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

java.lang.Object
  extended by org.biojava.bio.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
GuiWrapper()
           
 
Method Summary
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)
           
 
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

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
Throws:
ClassNotFoundException
NoSuchMethodException
InvocationTargetException
IllegalAccessException

getAtomArray

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