- private final static int WIGGLE = 2;
- private final static int LIMIT_FOR_HQ_RENDERING = 1000;
- private final static int CONFIDENCE_LEFT_MARGIN = 4;
- // TODO "rendering_hints" was static before. Need to make sure everything is OK with it not
- // being static anymore (02/20/2009).
- private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
- RenderingHints.VALUE_RENDER_DEFAULT );
- private File _treefile = null;
- private Configuration _configuration = null;
- private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
- private int _node_frame_index = 0;
- private Phylogeny _phylogeny = null;
- private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
- private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
- private int _subtree_index = 0;
- private MainPanel _main_panel = null;
- private Set<Integer> _found_nodes = null;
- private PhylogenyNode _highlight_node = null;
- private JPopupMenu _node_popup_menu = null;
- private JMenuItem _node_popup_menu_items[] = null;
- private int _longest_ext_node_info = 0;
- private float _x_correction_factor = 0.0f;
- private float _ov_x_correction_factor = 0.0f;
- private float _x_distance = 0.0f;
- private float _y_distance = 0.0f;
- private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
- private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
- private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
- private float _last_drag_point_x = 0;
- private float _last_drag_point_y = 0;
- private ControlPanel _control_panel = null;
- private int _external_node_index = 0;
- private final Polygon _polygon = new Polygon();
- private final StringBuilder _sb = new StringBuilder();
- private JColorChooser _color_chooser = null;
- private double _scale_distance = 0.0;
- private String _scale_label = null;
- private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
- private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
- private final Line2D _line = new Line2D.Float();
- private final Ellipse2D _ellipse = new Ellipse2D.Float();
- private final Rectangle2D _rectangle = new Rectangle2D.Float();
- private Options _options = null;
- private float _ov_max_width = 0;
- private float _ov_max_height = 0;
- private int _ov_x_position = 0;
- private int _ov_y_position = 0;
- private int _ov_y_start = 0;
- private float _ov_y_distance = 0;
- private float _ov_x_distance = 0;
- private boolean _ov_on = false;
- private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
- private float _urt_factor = 1;
- private float _urt_factor_ov = 1;
+ private final static int WIGGLE = 2;
+ private final static int LIMIT_FOR_HQ_RENDERING = 1000;
+ private final static int CONFIDENCE_LEFT_MARGIN = 4;
+ private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_DEFAULT );
+ private File _treefile = null;
+ private Configuration _configuration = null;
+ private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
+ private int _node_frame_index = 0;
+ private Phylogeny _phylogeny = null;
+ private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
+ private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
+ private int _subtree_index = 0;
+ private MainPanel _main_panel = null;
+ private Set<Integer> _found_nodes = null;
+ private PhylogenyNode _highlight_node = null;
+ private JPopupMenu _node_popup_menu = null;
+ private JMenuItem _node_popup_menu_items[] = null;
+ private int _longest_ext_node_info = 0;
+ private float _x_correction_factor = 0.0f;
+ private float _ov_x_correction_factor = 0.0f;
+ private float _x_distance = 0.0f;
+ private float _y_distance = 0.0f;
+ private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
+ private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
+ private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
+ private float _last_drag_point_x = 0;
+ private float _last_drag_point_y = 0;
+ private ControlPanel _control_panel = null;
+ private int _external_node_index = 0;
+ private final Polygon _polygon = new Polygon();
+ private final StringBuilder _sb = new StringBuilder();
+ private JColorChooser _color_chooser = null;
+ private double _scale_distance = 0.0;
+ private String _scale_label = null;
+ private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
+ private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
+ private final Line2D _line = new Line2D.Float();
+ private final Ellipse2D _ellipse = new Ellipse2D.Float();
+ private final Rectangle2D _rectangle = new Rectangle2D.Float();
+ private Options _options = null;
+ private float _ov_max_width = 0;
+ private float _ov_max_height = 0;
+ private int _ov_x_position = 0;
+ private int _ov_y_position = 0;
+ private int _ov_y_start = 0;
+ private float _ov_y_distance = 0;
+ private float _ov_x_distance = 0;
+ private boolean _ov_on = false;
+ private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
+ private float _urt_factor = 1;
+ private float _urt_factor_ov = 1;