org.biojava.nbio.structure.align.ce

Class GuiWrapper

java.lang.Object

org.biojava.nbio.structure.align.ce.GuiWrapper

public class GuiWrapper
extends Object

A class to wrap some of the strucutre.gui classes using Reflection

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
GuiWrapper()

Method Summary

Methods

Modifier and Type	Method and Description
static Object	display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static Structure	getAlignedStructure(Atom[] ca1, Atom[] ca2)
static Atom[]	getAtomArray(Atom[] ca, List<Group> hetatoms, List<Group> nucs)
static JPanel	getScaleableMatrixPanel(Matrix m)
static boolean	isGuiModuleInstalled()
static Group[]	prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	showAlignmentGUI()
static void	showAlignmentImage(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Object jmol)
static void	showDBResults(StartupParameters params)
static void	showStructure(Structure structure) Shows a structure in Jmol

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GuiWrapper

public GuiWrapper()

Method Detail

isGuiModuleInstalled

public static boolean isGuiModuleInstalled()

display

public static Object display(AFPChain afpChain,
             Atom[] ca1,
             Atom[] ca2)
                      throws ClassNotFoundException,
                             NoSuchMethodException,
                             InvocationTargetException,
                             IllegalAccessException

Throws:

ClassNotFoundException

NoSuchMethodException

InvocationTargetException

IllegalAccessException

showAlignmentImage

public static void showAlignmentImage(AFPChain afpChain,
                      Atom[] ca1,
                      Atom[] ca2,
                      Object jmol)
                               throws ClassNotFoundException,
                                      NoSuchMethodException,
                                      InvocationTargetException,
                                      IllegalAccessException

Throws:

ClassNotFoundException

NoSuchMethodException

InvocationTargetException

IllegalAccessException

showStructure

public static void showStructure(Structure structure)
                          throws ClassNotFoundException,
                                 NoSuchMethodException,
                                 InvocationTargetException,
                                 IllegalAccessException,
                                 InstantiationException

Shows a structure in Jmol

Throws:

ClassNotFoundException

NoSuchMethodException

InvocationTargetException

IllegalAccessException

InstantiationException

Since:

3.0.5

showAlignmentGUI

public static void showAlignmentGUI()
                             throws ClassNotFoundException,
                                    NoSuchMethodException,
                                    InvocationTargetException,
                                    IllegalAccessException

Throws:

ClassNotFoundException

NoSuchMethodException

InvocationTargetException

IllegalAccessException

getAlignedStructure

public static Structure getAlignedStructure(Atom[] ca1,
                            Atom[] ca2)
                                     throws ClassNotFoundException,
                                            NoSuchMethodException,
                                            InvocationTargetException,
                                            IllegalAccessException

Throws:

ClassNotFoundException

NoSuchMethodException

InvocationTargetException

IllegalAccessException

getScaleableMatrixPanel

public static JPanel getScaleableMatrixPanel(Matrix m)
                                      throws ClassNotFoundException,
                                             NoSuchMethodException,
                                             InvocationTargetException,
                                             IllegalAccessException,
                                             InstantiationException

Throws:

ClassNotFoundException

NoSuchMethodException

InvocationTargetException

IllegalAccessException

InstantiationException

prepareGroupsForDisplay

public static Group[] prepareGroupsForDisplay(AFPChain afpChain,
                              Atom[] ca1,
                              Atom[] ca2)
                                       throws ClassNotFoundException,
                                              NoSuchMethodException,
                                              InvocationTargetException,
                                              IllegalAccessException

Parameters:

afpChain -

ca1 -

ca2 -

Returns:

Throws:

ClassNotFoundException - If an error occurs when invoking jmol

NoSuchMethodException - If an error occurs when invoking jmol

InvocationTargetException - If an error occurs when invoking jmol

IllegalAccessException - If an error occurs when invoking jmol

getAtomArray

public static Atom[] getAtomArray(Atom[] ca,
                  List<Group> hetatoms,
                  List<Group> nucs)
                           throws ClassNotFoundException,
                                  NoSuchMethodException,
                                  InvocationTargetException,
                                  IllegalAccessException

Throws:

ClassNotFoundException

NoSuchMethodException

InvocationTargetException

IllegalAccessException

showDBResults

public static void showDBResults(StartupParameters params)

Since:

3.0.5