Serialized Form

Package uk.ac.ed.simulator_pdb

Class uk.ac.ed.simulator_pdb.InstanceJava3DView extends Java3DView implements Serializable

Serialized Fields

instance_file_listener

InstanceFile.InstanceFileListener instance_file_listener

selected_object_listener

InstanceBuilderModel.SelectedObjectAdapter selected_object_listener

Class uk.ac.ed.simulator_pdb.InstancePropertiesView extends PropertiesView implements Serializable

Class uk.ac.ed.simulator_pdb.InstanceToolbarView extends javax.swing.JPanel implements Serializable

Serialized Fields

open_icon

javax.swing.ImageIcon open_icon

save_icon

javax.swing.ImageIcon save_icon

file_toolbar

javax.swing.JToolBar file_toolbar

new_button

javax.swing.JButton new_button

open_button

javax.swing.JButton open_button

save_button

javax.swing.JButton save_button

new_sim_object_button

javax.swing.JButton new_sim_object_button

model

Model model

Class uk.ac.ed.simulator_pdb.InstanceTreeView extends TreeView implements Serializable

Serialized Fields

instance_listener

InstanceFile.InstanceFileListener instance_listener

selected_object_listener

InstanceBuilderModel.SelectedObjectAdapter selected_object_listener

tree_popup_menu

javax.swing.JPopupMenu tree_popup_menu

new_submenu

javax.swing.JMenu new_submenu

new_object_submenu

javax.swing.JMenuItem new_object_submenu

one_new_object_menu_item

javax.swing.JMenuItem one_new_object_menu_item

ten_new_objects_menu_item

javax.swing.JMenuItem ten_new_objects_menu_item

one_hundred_new_objects_menu_item

javax.swing.JMenuItem one_hundred_new_objects_menu_item

cut_menu_item

javax.swing.JMenuItem cut_menu_item

copy_menu_item

javax.swing.JMenuItem copy_menu_item

paste_menu_item

javax.swing.JMenuItem paste_menu_item

delete_menu_item

javax.swing.JMenuItem delete_menu_item

Class uk.ac.ed.simulator_pdb.Java3DView extends javax.swing.JPanel implements Serializable

Serialized Fields

panel

uk.ac.ed.java3d_handler.Java3DPanel panel

model

Model model

scale

float scale

inverse_scale

float inverse_scale

Class uk.ac.ed.simulator_pdb.PropertiesView extends javax.swing.JPanel implements Serializable

Serialized Fields

properties_scrollpane

javax.swing.JScrollPane properties_scrollpane

blank_panel

javax.swing.JPanel blank_panel

template_file_scrollpane

javax.swing.JScrollPane template_file_scrollpane

template_file_panel

javax.swing.JPanel template_file_panel

instance_file_scrollpane

javax.swing.JScrollPane instance_file_scrollpane

instance_file_panel

javax.swing.JPanel instance_file_panel

pdbfile_scrollpane

javax.swing.JScrollPane pdbfile_scrollpane

pdbfile_template_panel

javax.swing.JPanel pdbfile_template_panel

pdbfile_type_combobox

javax.swing.JComboBox pdbfile_type_combobox

pdbfile_clustered_checkbox

javax.swing.JCheckBox pdbfile_clustered_checkbox

pdbfile_number_of_cluster

javax.swing.JSpinner pdbfile_number_of_cluster

object_template_scrollpane

javax.swing.JScrollPane object_template_scrollpane

object_template_panel

javax.swing.JPanel object_template_panel

object_template_id_text_field

javax.swing.JTextField object_template_id_text_field

object_template_mass_text_field

javax.swing.JFormattedTextField object_template_mass_text_field

object_template_radius_text_field

javax.swing.JFormattedTextField object_template_radius_text_field

subparticle_scrollpane

javax.swing.JScrollPane subparticle_scrollpane

subparticle_panel

javax.swing.JPanel subparticle_panel

subparticle_position_text_field

javax.swing.JFormattedTextField subparticle_position_text_field

subparticle_orientation_text_field

javax.swing.JFormattedTextField subparticle_orientation_text_field

particle_template_scrollpane

javax.swing.JScrollPane particle_template_scrollpane

particle_template_panel

javax.swing.JPanel particle_template_panel

particle_template_id_text_field

javax.swing.JTextField particle_template_id_text_field

particle_template_mass_text_field

javax.swing.JFormattedTextField particle_template_mass_text_field

particle_template_volume_text_field

javax.swing.JFormattedTextField particle_template_volume_text_field

particle_template_color_editor

PropertiesView.ColorEditor particle_template_color_editor

particle_template_shape_combobox

javax.swing.JComboBox particle_template_shape_combobox

particle_template_dimensions_panel

javax.swing.JPanel particle_template_dimensions_panel

particle_template_sphere_dimensions_panel

javax.swing.JPanel particle_template_sphere_dimensions_panel

particle_template_radius_label

javax.swing.JLabel particle_template_radius_label

particle_template_radius_text_field

javax.swing.JFormattedTextField particle_template_radius_text_field

particle_template_height_label

javax.swing.JLabel particle_template_height_label

particle_template_height_text_field

javax.swing.JFormattedTextField particle_template_height_text_field

particle_template_width_label

javax.swing.JLabel particle_template_width_label

particle_template_width_text_field

javax.swing.JFormattedTextField particle_template_width_text_field

particle_template_breadth_label

javax.swing.JLabel particle_template_breadth_label

particle_template_breadth_text_field

javax.swing.JFormattedTextField particle_template_breadth_text_field

particle_template_transparency_text_field

javax.swing.JFormattedTextField particle_template_transparency_text_field

bondsite_scrollpane

javax.swing.JScrollPane bondsite_scrollpane

bondsite_panel

javax.swing.JPanel bondsite_panel

bondsite_position_text_field

javax.swing.JFormattedTextField bondsite_position_text_field

bondsite_orientation_text_field

javax.swing.JFormattedTextField bondsite_orientation_text_field

bond_template_scrollpane

javax.swing.JScrollPane bond_template_scrollpane

bond_template_panel

javax.swing.JPanel bond_template_panel

bond_template_id_text_field

javax.swing.JTextField bond_template_id_text_field

bond_template_rules_model

javax.swing.DefaultListModel bond_template_rules_model

bond_template_rules

javax.swing.JList bond_template_rules

bond_template_new_rule_button

javax.swing.JButton bond_template_new_rule_button

bond_template_remove_rule_button

javax.swing.JButton bond_template_remove_rule_button

rule_template_scrollpane

javax.swing.JScrollPane rule_template_scrollpane

rule_template_panel

javax.swing.JPanel rule_template_panel

rule_template_id_text_field

javax.swing.JTextField rule_template_id_text_field

rule_template_type_combobox

javax.swing.JComboBox rule_template_type_combobox

rule_template_ifs

javax.swing.JList rule_template_ifs

rule_template_if_text_field

javax.swing.JTextField rule_template_if_text_field

rule_template_ifs_model

javax.swing.DefaultListModel rule_template_ifs_model

rule_template_new_if_button

javax.swing.JButton rule_template_new_if_button

rule_template_remove_if_button

javax.swing.JButton rule_template_remove_if_button

rule_template_prob_text_field

javax.swing.JFormattedTextField rule_template_prob_text_field

rule_template_time_text_field

javax.swing.JFormattedTextField rule_template_time_text_field

rule_template_likelyhoods_model

javax.swing.DefaultListModel rule_template_likelyhoods_model

rule_template_likelyhoods

javax.swing.JList rule_template_likelyhoods

rule_template_new_likelyhood_button

javax.swing.JButton rule_template_new_likelyhood_button

rule_template_remove_likelyhood_button

javax.swing.JButton rule_template_remove_likelyhood_button

object_scrollpane

javax.swing.JScrollPane object_scrollpane

object_panel

javax.swing.JPanel object_panel

object_id_text_field

javax.swing.JTextField object_id_text_field

object

java.lang.Object object

model

Model model

Class uk.ac.ed.simulator_pdb.SettingsView extends java.awt.Frame implements Serializable

Serialized Fields

panel

javax.swing.JPanel panel

tabbedPane

javax.swing.JTabbedPane tabbedPane

button_panel

javax.swing.JPanel button_panel

ok_button

javax.swing.JButton ok_button

landscape_combobox

javax.swing.JComboBox landscape_combobox

clustering_type_combobox

javax.swing.JComboBox clustering_type_combobox

number_of_clusters_textfield

javax.swing.JTextField number_of_clusters_textfield

time_value_textfield

javax.swing.JFormattedTextField time_value_textfield

time_unit_combo_box

javax.swing.JComboBox time_unit_combo_box

frame_delay_textfield

javax.swing.JFormattedTextField frame_delay_textfield

model

Model model

Class uk.ac.ed.simulator_pdb.SimulationJava3DView extends Java3DView implements Serializable

Class uk.ac.ed.simulator_pdb.SimulationToolbarView extends javax.swing.JPanel implements Serializable

Serialized Fields

open_icon

javax.swing.ImageIcon open_icon

save_icon

javax.swing.ImageIcon save_icon

simulation_toolbar

javax.swing.JToolBar simulation_toolbar

open_button

javax.swing.JButton open_button

play_button

javax.swing.JButton play_button

pause_button

javax.swing.JButton pause_button

stop_button

javax.swing.JButton stop_button

model

Model model

Class uk.ac.ed.simulator_pdb.SwingView extends java.awt.Frame implements Serializable

Serialized Fields

menuBar

java.awt.MenuBar menuBar

file_menu

java.awt.Menu file_menu

open_file_menu_item

java.awt.MenuItem open_file_menu_item

edit_settings_menu_item

java.awt.MenuItem edit_settings_menu_item

exit_menu_item

java.awt.MenuItem exit_menu_item

settings_view

SettingsView settings_view

tabbedPane

javax.swing.JTabbedPane tabbedPane

template_builder_panel

javax.swing.JPanel template_builder_panel

instance_builder_panel

javax.swing.JPanel instance_builder_panel

simulation_panel

javax.swing.JPanel simulation_panel

template_splitpane

javax.swing.JSplitPane template_splitpane

template_leftsplitpane

javax.swing.JSplitPane template_leftsplitpane

template_toolbar_view

TemplateToolbarView template_toolbar_view

template_tree_view

TemplateTreeView template_tree_view

template_properties_panel

TemplatePropertiesView template_properties_panel

template_java3d_view

TemplateJava3DView template_java3d_view

instance_splitpane

javax.swing.JSplitPane instance_splitpane

instance_leftsplitpane

javax.swing.JSplitPane instance_leftsplitpane

instance_toolbar_view

InstanceToolbarView instance_toolbar_view

instance_tree_view

InstanceTreeView instance_tree_view

instance_properties_panel

InstancePropertiesView instance_properties_panel

instance_java3d_view

InstanceJava3DView instance_java3d_view

simulation_toolbar_view

SimulationToolbarView simulation_toolbar_view

simulation_java3d_view

SimulationJava3DView simulation_java3d_view

model

Model model

Class uk.ac.ed.simulator_pdb.TemplateJava3DView extends Java3DView implements Serializable

Serialized Fields

file_listener

TemplateBuilderModel.FileListener file_listener

pdb_file_listener

PDBFile.PDBListener pdb_file_listener

template_file_listener

TemplateFile.TemplateFileListener template_file_listener

selected_object_listener

TemplateBuilderModel.SelectedObjectAdapter selected_object_listener

object_template_listener

SimObjectTemplate.SimObjectTemplateListener object_template_listener

template_listener

TemplateFileObject.TemplateFileObjectListener template_listener

Class uk.ac.ed.simulator_pdb.TemplatePropertiesView extends PropertiesView implements Serializable

Class uk.ac.ed.simulator_pdb.TemplateToolbarView extends javax.swing.JPanel implements Serializable

Serialized Fields

open_icon

javax.swing.ImageIcon open_icon

save_icon

javax.swing.ImageIcon save_icon

file_toolbar

javax.swing.JToolBar file_toolbar

new_button

javax.swing.JButton new_button

open_button

javax.swing.JButton open_button

save_button

javax.swing.JButton save_button

toolbar

javax.swing.JToolBar toolbar

new_sim_template_button

javax.swing.JButton new_sim_template_button

new_sim_sub_particle_button

javax.swing.JButton new_sim_sub_particle_button

new_sim_bond_site_button

javax.swing.JButton new_sim_bond_site_button

delete_sim_template_button

javax.swing.JButton delete_sim_template_button

model

Model model

Class uk.ac.ed.simulator_pdb.TemplateTreeView extends TreeView implements Serializable

Serialized Fields

template_listener

TemplateFile.TemplateFileListener template_listener

object_template_listener

SimObjectTemplate.SimObjectTemplateListener object_template_listener

tree_popup_menu

javax.swing.JPopupMenu tree_popup_menu

new_submenu

javax.swing.JMenu new_submenu

new_object_template_menu_item

javax.swing.JMenuItem new_object_template_menu_item

new_particle_template_menu_item

javax.swing.JMenuItem new_particle_template_menu_item

new_bond_template_menu_item

javax.swing.JMenuItem new_bond_template_menu_item

new_rule_template_menu_item

javax.swing.JMenuItem new_rule_template_menu_item

new_subparticle_template_menu_item

javax.swing.JMenuItem new_subparticle_template_menu_item

new_bondsite_template_menu_item

javax.swing.JMenuItem new_bondsite_template_menu_item

cut_menu_item

javax.swing.JMenuItem cut_menu_item

copy_menu_item

javax.swing.JMenuItem copy_menu_item

paste_menu_item

javax.swing.JMenuItem paste_menu_item

delete_menu_item

javax.swing.JMenuItem delete_menu_item

Class uk.ac.ed.simulator_pdb.TreeView extends javax.swing.JPanel implements Serializable

Serialized Fields

tree

javax.swing.JTree tree

renderer

TreeView.TreeRenderer renderer

tree_scrollpane

javax.swing.JScrollPane tree_scrollpane

root

javax.swing.tree.TreeNode root

instances

javax.swing.tree.DefaultMutableTreeNode instances

objects_instances

javax.swing.tree.DefaultMutableTreeNode objects_instances

tree_model

javax.swing.tree.DefaultTreeModel tree_model

model

Model model

node_mappings

java.util.Hashtable node_mappings

Class uk.ac.ed.simulator_pdb.View.ChooserDialog extends javax.swing.JComponent implements Serializable

Serialized Fields

choosen_object

java.lang.Object choosen_object

dialog

javax.swing.JDialog dialog

panel

javax.swing.JPanel panel

scrollPane

javax.swing.JScrollPane scrollPane

list

javax.swing.JList list

button_panel

javax.swing.JPanel button_panel

ok_button

javax.swing.JButton ok_button

cancel_button

javax.swing.JButton cancel_button

return_value

int return_value

Package uk.ac.ed.simulator_pdb.model

Class uk.ac.ed.simulator_pdb.model.InstanceBuilderModel.FileEvent extends java.util.EventObject implements Serializable

Serialized Fields

instance_file

InstanceFile instance_file

Class uk.ac.ed.simulator_pdb.model.InstanceBuilderModel.SelectedObjectEvent extends java.util.EventObject implements Serializable

Serialized Fields

selected_object

java.lang.Object selected_object

deselected_object

java.lang.Object deselected_object

transform_matrix

javax.vecmath.Matrix4d transform_matrix

Class uk.ac.ed.simulator_pdb.model.InstanceFile.InstanceFileEvent extends java.util.EventObject implements Serializable

Serialized Fields

instance_file_object

InstanceFileObject instance_file_object

scale

double scale

Class uk.ac.ed.simulator_pdb.model.InstanceFileObject.InstanceFileObjectEvent extends java.util.EventObject implements Serializable

Serialized Fields

instance_file_object

InstanceFileObject instance_file_object

Class uk.ac.ed.simulator_pdb.model.PDBFile.PDBEvent extends java.util.EventObject implements Serializable

Serialized Fields

scale

double scale

template_file_object

TemplateFileObject template_file_object

pdb_file

PDBFile pdb_file

Class uk.ac.ed.simulator_pdb.model.SimObjectTemplate.SimObjectTemplateEvent extends java.util.EventObject implements Serializable

Serialized Fields

template

SimObjectTemplate template

sub_particle

SimSubParticle sub_particle

bond_site

SimBondSite bond_site

Class uk.ac.ed.simulator_pdb.model.SimulatorModel.SimulationEvent extends java.util.EventObject implements Serializable

Serialized Fields

simulation_state

int simulation_state

new_value

double new_value

old_value

double old_value

new_frame_delay

long new_frame_delay

old_frame_delay

long old_frame_delay

cluster

SimCluster cluster

new_transform

javax.vecmath.Matrix4d new_transform

Class uk.ac.ed.simulator_pdb.model.TemplateBuilderModel.FileEvent extends java.util.EventObject implements Serializable

Serialized Fields

pdb_file

PDBFile pdb_file

template_file

TemplateFile template_file

Class uk.ac.ed.simulator_pdb.model.TemplateBuilderModel.SelectedObjectEvent extends java.util.EventObject implements Serializable

Serialized Fields

selected_object

java.lang.Object selected_object

deselected_object

java.lang.Object deselected_object

transform_matrix

javax.vecmath.Matrix4d transform_matrix

Class uk.ac.ed.simulator_pdb.model.TemplateFile.TemplateFileEvent extends java.util.EventObject implements Serializable

Serialized Fields

template_file_object

TemplateFileObject template_file_object

scale

double scale

Class uk.ac.ed.simulator_pdb.model.TemplateFileObject.TemplateFileObjectEvent extends java.util.EventObject implements Serializable

Serialized Fields

template_file_object

TemplateFileObject template_file_object

old_id

java.lang.String old_id

new_id

java.lang.String new_id