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

jalview::appletgui::ExtJmol Class Reference

Inheritance diagram for jalview::appletgui::ExtJmol:
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Collaboration diagram for jalview::appletgui::ExtJmol:
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List of all members.

Public Member Functions

void addSequence (int pe, SequenceI[] seq)
synchronized PDBEntry[] addSequenceAndChain (PDBEntry[] pdbe, SequenceI[][] seq, String[][] chns)
void allocateViewer (Container renderPanel, boolean jmolfileio, String htmlName, URL documentBase, URL codeBase, String commandOptions)
void allocateViewer (Container renderPanel, boolean jmolfileio, String htmlName, URL documentBase, URL codeBase, String commandOptions, final Container consolePanel, String buttonsToShow)
void centerViewer (Vector chainList)
void closeViewer ()
void colourByChain ()
void colourByCharge ()
void colourBySequence (boolean showFeatures, jalview.api.AlignmentViewPanel alignmentv)
void componentHidden (ComponentEvent e)
void componentMoved (ComponentEvent e)
void componentResized (ComponentEvent e)
void componentShown (ComponentEvent e)
String createImage (String fileName, String type, Object textOrBytes, int quality)
void createImage (String file, String type, int quality)
String eval (String strEval)
void evalStateCommand (String command)
 ExtJmol (JmolViewer viewer, AlignmentPanel alignPanel, SequenceI[][] seqs)
float[][] functionXY (String functionName, int x, int y)
float[][][] functionXYZ (String functionName, int nx, int ny, int nz)
Color getColour (int atomIndex, int pdbResNum, String chain, String pdbfile)
FeatureRenderer getFeatureRenderer (AlignmentViewPanel alignment)
long getLoadNotifiesHandled ()
synchronized String[] getPdbFile ()
Map getRegistryInfo ()
SequenceRenderer getSequenceRenderer (AlignmentViewPanel alignment)
String getViewerTitle ()
void handlePopupMenu (int x, int y)
void highlightAtom (int atomIndex, int pdbResNum, String chain, String pdbfile)
boolean isColourBySequence ()
boolean isFinishedInit ()
boolean isLoadingFromArchive ()
void loadInline (String string)
void mouseOverStructure (int atomIndex, String strInfo)
void notifyAtomHovered (int atomIndex, String strInfo, String data)
void notifyAtomPicked (int atomIndex, String strInfo, String strData)
void notifyCallback (int type, Object[] data)
boolean notifyEnabled (int callbackPick)
void notifyFileLoaded (String fullPathName, String fileName2, String modelName, String errorMsg, int modelParts)
void notifyNewPickingModeMeasurement (int iatom, String strMeasure)
void notifyScriptTermination (String strStatus, int msWalltime)
String printMapping (String pdbfile)
void refreshGUI ()
void refreshPdbEntries ()
void releaseReferences (Object svl)
void selectionChanged (BitSet arg0)
void sendConsoleEcho (String strEcho)
void sendConsoleMessage (String strStatus)
void setBackgroundColour (java.awt.Color col)
void setCallbackFunction (String callbackType, String callbackFunction)
void setColourBySequence (boolean colourBySequence)
void setFinishedInit (boolean finishedInit)
void setJalviewColourScheme (ColourSchemeI cs)
void setLoadingFromArchive (boolean loadingFromArchive)
void showConsole (boolean show)
void showHelp ()
void showUrl (String arg0)
void showUrl (String url, String target)
void superposeStructures (AlignmentI alignment, int refStructure)
void superposeStructures (AlignmentI alignment, int refStructure, ColumnSelection hiddenCols)
void superposeStructures (AlignmentI alignment)
void superposeStructures (AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols)
void updateColours (Object source)

Public Attributes

Vector chainNames
String fileLoadingError
PDBEntry[] pdbentry
SequenceI[][] sequence
StructureSelectionManager ssm
JmolViewer viewer

Protected Member Functions

JmolAppConsoleInterface createJmolConsole (JmolViewer viewer2, Container consolePanel, String buttonsToShow)
 ExtJmol (jalview.appletgui.AlignFrame alframe, PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains, String protocol)
void releaseUIResources ()

Protected Attributes

String[][] chains
org.jmol.api.JmolAppConsoleInterface console = null
JmolPopup jmolpopup

Package Attributes

boolean allChainsSelected = false
Vector atomsPicked = new Vector()
Hashtable chainFile
boolean colourBySequence = true
boolean debug = true
StringBuffer eval = new StringBuffer()
int frameNo = 0
String lastCommand
String lastMessage
boolean loadedInline
String[] modelFileNames = null
String protocol = null
StringBuffer resetLastRes = new StringBuffer()

Private Attributes

AlignmentPanel ap

Detailed Description

bind an alignment view to an external Jmol instance.

Author:
JimP

Definition at line 42 of file ExtJmol.java.


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

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