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

  Parameters:

  afpChain -

  ca1 -

  ca2 -

  Returns:

  Throws:

  java.lang.ClassNotFoundException - If an error occurs when invoking jmol

  java.lang.NoSuchMethodException - If an error occurs when invoking jmol

  java.lang.reflect.InvocationTargetException - If an error occurs when invoking jmol

  java.lang.IllegalAccessException - If an error occurs when invoking jmol

• 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