org.biojava.bio.structure.align.ce

Class GuiWrapper

java.lang.Object

org.biojava.bio.structure.align.ce.GuiWrapper

public class GuiWrapper
extends java.lang.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 java.lang.Object	display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static Structure	getAlignedStructure(Atom[] ca1, Atom[] ca2)
static Atom[]	getAtomArray(Atom[] ca, java.util.List<Group> hetatoms, java.util.List<Group> nucs)
static javax.swing.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, java.lang.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 java.lang.Object display(AFPChain afpChain,
                       Atom[] ca1,
                       Atom[] ca2)
                                throws java.lang.ClassNotFoundException,
                                       java.lang.NoSuchMethodException,
                                       java.lang.reflect.InvocationTargetException,
                                       java.lang.IllegalAccessException

Throws:

java.lang.ClassNotFoundException

java.lang.NoSuchMethodException

java.lang.reflect.InvocationTargetException

java.lang.IllegalAccessException

showAlignmentImage

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

Throws:

java.lang.ClassNotFoundException

java.lang.NoSuchMethodException

java.lang.reflect.InvocationTargetException

java.lang.IllegalAccessException

showStructure

public static void showStructure(Structure structure)
                          throws java.lang.ClassNotFoundException,
                                 java.lang.NoSuchMethodException,
                                 java.lang.reflect.InvocationTargetException,
                                 java.lang.IllegalAccessException,
                                 java.lang.InstantiationException

Shows a structure in Jmol

Throws:

java.lang.ClassNotFoundException

java.lang.NoSuchMethodException

java.lang.reflect.InvocationTargetException

java.lang.IllegalAccessException

java.lang.InstantiationException

Since:

3.0.5

showAlignmentGUI

public static void showAlignmentGUI()
                             throws java.lang.ClassNotFoundException,
                                    java.lang.NoSuchMethodException,
                                    java.lang.reflect.InvocationTargetException,
                                    java.lang.IllegalAccessException

Throws:

java.lang.ClassNotFoundException

java.lang.NoSuchMethodException

java.lang.reflect.InvocationTargetException

java.lang.IllegalAccessException

getAlignedStructure

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

Throws:

java.lang.ClassNotFoundException

java.lang.NoSuchMethodException

java.lang.reflect.InvocationTargetException

java.lang.IllegalAccessException

getScaleableMatrixPanel

public static javax.swing.JPanel getScaleableMatrixPanel(Matrix m)
                                                  throws java.lang.ClassNotFoundException,
                                                         java.lang.NoSuchMethodException,
                                                         java.lang.reflect.InvocationTargetException,
                                                         java.lang.IllegalAccessException,
                                                         java.lang.InstantiationException

Throws:

java.lang.ClassNotFoundException

java.lang.NoSuchMethodException

java.lang.reflect.InvocationTargetException

java.lang.IllegalAccessException

java.lang.InstantiationException

prepareGroupsForDisplay

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

Throws:

java.lang.ClassNotFoundException

java.lang.NoSuchMethodException

java.lang.reflect.InvocationTargetException

java.lang.IllegalAccessException

getAtomArray

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

Throws:

java.lang.ClassNotFoundException

java.lang.NoSuchMethodException

java.lang.reflect.InvocationTargetException

java.lang.IllegalAccessException

showDBResults

public static void showDBResults(StartupParameters params)

Since:

3.0.5