org.biojava.spice
Interface SPICEFrame

All Known Implementing Classes:

SpiceApplication

public interface SPICEFrame

an interface that defines methods provided by the master application.

Author:

Andreas Prlic

Method Summary

BrowserPane	getBrowserPane() get the BrowserPane that is doing the 2D display
Chain	getChain(int chainnumber) retreive info regarding structure
RegistryConfiguration	getConfiguration() retrieve configuration for DAS servers to use
String	getENSPCode()
Container	getParent() returns the java.awt.Container of the spice object
String	getPDBCode() returns currently displayed PDB code; null if none
String	getPreferredStructureAlignmentServerName()
SpiceServer	getSpiceServer()
SpiceStartParameters	getSpiceStartParameters() get the parameters that are used while loading the next molecule
SpiceTabbedPane	getSpiceTabbedPane()
Structure	getStructure() retreive the internal Structure object
String	getUniProtCode() returns currently displayed UniProt code; null if none
JmolViewer	getViewer() get the Jmol viewer
void	load(String type, String code) starts a new thread and loads a new biological object into spice
void	reload() reload the currently displayed data
void	resetDisplay() reset the display, but do not change data
void	setPreferredStructureAlignmentServerName(String name)
void	setSpiceStartParameters(SpiceStartParameters params) set which parameters should be used for loading the next molecule.
void	setSpiceTabbedPane(SpiceTabbedPane tab)
void	setStructure(Structure s)
void	showConfig() show Config

Method Detail

getParent

public Container getParent()

returns the java.awt.Container of the spice object

Returns:

Container

load

public void load(String type,
                 String code)

starts a new thread and loads a new biological object into spice

Parameters:

type - the type of the code provided. currently supported: PDB, UniProt, ENSP

code - the code of the entry. e.g. 1a4a, P00280, 1q22

reload

public void reload()

reload the currently displayed data

getPreferredStructureAlignmentServerName

public String getPreferredStructureAlignmentServerName()

setPreferredStructureAlignmentServerName

public void setPreferredStructureAlignmentServerName(String name)

getConfiguration

public RegistryConfiguration getConfiguration()

retrieve configuration for DAS servers to use

Returns:

RegistryConfiguration the config

getSpiceServer

public SpiceServer getSpiceServer()

setSpiceTabbedPane

public void setSpiceTabbedPane(SpiceTabbedPane tab)

getSpiceTabbedPane

public SpiceTabbedPane getSpiceTabbedPane()

getViewer

public JmolViewer getViewer()

get the Jmol viewer

Returns:

JmolViewer the Jmol viewer doing the 3D visualisation

getBrowserPane

public BrowserPane getBrowserPane()

get the BrowserPane that is doing the 2D display

Returns:

returns the 2D sequence and feature panels

getStructure

public Structure getStructure()

retreive the internal Structure object

Returns:

Structure the internal structure representing the PDB object

setStructure

public void setStructure(Structure s)

resetDisplay

public void resetDisplay()

reset the display, but do not change data

showConfig

public void showConfig()

show Config

getChain

public Chain getChain(int chainnumber)

retreive info regarding structure

Parameters:

chainnumber - the number of the chain

Returns:

the Chain object

getPDBCode

public String getPDBCode()

returns currently displayed PDB code; null if none

Returns:

String the PDB code

getUniProtCode

public String getUniProtCode()

returns currently displayed UniProt code; null if none

Returns:

the Uniprot code

getENSPCode

public String getENSPCode()

setSpiceStartParameters

public void setSpiceStartParameters(SpiceStartParameters params)

set which parameters should be used for loading the next molecule. typically set before doing a new load(type,code) call.

Parameters:

params -

getSpiceStartParameters

public SpiceStartParameters getSpiceStartParameters()

get the parameters that are used while loading the next molecule

Returns:

the startup parameters