useToAlign, boolean leaveColouringToJmol, String loadStatus, Rectangle bounds, String viewid)
void backGround_actionPerformed (ActionEvent actionEvent)
void buriedColour_actionPerformed (ActionEvent actionEvent)
void chainColour_actionPerformed (ActionEvent actionEvent)
void chargeColour_actionPerformed (ActionEvent actionEvent)
void eps_actionPerformed (ActionEvent e)
void excludeAlignmentPanelForColourbyseq (AlignmentPanel nap)
void excludeAlignmentPanelForSuperposition (AlignmentPanel nap)
AlignmentPanel getAlignmentPanelFor (AlignmentI alignment)
AlignmentPanel[] getAllAlignmentPanels ()
String getViewId ()
void helixColour_actionPerformed (ActionEvent actionEvent)
void hydroColour_actionPerformed (ActionEvent actionEvent)
boolean isColouredByJmol ()
boolean isLinkedWith (AlignmentPanel ap2)
boolean isUsedforaligment (AlignmentPanel ap2)
boolean isUsedforcolourby (AlignmentPanel ap2)
void jmolColour_actionPerformed (ActionEvent actionEvent)
void jmolHelp_actionPerformed (ActionEvent actionEvent)
void pdbFile_actionPerformed (ActionEvent actionEvent)
void png_actionPerformed (ActionEvent e)
void removeAlignmentPanel (AlignmentPanel nap)
void run ()
void seqColour_actionPerformed (ActionEvent actionEvent)
void setJalviewColourScheme (ColourSchemeI ucs)
void showConsole (boolean showConsole)
void strandColour_actionPerformed (ActionEvent actionEvent)
void taylorColour_actionPerformed (ActionEvent actionEvent)
void turnColour_actionPerformed (ActionEvent actionEvent)
void updateTitleAndMenus ()
void useAlignmentPanelForColourbyseq (AlignmentPanel nap)
void useAlignmentPanelForColourbyseq (AlignmentPanel nap, boolean enableColourBySeq)
void useAlignmentPanelForSuperposition (AlignmentPanel nap)
void userColour_actionPerformed (ActionEvent actionEvent)
void viewMapping_actionPerformed (ActionEvent actionEvent)
void zappoColour_actionPerformed (ActionEvent actionEvent)

Protected Member Functions

void alignStructs_actionPerformed (ActionEvent actionEvent)
void buildJmolActionMenu ()

Protected Attributes

JMenuItem alignStructs = new JMenuItem()
JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem()
JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem()
JMenu chainMenu = new JMenu()
JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem()
ButtonGroup colourButtons = new ButtonGroup()
JMenu colourMenu = new JMenu()
JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem()
JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem()
JMenu jmolActionMenu = new JMenu()
JRadioButtonMenuItem jmolColour = new JRadioButtonMenuItem()
JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem()
JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem()
JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem()
JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem()
JRadioButtonMenuItem userColour = new JRadioButtonMenuItem()
JMenu viewMenu = new JMenu()
JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem()

Package Functions

void centerViewer ()
void closeViewer ()
void initJmol (String command)
void makePDBImage (int type)
void setChainMenuItems (Vector chains)

Package Attributes

Vector< AlignmentPanel_alignwith = new Vector<AlignmentPanel>()
ArrayList< String > _aps = new ArrayList()
Vector< AlignmentPanel_colourwith = new Vector<AlignmentPanel>()
boolean allChainsSelected = false
AlignmentPanel ap
Vector atomsPicked = new Vector()
JMenuItem backGround = new JMenuItem()
JMenuItem eps = new JMenuItem()
JMenu fileMenu = new JMenu()
JMenu helpMenu = new JMenu()
AppJmolBinding jmb
JMenu jMenu1 = new JMenu()
JMenuItem jmolHelp = new JMenuItem()
JMenuBar menuBar = new JMenuBar()
JMenuItem pdbFile = new JMenuItem()
JMenuItem png = new JMenuItem()
IProgressIndicator progressBar = null
RenderPanel renderPanel
JMenu savemenu = new JMenu()
JPanel scriptWindow
ViewSelectionMenu seqColourBy
JSplitPane splitPane
String viewId = null
JMenuItem viewMapping = new JMenuItem()

Private Member Functions

void addStructure (final PDBEntry pdbentry, final SequenceI[] seq, final String[] chains, final boolean b, final IProgressIndicator alignFrame)
void alignStructs_withAllAlignPanels ()
Vector getJmolsFor (AlignmentPanel ap2)
void initMenus ()
void openNewJmol (AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs)

Private Attributes

boolean _started = false
boolean addingStructures = false
boolean alignAddedStructures = false
Thread worker = null

Detailed Description

Definition at line 39 of file AppJmol.java.

The documentation for this class was generated from the following file:

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