Serialized Form (Forester 1.038 API)

Package org.forester.analysis
- Class org.forester.analysis.AncestralTaxonomyInferenceException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L

Package org.forester.archaeopteryx

Class org.forester.archaeopteryx.ArchaeopteryxA extends JApplet implements Serializable

serialVersionUID:

2314899014580484146L
- Serialized Fields
  - _mainframe_applet
```
MainFrameApplet _mainframe_applet
```
  - _tree_url_str
```
String _tree_url_str
```
  - _species_tree_url_str
```
String _species_tree_url_str
```
  - _message_1
```
String _message_1
```
  - _message_2
```
String _message_2
```

Class org.forester.archaeopteryx.ArchaeopteryxE extends JApplet implements Serializable

serialVersionUID:: -1220055577935759443L

Serialized Fields

_configuration
```
Configuration _configuration
```
_mainpanel
```
MainPanel _mainpanel
```
_jmenubar
```
JMenuBar _jmenubar
```
_options_jmenu
```
JMenu _options_jmenu
```
_font_size_menu
```
JMenu _font_size_menu
```
_super_tiny_fonts_mi
```
JMenuItem _super_tiny_fonts_mi
```
_tiny_fonts_mi
```
JMenuItem _tiny_fonts_mi
```
_small_fonts_mi
```
JMenuItem _small_fonts_mi
```
_medium_fonts_mi
```
JMenuItem _medium_fonts_mi
```
_large_fonts_mi
```
JMenuItem _large_fonts_mi
```
_tools_menu
```
JMenu _tools_menu
```
_taxcolor_item
```
JMenuItem _taxcolor_item
```
_confcolor_item
```
JMenuItem _confcolor_item
```
_midpoint_root_item
```
JMenuItem _midpoint_root_item
```
_view_jmenu
```
JMenu _view_jmenu
```
_view_as_XML_item
```
JMenuItem _view_as_XML_item
```
_view_as_NH_item
```
JMenuItem _view_as_NH_item
```
_view_as_nexus_item
```
JMenuItem _view_as_nexus_item
```

_display_basic_information_item

JMenuItem _display_basic_information_item

_type_menu
```
JMenu _type_menu
```

_rectangular_type_cbmi

JCheckBoxMenuItem _rectangular_type_cbmi

_triangular_type_cbmi
```
JCheckBoxMenuItem _triangular_type_cbmi
```
_curved_type_cbmi
```
JCheckBoxMenuItem _curved_type_cbmi
```
_convex_type_cbmi
```
JCheckBoxMenuItem _convex_type_cbmi
```
_euro_type_cbmi
```
JCheckBoxMenuItem _euro_type_cbmi
```
_rounded_type_cbmi
```
JCheckBoxMenuItem _rounded_type_cbmi
```
_unrooted_type_cbmi
```
JCheckBoxMenuItem _unrooted_type_cbmi
```
_circular_type_cbmi
```
JCheckBoxMenuItem _circular_type_cbmi
```
_help_item
```
JMenuItem _help_item
```
_about_item
```
JMenuItem _about_item
```
_help_jmenu
```
JMenu _help_jmenu
```
_website_item
```
JMenuItem _website_item
```
_phyloxml_website_item
```
JMenuItem _phyloxml_website_item
```
_phyloxml_ref_item
```
JMenuItem _phyloxml_ref_item
```
_aptx_ref_item
```
JMenuItem _aptx_ref_item
```
_remove_branch_color_item
```
JMenuItem _remove_branch_color_item
```
_remove_visual_styles_item
```
JMenuItem _remove_visual_styles_item
```
_show_domain_labels
```
JCheckBoxMenuItem _show_domain_labels
```

_show_annotation_ref_source

JCheckBoxMenuItem _show_annotation_ref_source

_color_labels_same_as_parent_branch

JCheckBoxMenuItem _color_labels_same_as_parent_branch

_abbreviate_scientific_names

JCheckBoxMenuItem _abbreviate_scientific_names

_screen_antialias_cbmi

JCheckBoxMenuItem _screen_antialias_cbmi

_background_gradient_cbmi

JCheckBoxMenuItem _background_gradient_cbmi

_color_by_taxonomic_group_cbmi

JCheckBoxMenuItem _color_by_taxonomic_group_cbmi

_non_lined_up_cladograms_rbmi

JRadioButtonMenuItem _non_lined_up_cladograms_rbmi

_uniform_cladograms_rbmi

JRadioButtonMenuItem _uniform_cladograms_rbmi

_ext_node_dependent_cladogram_rbmi

JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi

_options
```
Options _options
```
_choose_font_mi
```
JMenuItem _choose_font_mi
```
_switch_colors_mi
```
JMenuItem _switch_colors_mi
```
_label_direction_cbmi
```
JCheckBoxMenuItem _label_direction_cbmi
```
_show_scale_cbmi
```
JCheckBoxMenuItem _show_scale_cbmi
```

_search_case_senstive_cbmi

JCheckBoxMenuItem _search_case_senstive_cbmi

_search_whole_words_only_cbmi

JCheckBoxMenuItem _search_whole_words_only_cbmi

_inverse_search_result_cbmi

JCheckBoxMenuItem _inverse_search_result_cbmi

_search_with_regex_cbmi

JCheckBoxMenuItem _search_with_regex_cbmi

_show_overview_cbmi
```
JCheckBoxMenuItem _show_overview_cbmi
```
_choose_minimal_confidence_mi
```
JMenuItem _choose_minimal_confidence_mi
```

_collapse_species_specific_subtrees

JMenuItem _collapse_species_specific_subtrees

_overview_placment_mi
```
JMenuItem _overview_placment_mi
```
_radio_group_1
```
ButtonGroup _radio_group_1
```

_show_default_node_shapes_internal_cbmi

JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi

_show_default_node_shapes_external_cbmi

JCheckBoxMenuItem _show_default_node_shapes_external_cbmi

_show_default_node_shapes_for_marked_cbmi

JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi

_cycle_node_shape_mi
```
JMenuItem _cycle_node_shape_mi
```
_cycle_node_fill_mi
```
JMenuItem _cycle_node_fill_mi
```
_choose_node_size_mi
```
JMenuItem _choose_node_size_mi
```

_show_confidence_stddev_cbmi

JCheckBoxMenuItem _show_confidence_stddev_cbmi

_textframes
```
LinkedList<E> _textframes
```
_analysis_menu
```
JMenu _analysis_menu
```
_gsdi_item
```
JMenuItem _gsdi_item
```
_gsdir_item
```
JMenuItem _gsdir_item
```
_species_tree
```
Phylogeny _species_tree
```

_right_line_up_domains_cbmi

JCheckBoxMenuItem _right_line_up_domains_cbmi

_line_up_renderable_data_cbmi

JCheckBoxMenuItem _line_up_renderable_data_cbmi

_save_item
```
JMenuItem _save_item
```
_print_item
```
JMenuItem _print_item
```
_write_to_pdf_item
```
JMenuItem _write_to_pdf_item
```
_write_to_jpg_item
```
JMenuItem _write_to_jpg_item
```
_write_to_gif_item
```
JMenuItem _write_to_gif_item
```
_write_to_tif_item
```
JMenuItem _write_to_tif_item
```
_write_to_png_item
```
JMenuItem _write_to_png_item
```
_write_to_bmp_item
```
JMenuItem _write_to_bmp_item
```
_file_jmenu
```
JMenu _file_jmenu
```
_writetopdf_filechooser
```
JFileChooser _writetopdf_filechooser
```
_current_dir
```
File _current_dir
```
_save_filechooser
```
JFileChooser _save_filechooser
```

_writetographics_filechooser

JFileChooser _writetographics_filechooser

_graphics_export_visible_only_cbmi

JCheckBoxMenuItem _graphics_export_visible_only_cbmi

_antialias_print_cbmi
```
JCheckBoxMenuItem _antialias_print_cbmi
```

_print_black_and_white_cbmi

JCheckBoxMenuItem _print_black_and_white_cbmi

_print_using_actual_size_cbmi

JCheckBoxMenuItem _print_using_actual_size_cbmi

_graphics_export_using_actual_size_cbmi

JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi

_print_size_mi
```
JMenuItem _print_size_mi
```
_choose_pdf_width_mi
```
JMenuItem _choose_pdf_width_mi
```

Class org.forester.archaeopteryx.FontChooser extends JDialog implements Serializable

serialVersionUID:: 62256323L

Serialized Fields

_font
```
Font _font
```
_option
```
int _option
```
_type
```
String _type
```
_style
```
int _style
```
_size
```
int _size
```
_font_list
```
JList<E> _font_list
```
_style_list
```
JList<E> _style_list
```
_size_list
```
JList<E> _size_list
```
_fonts_tf
```
JTextField _fonts_tf
```
_style_tf
```
JTextField _style_tf
```
_size_tf
```
JTextField _size_tf
```
_fonts_label
```
JLabel _fonts_label
```
_style_label
```
JLabel _style_label
```
_size_label
```
JLabel _size_label
```
_font_jsp
```
JScrollPane _font_jsp
```
_style_jsp
```
JScrollPane _style_jsp
```
_size_jsp
```
JScrollPane _size_jsp
```
_ok_button
```
JButton _ok_button
```
_cancel_button
```
JButton _cancel_button
```
_test_tf
```
JTextField _test_tf
```

Class org.forester.archaeopteryx.MainFrame extends JFrame implements Serializable

serialVersionUID:: 3655000897845508358L

Serialized Fields

_jmenubar
```
JMenuBar _jmenubar
```
_file_jmenu
```
JMenu _file_jmenu
```
_tools_menu
```
JMenu _tools_menu
```
_view_jmenu
```
JMenu _view_jmenu
```
_options_jmenu
```
JMenu _options_jmenu
```
_font_size_menu
```
JMenu _font_size_menu
```
_help_jmenu
```
JMenu _help_jmenu
```

_load_phylogeny_from_webservice_menu_items

JMenuItem[] _load_phylogeny_from_webservice_menu_items

_analysis_menu
```
JMenu _analysis_menu
```
_load_species_tree_item
```
JMenuItem _load_species_tree_item
```
_gsdi_item
```
JMenuItem _gsdi_item
```
_gsdir_item
```
JMenuItem _gsdir_item
```
_lineage_inference
```
JMenuItem _lineage_inference
```
_open_item
```
JMenuItem _open_item
```
_open_url_item
```
JMenuItem _open_url_item
```
_save_item
```
JMenuItem _save_item
```
_save_all_item
```
JMenuItem _save_all_item
```
_close_item
```
JMenuItem _close_item
```
_exit_item
```
JMenuItem _exit_item
```
_new_item
```
JMenuItem _new_item
```
_print_item
```
JMenuItem _print_item
```
_write_to_pdf_item
```
JMenuItem _write_to_pdf_item
```
_write_to_jpg_item
```
JMenuItem _write_to_jpg_item
```
_write_to_gif_item
```
JMenuItem _write_to_gif_item
```
_write_to_tif_item
```
JMenuItem _write_to_tif_item
```
_write_to_png_item
```
JMenuItem _write_to_png_item
```
_write_to_bmp_item
```
JMenuItem _write_to_bmp_item
```
_midpoint_root_item
```
JMenuItem _midpoint_root_item
```
_taxcolor_item
```
JMenuItem _taxcolor_item
```
_confcolor_item
```
JMenuItem _confcolor_item
```
_color_rank_jmi
```
JMenuItem _color_rank_jmi
```

_collapse_species_specific_subtrees

JMenuItem _collapse_species_specific_subtrees

_obtain_detailed_taxonomic_information_jmi

JMenuItem _obtain_detailed_taxonomic_information_jmi

_obtain_detailed_taxonomic_information_deleting_jmi

JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi

_obtain_seq_information_jmi
```
JMenuItem _obtain_seq_information_jmi
```

_move_node_names_to_tax_sn_jmi

JMenuItem _move_node_names_to_tax_sn_jmi

_move_node_names_to_seq_names_jmi

JMenuItem _move_node_names_to_seq_names_jmi

_extract_tax_code_from_node_names_jmi

JMenuItem _extract_tax_code_from_node_names_jmi

_annotate_item
```
JMenuItem _annotate_item
```
_remove_branch_color_item
```
JMenuItem _remove_branch_color_item
```
_remove_visual_styles_item
```
JMenuItem _remove_visual_styles_item
```
_delete_selected_nodes_item
```
JMenuItem _delete_selected_nodes_item
```

_delete_not_selected_nodes_item

JMenuItem _delete_not_selected_nodes_item

_super_tiny_fonts_item
```
JMenuItem _super_tiny_fonts_item
```
_tiny_fonts_item
```
JMenuItem _tiny_fonts_item
```
_small_fonts_item
```
JMenuItem _small_fonts_item
```
_medium_fonts_item
```
JMenuItem _medium_fonts_item
```
_large_fonts_item
```
JMenuItem _large_fonts_item
```
_choose_font_mi
```
JMenuItem _choose_font_mi
```
_switch_colors_mi
```
JMenuItem _switch_colors_mi
```
_label_direction_cbmi
```
JCheckBoxMenuItem _label_direction_cbmi
```

_screen_antialias_cbmi

JCheckBoxMenuItem _screen_antialias_cbmi

_background_gradient_cbmi

JCheckBoxMenuItem _background_gradient_cbmi

_non_lined_up_cladograms_rbmi

JRadioButtonMenuItem _non_lined_up_cladograms_rbmi

_uniform_cladograms_rbmi

JRadioButtonMenuItem _uniform_cladograms_rbmi

_ext_node_dependent_cladogram_rbmi

JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi

_color_by_taxonomic_group_cbmi

JCheckBoxMenuItem _color_by_taxonomic_group_cbmi

_show_scale_cbmi
```
JCheckBoxMenuItem _show_scale_cbmi
```
_show_overview_cbmi
```
JCheckBoxMenuItem _show_overview_cbmi
```
_show_domain_labels
```
JCheckBoxMenuItem _show_domain_labels
```

_show_annotation_ref_source

JCheckBoxMenuItem _show_annotation_ref_source

_abbreviate_scientific_names

JCheckBoxMenuItem _abbreviate_scientific_names

_color_labels_same_as_parent_branch

JCheckBoxMenuItem _color_labels_same_as_parent_branch

_overview_placment_mi
```
JMenuItem _overview_placment_mi
```
_choose_minimal_confidence_mi
```
JMenuItem _choose_minimal_confidence_mi
```

_show_default_node_shapes_internal_cbmi

JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi

_show_default_node_shapes_external_cbmi

JCheckBoxMenuItem _show_default_node_shapes_external_cbmi

_show_default_node_shapes_for_marked_cbmi

JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi

_cycle_node_shape_mi
```
JMenuItem _cycle_node_shape_mi
```
_cycle_node_fill_mi
```
JMenuItem _cycle_node_fill_mi
```
_choose_node_size_mi
```
JMenuItem _choose_node_size_mi
```
_cycle_data_return
```
JMenuItem _cycle_data_return
```

_show_confidence_stddev_cbmi

JCheckBoxMenuItem _show_confidence_stddev_cbmi

_right_line_up_domains_cbmi

JCheckBoxMenuItem _right_line_up_domains_cbmi

_line_up_renderable_data_cbmi

JCheckBoxMenuItem _line_up_renderable_data_cbmi

_graphics_export_visible_only_cbmi

JCheckBoxMenuItem _graphics_export_visible_only_cbmi

_antialias_print_cbmi
```
JCheckBoxMenuItem _antialias_print_cbmi
```

_print_black_and_white_cbmi

JCheckBoxMenuItem _print_black_and_white_cbmi

_print_using_actual_size_cbmi

JCheckBoxMenuItem _print_using_actual_size_cbmi

_graphics_export_using_actual_size_cbmi

JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi

_print_size_mi
```
JMenuItem _print_size_mi
```
_choose_pdf_width_mi
```
JMenuItem _choose_pdf_width_mi
```

_internal_number_are_confidence_for_nh_parsing_cbmi

JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi

_extract_taxonomy_no_rbmi

JRadioButtonMenuItem _extract_taxonomy_no_rbmi

_extract_taxonomy_agressive_rbmi

JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi

_extract_taxonomy_pfam_strict_rbmi

JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi

_extract_taxonomy_pfam_relaxed_rbmi

JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi

_replace_underscores_cbmi

JCheckBoxMenuItem _replace_underscores_cbmi

_allow_errors_in_distance_to_parent_cbmi

JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi

_use_brackets_for_conf_in_nh_export_cbmi

JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi

_use_internal_names_for_conf_in_nh_export_cbmi

JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi

_search_case_senstive_cbmi

JCheckBoxMenuItem _search_case_senstive_cbmi

_search_whole_words_only_cbmi

JCheckBoxMenuItem _search_whole_words_only_cbmi

_inverse_search_result_cbmi

JCheckBoxMenuItem _inverse_search_result_cbmi

_search_with_regex_cbmi

JCheckBoxMenuItem _search_with_regex_cbmi

_type_menu
```
JMenu _type_menu
```

_rectangular_type_cbmi

JCheckBoxMenuItem _rectangular_type_cbmi

_triangular_type_cbmi
```
JCheckBoxMenuItem _triangular_type_cbmi
```
_curved_type_cbmi
```
JCheckBoxMenuItem _curved_type_cbmi
```
_convex_type_cbmi
```
JCheckBoxMenuItem _convex_type_cbmi
```
_euro_type_cbmi
```
JCheckBoxMenuItem _euro_type_cbmi
```
_rounded_type_cbmi
```
JCheckBoxMenuItem _rounded_type_cbmi
```
_unrooted_type_cbmi
```
JCheckBoxMenuItem _unrooted_type_cbmi
```
_circular_type_cbmi
```
JCheckBoxMenuItem _circular_type_cbmi
```
_view_as_NH_item
```
JMenuItem _view_as_NH_item
```
_view_as_XML_item
```
JMenuItem _view_as_XML_item
```
_view_as_nexus_item
```
JMenuItem _view_as_nexus_item
```

_display_basic_information_item

JMenuItem _display_basic_information_item

_about_item
```
JMenuItem _about_item
```
_help_item
```
JMenuItem _help_item
```
_website_item
```
JMenuItem _website_item
```
_phyloxml_website_item
```
JMenuItem _phyloxml_website_item
```
_phyloxml_ref_item
```
JMenuItem _phyloxml_ref_item
```
_aptx_ref_item
```
JMenuItem _aptx_ref_item
```
_current_dir
```
File _current_dir
```
_writetopdf_filechooser
```
JFileChooser _writetopdf_filechooser
```
_save_filechooser
```
JFileChooser _save_filechooser
```

_writetographics_filechooser

JFileChooser _writetographics_filechooser

_process_menu
```
JMenu _process_menu
```
_mainpanel
```
MainPanel _mainpanel
```
_contentpane
```
Container _contentpane
```
_textframes
```
LinkedList<E> _textframes
```
_configuration
```
Configuration _configuration
```
_options
```
Options _options
```
_species_tree
```
Phylogeny _species_tree
```
_inference_manager
```
InferenceManager _inference_manager
```
_process_pool
```
ProcessPool _process_pool
```
_previous_node_annotation_ref
```
String _previous_node_annotation_ref
```

Class org.forester.archaeopteryx.MainFrameApplet extends MainFrame implements Serializable

serialVersionUID:

1941019292746717053L
- Serialized Fields
  - _applet
```
ArchaeopteryxA _applet
```
  - _radio_group_1
```
ButtonGroup _radio_group_1
```

Class org.forester.archaeopteryx.MainFrameApplication extends MainFrame implements Serializable

serialVersionUID:: -799735726778865234L

Serialized Fields

_values_filechooser
```
JFileChooser _values_filechooser
```
_sequences_filechooser
```
JFileChooser _sequences_filechooser
```
_open_filechooser
```
JFileChooser _open_filechooser
```
_msa_filechooser
```
JFileChooser _msa_filechooser
```
_seqs_pi_filechooser
```
JFileChooser _seqs_pi_filechooser
```

_open_filechooser_for_species_tree

JFileChooser _open_filechooser_for_species_tree

_collapse_below_threshold
```
JMenuItem _collapse_below_threshold
```
_collapse_below_branch_length
```
JMenuItem _collapse_below_branch_length
```
_radio_group_1
```
ButtonGroup _radio_group_1
```
_radio_group_2
```
ButtonGroup _radio_group_2
```
_min_not_collapse
```
double _min_not_collapse
```
_min_not_collapse_bl
```
double _min_not_collapse_bl
```
_inference_menu
```
JMenu _inference_menu
```
_inference_from_msa_item
```
JMenuItem _inference_from_msa_item
```
_inference_from_seqs_item
```
JMenuItem _inference_from_seqs_item
```

_phylogenetic_inference_options

PhylogeneticInferenceOptions _phylogenetic_inference_options

_msa
```
Msa _msa
```
_msa_file
```
File _msa_file
```
_seqs
```
List<E> _seqs
```
_seqs_file
```
File _seqs_file
```
_read_values_jmi
```
JMenuItem _read_values_jmi
```
_read_seqs_jmi
```
JMenuItem _read_seqs_jmi
```

Class org.forester.archaeopteryx.MainPanel extends JPanel implements Serializable

serialVersionUID:: -2682765312661416435L

Serialized Fields

_mainframe
```
MainFrame _mainframe
```
_treepanels
```
List<E> _treepanels
```

_control_panel

org.forester.archaeopteryx.ControlPanel _control_panel

_treegraphic_scroll_panes
```
List<E> _treegraphic_scroll_panes
```
_treegraphic_scroll_pane_panels
```
List<E> _treegraphic_scroll_pane_panels
```
_configuration
```
Configuration _configuration
```
_tabbed_pane
```
JTabbedPane _tabbed_pane
```
_colorset
```
TreeColorSet _colorset
```
_fontset
```
TreeFontSet _fontset
```
_cut_or_copied_tree
```
Phylogeny _cut_or_copied_tree
```
_copied_and_pasted_nodes
```
Set<E> _copied_and_pasted_nodes
```
_image_map
```
Hashtable<K,V> _image_map
```

Class org.forester.archaeopteryx.TreePanel extends JPanel implements Serializable

serialVersionUID:: -978349745916505029L

Serialized Fields

_nodeid_dist_to_leaf
```
HashMap<K,V> _nodeid_dist_to_leaf
```
_arc
```
Arc2D _arc
```
_at
```
AffineTransform _at
```
_circ_max_depth
```
int _circ_max_depth
```
_collapsed_external_nodeid_set
```
Set<E> _collapsed_external_nodeid_set
```
_color_chooser
```
JColorChooser _color_chooser
```
_configuration
```
Configuration _configuration
```

_control_panel

org.forester.archaeopteryx.ControlPanel _control_panel

_cubic_curve
```
CubicCurve2D _cubic_curve
```
_current_external_nodes
```
Set<E> _current_external_nodes
```

_current_external_nodes_data_buffer

StringBuilder _current_external_nodes_data_buffer

_current_external_nodes_data_buffer_change_counter

int _current_external_nodes_data_buffer_change_counter

_domain_structure_e_value_thr_exp
```
int _domain_structure_e_value_thr_exp
```
_domain_structure_width
```
double _domain_structure_width
```
_dynamic_hiding_factor
```
int _dynamic_hiding_factor
```
_edited
```
boolean _edited
```
_ellipse
```
Ellipse2D _ellipse
```
_external_node_index
```
int _external_node_index
```
_found_nodes_0
```
Set<E> _found_nodes_0
```
_found_nodes_1
```
Set<E> _found_nodes_1
```
_frc
```
FontRenderContext _frc
```

_graphics_type

Options.PHYLOGENY_GRAPHICS_TYPE _graphics_type

_highlight_node
```
PhylogenyNode _highlight_node
```
_in_ov
```
boolean _in_ov
```
_in_ov_rect
```
boolean _in_ov_rect
```
_last_drag_point_x
```
float _last_drag_point_x
```
_last_drag_point_y
```
float _last_drag_point_y
```
_line
```
Line2D _line
```
_longest_ext_node_info
```
int _longest_ext_node_info
```

_ext_node_with_longest_txt_info

PhylogenyNode _ext_node_with_longest_txt_info

_main_panel
```
MainPanel _main_panel
```
_max_distance_to_root
```
double _max_distance_to_root
```
_node_desc_popup
```
Popup _node_desc_popup
```
_node_frame_index
```
int _node_frame_index
```

_node_frames

org.forester.archaeopteryx.NodeFrame[] _node_frames

_node_popup_menu
```
JPopupMenu _node_popup_menu
```
_node_popup_menu_items
```
JMenuItem[] _node_popup_menu_items
```
_nodes_in_preorder
```
PhylogenyNode[] _nodes_in_preorder
```
_options
```
Options _options
```
_ov_max_height
```
float _ov_max_height
```
_ov_max_width
```
float _ov_max_width
```
_ov_on
```
boolean _ov_on
```
_ov_rectangle
```
Rectangle2D _ov_rectangle
```
_ov_virtual_rectangle
```
Rectangle _ov_virtual_rectangle
```
_ov_x_correction_factor
```
float _ov_x_correction_factor
```
_ov_x_distance
```
float _ov_x_distance
```
_ov_x_position
```
int _ov_x_position
```
_ov_y_distance
```
float _ov_y_distance
```
_ov_y_position
```
int _ov_y_position
```
_ov_y_start
```
int _ov_y_start
```
_phy_has_branch_lengths
```
boolean _phy_has_branch_lengths
```
_phylogeny
```
Phylogeny _phylogeny
```
_polygon
```
Path2D.Float _polygon
```
_popup_buffer
```
StringBuffer _popup_buffer
```
_quad_curve
```
QuadCurve2D _quad_curve
```
_query_sequence
```
Sequence _query_sequence
```
_rectangle
```
Rectangle2D _rectangle
```
_rendering_hints
```
RenderingHints _rendering_hints
```
_rollover_popup
```
JTextArea _rollover_popup
```
_root
```
PhylogenyNode _root
```
_sb
```
StringBuilder _sb
```
_scale_distance
```
double _scale_distance
```
_scale_label
```
String _scale_label
```

_statistics_for_vector_data

DescriptiveStatistics _statistics_for_vector_data

_sub_phylogenies
```
Phylogeny[] _sub_phylogenies
```

_sub_phylogenies_temp_roots

PhylogenyNode[] _sub_phylogenies_temp_roots

_subtree_index
```
int _subtree_index
```
_treefile
```
File _treefile
```
_urt_factor
```
float _urt_factor
```
_urt_factor_ov
```
float _urt_factor_ov
```
_urt_nodeid_angle_map
```
HashMap<K,V> _urt_nodeid_angle_map
```
_urt_nodeid_index_map
```
HashMap<K,V> _urt_nodeid_index_map
```
_urt_starting_angle
```
double _urt_starting_angle
```
_x_correction_factor
```
float _x_correction_factor
```
_x_distance
```
float _x_distance
```
_y_distance
```
float _y_distance
```
_length_of_longest_text
```
int _length_of_longest_text
```
_longest_domain
```
int _longest_domain
```

Package org.forester.archaeopteryx.tools

Class org.forester.archaeopteryx.tools.PhyloInferenceDialog extends JDialog implements Serializable

serialVersionUID:: 8337543508238133614L

Serialized Fields

_pnl
```
JPanel _pnl
```
_launch_btn
```
JButton _launch_btn
```
_cancel_btn
```
JButton _cancel_btn
```
_bootstrap_tf
```
JFormattedTextField _bootstrap_tf
```
_bootstrap_cb
```
JCheckBox _bootstrap_cb
```
_opts
```
PhylogeneticInferenceOptions _opts
```
_input_msa_file_tf
```
JTextField _input_msa_file_tf
```
_select_input_msa_btn
```
JButton _select_input_msa_btn
```
_parent_frame
```
MainFrameApplication _parent_frame
```
_msa_length_tf
```
JTextField _msa_length_tf
```
_msa_size_tf
```
JTextField _msa_size_tf
```
_msa_type_tf
```
JTextField _msa_type_tf
```
_distance_calc_kimura_rb
```
JRadioButton _distance_calc_kimura_rb
```
_distance_calc_poisson_rb
```
JRadioButton _distance_calc_poisson_rb
```

_distance_calc_fract_dissimilarity_rb

JRadioButton _distance_calc_fract_dissimilarity_rb

_value
```
int _value
```
_input_seqs_tf
```
JTextField _input_seqs_tf
```
_select_input_seqs_btn
```
JButton _select_input_seqs_btn
```
_input_seqs_number_tf
```
JTextField _input_seqs_number_tf
```
_input_seqs_median_length_tf
```
JTextField _input_seqs_median_length_tf
```
_input_seqs_min_length_tf
```
JTextField _input_seqs_min_length_tf
```
_input_seqs_max_length_tf
```
JTextField _input_seqs_max_length_tf
```
_input_seqs_type_tf
```
JTextField _input_seqs_type_tf
```
_mafft_paramenters_tf
```
JTextField _mafft_paramenters_tf
```

_msa_processing_max_allowed_gap_ratio_tf

JTextField _msa_processing_max_allowed_gap_ratio_tf

_msa_processing_min_allowed_length_tf

JTextField _msa_processing_min_allowed_length_tf

_random_seed_tf
```
JTextField _random_seed_tf
```
_execute_msa_processing_cb
```
JCheckBox _execute_msa_processing_cb
```

_msa_processing_remove_all_gap_columns_cb

JCheckBox _msa_processing_remove_all_gap_columns_cb

_mafft_cb
```
JCheckBox _mafft_cb
```
_save_pwd_file_cb
```
JCheckBox _save_pwd_file_cb
```
_save_processed_msa_cb
```
JCheckBox _save_processed_msa_cb
```
_save_original_msa_cb
```
JCheckBox _save_original_msa_cb
```
_pwd_outfile_tf
```
JTextField _pwd_outfile_tf
```
_processed_msa_outfile_tf
```
JTextField _processed_msa_outfile_tf
```
_original_msa_outfile_tf
```
JTextField _original_msa_outfile_tf
```

Package org.forester.development
- Class org.forester.development.AbstractRenderer extends JComponent implements Serializable
  
  serialVersionUID:
  
  7236434322552764776L
  - Serialized Fields
    - _x
```
int _x
```
    - _y
```
int _y
```
    - _well_size
```
int _well_size
```
    - _status
```
byte _status
```
- Class org.forester.development.MsaRenderer extends JComponent implements Serializable
  
  serialVersionUID:
  
  -68078011081748093L
  - Serialized Fields
    - _rows
```
int _rows
```
    - _columns
```
int _columns
```
    - _wellSize
```
int _wellSize
```
    - _wells
```
AbstractRenderer[][] _wells
```
    - _min
```
double _min
```
    - _max
```
double _max
```
    - _mean
```
double _mean
```
    - _minColor
```
Color _minColor
```
    - _maxColor
```
Color _maxColor
```
    - _meanColor
```
Color _meanColor
```
    - _useMean
```
boolean _useMean
```
    - _msa
```
Msa _msa
```
    - _parent
```
JComponent _parent
```
- Class org.forester.development.ResidueRenderer extends AbstractRenderer implements Serializable
  
  serialVersionUID:
  
  -2331160296913478874L
  - Serialized Fields
    - _value
```
char _value
```
    - _wellColor
```
Color _wellColor
```
    - _isMarked
```
boolean _isMarked
```
    - _isSelected
```
boolean _isSelected
```
    - _parentPlateRenderer
```
MsaRenderer _parentPlateRenderer
```
Package org.forester.io.parsers.nexus
- Class org.forester.io.parsers.nexus.NexusFormatException extends IOException implements Serializable
  
  serialVersionUID:
  
  -8750474393398183410L
Package org.forester.io.parsers.nhx
- Class org.forester.io.parsers.nhx.NHXFormatException extends IOException implements Serializable
  
  serialVersionUID:
  
  3756209394438250170L
Package org.forester.io.parsers.phyloxml
- Class org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException extends IOException implements Serializable
  
  serialVersionUID:
  
  3756209394438250170L
- Class org.forester.io.parsers.phyloxml.PhyloXmlException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  3756209394438250170L
Package org.forester.io.parsers.util
- Class org.forester.io.parsers.util.PhylogenyParserException extends IOException implements Serializable
  
  serialVersionUID:
  
  -4810333295377881086L
Package org.forester.msa
- Class org.forester.msa.MsaFormatException extends IOException implements Serializable
  
  serialVersionUID:
  
  690079849050106491L
Package org.forester.msa_compactor
- Class org.forester.msa_compactor.Chart extends JDialog implements Serializable
  
  serialVersionUID:
  
  -5292420246132943515L
  - Serialized Fields
    - _chart_panel
```
com.approximatrix.charting.swing.ChartPanel _chart_panel
```
    - _initial_number_of_seqs
```
int _initial_number_of_seqs
```
    - _m_exit
```
JMenuItem _m_exit
```
    - _msa_props
```
List<E> _msa_props
```
    - _show_msa_qual
```
boolean _show_msa_qual
```
    - _title
```
String _title
```
Package org.forester.rio
- Class org.forester.rio.RIOException extends Exception implements Serializable
  
  serialVersionUID:
  
  4691098852783522097L
Package org.forester.sdi
- Class org.forester.sdi.SDIException extends Exception implements Serializable
  
  serialVersionUID:
  
  5154733429066500435L
Package org.forester.util
- Class org.forester.util.FailedConditionCheckException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -860013990231493438L
- Class org.forester.util.IllegalFormatUseException extends IllegalArgumentException implements Serializable
  
  serialVersionUID:
  
  -1126329548396073983L

Serialized Form

Package org.forester.analysis

Class org.forester.analysis.AncestralTaxonomyInferenceException extends Exception implements Serializable

Package org.forester.archaeopteryx

Class org.forester.archaeopteryx.ArchaeopteryxA extends JApplet implements Serializable

Serialized Fields

_mainframe_applet

_tree_url_str

_species_tree_url_str

_message_1

_message_2

Class org.forester.archaeopteryx.ArchaeopteryxE extends JApplet implements Serializable

Serialized Fields

_configuration

_mainpanel

_jmenubar

_options_jmenu

_font_size_menu

_super_tiny_fonts_mi

_tiny_fonts_mi

_small_fonts_mi

_medium_fonts_mi

_large_fonts_mi

_tools_menu

_taxcolor_item

_confcolor_item

_midpoint_root_item

_view_jmenu

_view_as_XML_item

_view_as_NH_item

_view_as_nexus_item

_display_basic_information_item

_type_menu

_rectangular_type_cbmi

_triangular_type_cbmi

_curved_type_cbmi

_convex_type_cbmi

_euro_type_cbmi

_rounded_type_cbmi

_unrooted_type_cbmi

_circular_type_cbmi

_help_item

_about_item

_help_jmenu

_website_item

_phyloxml_website_item

_phyloxml_ref_item

_aptx_ref_item

_remove_branch_color_item

_remove_visual_styles_item

_show_domain_labels

_show_annotation_ref_source

_color_labels_same_as_parent_branch

_abbreviate_scientific_names

_screen_antialias_cbmi

_background_gradient_cbmi

_color_by_taxonomic_group_cbmi

_non_lined_up_cladograms_rbmi

_uniform_cladograms_rbmi

_ext_node_dependent_cladogram_rbmi

_options

_choose_font_mi

_switch_colors_mi

_label_direction_cbmi

_show_scale_cbmi

_search_case_senstive_cbmi

_search_whole_words_only_cbmi

_inverse_search_result_cbmi

_search_with_regex_cbmi

_show_overview_cbmi

_choose_minimal_confidence_mi

_collapse_species_specific_subtrees

_overview_placment_mi

_radio_group_1

_show_default_node_shapes_internal_cbmi

_show_default_node_shapes_external_cbmi

_show_default_node_shapes_for_marked_cbmi

_cycle_node_shape_mi

_cycle_node_fill_mi

_choose_node_size_mi