private boolean _color_labels_same_as_parent_branch = false;
private int _default_bootstrap_samples = -1;
private boolean _show_default_node_shapes = false;
- private NodeShape _default_node_shape = NodeShape.NONE;
+ private NodeShape _default_node_shape = NodeShape.CIRCLE;
private NodeFill _default_node_fill = NodeFill.GRADIENT;
private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
- private boolean _taxonomy_colorize_node_shapes = false;
+ private boolean _taxonomy_colorize_node_shapes = false;
final static int display_as_phylogram = 0;
final static int show_node_names = 1;
final static int show_tax_code = 2;
{ "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
{ "Annotation", "nodisplay", "no" }, { "Confidence Value", "display", "?" }, { "Event", "display", "?" },
{ "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" },
- { "Use Branch-Width", "nodisplay", "no" }, { "Show Custom Nodes", "display", "yes"}, { "Domains", "nodisplay", "no" },
- { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
- { "Prot/Gene Name", "display", "no" }, { "Prot/Gene Acc", "display", "no" },
- { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
- { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
- { "Annotation Colorize", "nodisplay", "no" }, { "Property", "nodisplay", "no" },
- { "Prot/Gene Symbol", "display", "no" }, { "Rollover", "display", "yes" },
- { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
- { "Taxonomy Images", "display", "no" } };
+ { "Use Branch-Width", "nodisplay", "no" }, { "Show Custom Nodes", "display", "yes" },
+ { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
+ { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "no" },
+ { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
+ { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
+ { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
+ { "Property", "nodisplay", "no" }, { "Prot/Gene Symbol", "display", "no" },
+ { "Rollover", "display", "yes" }, { "Relation Confidence", "display", "no" },
+ { "Vector Data", "display", "no" }, { "Taxonomy Images", "display", "no" } };
final static String clickto_options[][] = {
{ "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
{ "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
return _cladogram_type;
}
-
private int getClickToIndex( final String name ) {
int index = -1;
if ( name.equals( "edit_info" ) ) {
else if ( key.equals( "domain_structure_base_color" ) ) {
_domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
}
- //
else if ( key.equals( "show_default_node_shapes" ) ) {
setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
}
}
else if ( key.equals( "default_node_shape" ) ) {
final String shape_str = ( ( String ) st.nextElement() ).trim();
- if ( shape_str.equalsIgnoreCase( Options.NodeShape.NONE.toString() ) ) {
- setDefaultNodeShape( NodeShape.NONE );
- }
- else if ( shape_str.equalsIgnoreCase( Options.NodeShape.CIRCLE.toString() ) ) {
+ if ( shape_str.equalsIgnoreCase( Options.NodeShape.CIRCLE.toString() ) ) {
setDefaultNodeShape( NodeShape.CIRCLE );
}
else if ( shape_str.equalsIgnoreCase( Options.NodeShape.RECTANGLE.toString() ) ) {
public boolean isTaxonomyColorizeNodeShapes() {
return _taxonomy_colorize_node_shapes;
}
-
+
public boolean isShowDefaultNodeShapes() {
- return _show_default_node_shapes;
- }
- private void setShowDefaultNodeShapes(boolean show_default_node_shapes) {
- _show_default_node_shapes =show_default_node_shapes;
- }
-
+ return _show_default_node_shapes;
+ }
+
+ private void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
+ _show_default_node_shapes = show_default_node_shapes;
+ }
}
import java.util.Locale;
import java.util.Map;
-import javax.swing.Icon;
import javax.swing.JApplet;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JFrame;
public abstract class MainFrame extends JFrame implements ActionListener {
- static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
- static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
- static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
- private static final long serialVersionUID = 3655000897845508358L;
- final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
- Font.PLAIN,
- 10 );
- static final String TYPE_MENU_HEADER = "Type";
- static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
- static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
- static final String CURVED_TYPE_CBMI_LABEL = "Curved";
- static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
- static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
- static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
- static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
- static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
- static final String OPTIONS_HEADER = "Options";
- static final String SEARCH_SUBHEADER = "Search:";
- static final String DISPLAY_SUBHEADER = "Display:";
- static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
- static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
- static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
- static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
- static final String DISPLAY_SCALE_LABEL = "Display Scale";
- static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
- static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
- static final String LABEL_DIRECTION_LABEL = "Radial Labels";
- static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
- static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
- static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
- static final String BG_GRAD_LABEL = "Background Color Gradient";
- static final String DISPLAY_NODE_BOXES_LABEL = "Display Node Shapes";
- static final String SHOW_OVERVIEW_LABEL = "Show Overview";
- static final String FONT_SIZE_MENU_LABEL = "Font Size";
- static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
- static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
- static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
- static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
- static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
- static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
- static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
- static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
+ static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
+ static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
+ static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
+ private static final long serialVersionUID = 3655000897845508358L;
+ final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
+ Font.PLAIN,
+ 10 );
+ static final String TYPE_MENU_HEADER = "Type";
+ static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
+ static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
+ static final String CURVED_TYPE_CBMI_LABEL = "Curved";
+ static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
+ static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
+ static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
+ static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
+ static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
+ static final String OPTIONS_HEADER = "Options";
+ static final String SEARCH_SUBHEADER = "Search:";
+ static final String DISPLAY_SUBHEADER = "Display:";
+ static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
+ static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
+ static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
+ static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
+ static final String DISPLAY_SCALE_LABEL = "Display Scale";
+ static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
+ static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
+ static final String LABEL_DIRECTION_LABEL = "Radial Labels";
+ static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
+ static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
+ static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
+ static final String BG_GRAD_LABEL = "Background Color Gradient";
+ static final String DISPLAY_NODE_BOXES_LABEL = "Display Node Shapes";
+ static final String SHOW_OVERVIEW_LABEL = "Show Overview";
+ static final String FONT_SIZE_MENU_LABEL = "Font Size";
+ static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
+ static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
+ static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
+ static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
+ static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
+ static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
+ static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
+ static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
JMenuBar _jmenubar;
JMenu _file_jmenu;
JMenu _tools_menu;
JMenuItem _confcolor_item;
JMenuItem _infer_common_sn_names_item;
JMenuItem _collapse_species_specific_subtrees;
- JMenuItem _collapse_below_threshold; //TODO implememt me
+ JMenuItem _collapse_below_threshold; //TODO implememt me
JMenuItem _obtain_detailed_taxonomic_information_jmi;
JMenuItem _obtain_uniprot_seq_information_jmi;
JMenuItem _move_node_names_to_tax_sn_jmi;
// _ screen display
JCheckBoxMenuItem _screen_antialias_cbmi;
JCheckBoxMenuItem _background_gradient_cbmi;
-
JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
JRadioButtonMenuItem _uniform_cladograms_rbmi;
JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
JCheckBoxMenuItem _show_branch_length_values_cbmi;
- JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
+ JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
JCheckBoxMenuItem _show_overview_cbmi;
JCheckBoxMenuItem _show_domain_labels;
JCheckBoxMenuItem _abbreviate_scientific_names;
JCheckBoxMenuItem _color_labels_same_as_parent_branch;
JMenuItem _overview_placment_mi;
JMenuItem _choose_minimal_confidence_mi;
-
JCheckBoxMenuItem _show_default_node_shapes_cbmi;
JMenuItem _cycle_node_shape_mi;
JMenuItem _cycle_node_fill_mi;
JMenuItem _choose_node_size_mi;
- JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
+ JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
// _ print
JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
JCheckBoxMenuItem _antialias_print_cbmi;
else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
updateOptions( getOptions() );
}
-
else if ( o == _non_lined_up_cladograms_rbmi ) {
updateOptions( getOptions() );
showWhole();
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _color_labels_same_as_parent_branch.isSelected() );
//TODO FIXME ~~
- options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null ) && _show_default_node_shapes_cbmi.isSelected() );
- options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
-
+ options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
+ && _show_default_node_shapes_cbmi.isSelected() );
+ options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
+ && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
//TODO FIXME ~~
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
_radio_group_1.add( _uniform_cladograms_rbmi );
_radio_group_1.add( _non_lined_up_cladograms_rbmi );
- _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
_options_jmenu
.add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
import java.util.Set;
import javax.swing.ButtonGroup;
-import javax.swing.Icon;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JFileChooser;
import javax.swing.JMenu;
private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
private final static DefaultFilter defaultfilter = new DefaultFilter();
private static final long serialVersionUID = -799735726778865234L;
-
private final JFileChooser _values_filechooser;
private final JFileChooser _open_filechooser;
private final JFileChooser _msa_filechooser;
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
_radio_group_1.add( _uniform_cladograms_rbmi );
_radio_group_1.add( _non_lined_up_cladograms_rbmi );
-
//
_options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
-
-
- _options_jmenu.add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL) );
- _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL));
- _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ));
- _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ));
+ _options_jmenu
+ .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
//
-
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
_options_jmenu
.add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
private NodeFill _default_node_fill;
private short _default_node_shape_size;
private boolean _taxonomy_colorize_node_shapes;
- private boolean _show_default_node_shapes;
+ private boolean _show_default_node_shapes;
private Options() {
init();
}
final private void init() {
- _default_node_shape = NodeShape.NONE;
+ _default_node_shape = NodeShape.CIRCLE;
_default_node_fill = NodeFill.GRADIENT;
_default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
_taxonomy_colorize_node_shapes = false;
return new Options();
}
- boolean isShowDefaultNodeShapes() {
- return _show_default_node_shapes;
- }
- void setShowDefaultNodeShapes(boolean show_default_node_shapes) {
- _show_default_node_shapes = show_default_node_shapes;
+ boolean isShowDefaultNodeShapes() {
+ return _show_default_node_shapes;
}
+
+ void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
+ _show_default_node_shapes = show_default_node_shapes;
+ }
+
final static Options createInstance( final Configuration configuration ) {
final Options instance = createDefaultInstance();
if ( configuration != null ) {
if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
}
- instance.setTaxonomyColorizeNodeShapes( configuration
- .isTaxonomyColorizeNodeShapes() );
+ instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() );
}
return instance;
}
enum NodeShape {
- NONE, CIRCLE, RECTANGLE
+ CIRCLE, RECTANGLE
}
static enum OVERVIEW_PLACEMENT_TYPE {
}
}
- final void assignGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node, final Graphics g ) {
+ final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ return ( PhylogenyMethods.getBranchColorValue( node ) );
}
else {
- g.setColor( getTreeColorSet().getBranchColor() );
+ return ( getTreeColorSet().getBranchColor() );
}
}
final private void paintBranchRectangular( final Graphics2D g,
final float x1,
final float x2,
- float y1,
+ final float y1,
final float y2,
final PhylogenyNode node,
final boolean to_pdf,
g.draw( _cubic_curve );
}
else {
- float x2a = x2;
- float x1a = x1;
+ final float x2a = x2;
+ final float x1a = x1;
// draw the vertical line
- boolean draw_horizontal = true;
+ // boolean draw_horizontal = true;
float y2_r = 0;
if ( node.isFirstChildNode() || node.isLastChildNode()
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- boolean draw_vertical = true;
- final PhylogenyNode parent = node.getParent();
- if ( ( ( ( getOptions().getDefaultNodeShape() != Options.NodeShape.NONE ) && !to_pdf && !to_graphics_file ) || ( ( getControlPanel()
- .isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) )
- && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) )
- && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent
- .isDuplication() ) ) {
- if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
- && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- if ( Math.abs( y2 - y1 ) <= _half_box_size ) {
- draw_vertical = false;
- }
- else {
- if ( y1 < y2 ) {
- y1 += _half_box_size;
- }
- else {
- if ( !to_pdf ) {
- y1 -= _half_box_size + 1;
- }
- else {
- y1 -= _half_box_size;
- }
- }
- }
- }
- if ( ( x2 - x1 ) <= _half_box_size ) {
- draw_horizontal = false;
- }
- else if ( !draw_vertical ) {
- x1a += _half_box_size;
- }
- if ( ( ( x2 - x1a ) > _half_box_size )
- && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node
- .isDuplication() ) ) {
- x2a -= _half_box_size;
- }
+ //boolean draw_vertical = true;
+ // final PhylogenyNode parent = node.getParent();
+ //TODO fix below -- actually this might not be necessay anymore? test pdf, though!
+ // if ( ( ( ( getOptions().isShowDefaultNodeShapes() ) && !to_pdf && !to_graphics_file ) || ( ( getControlPanel()
+ // .isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) )
+ // && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) )
+ // && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent
+ // .isDuplication() ) ) {
+ // if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
+ // && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
+ // if ( Math.abs( y2 - y1 ) <= _half_box_size ) {
+ // draw_vertical = false;
+ // }
+ // else {
+ // if ( y1 < y2 ) {
+ // y1 += _half_box_size;
+ // }
+ // else {
+ // if ( !to_pdf ) {
+ // y1 -= _half_box_size + 1;
+ // }
+ // else {
+ // y1 -= _half_box_size;
+ // }
+ // }
+ // }
+ // }
+ // if ( ( x2 - x1 ) <= _half_box_size ) {
+ // draw_horizontal = false;
+ // }
+ // else if ( !draw_vertical ) {
+ // x1a += _half_box_size;
+ // }
+ // if ( ( ( x2 - x1a ) > _half_box_size )
+ // && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node
+ // .isDuplication() ) ) {
+ // x2a -= _half_box_size;
+ // }
+ // }
+ //if ( draw_vertical ) {
+ if ( !to_graphics_file
+ && !to_pdf
+ && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
+ .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
+ // Do nothing.
}
- if ( draw_vertical ) {
- if ( !to_graphics_file
- && !to_pdf
- && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
- .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
- // Do nothing.
- }
- else {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- float x2c = x1 + EURO_D;
- if ( x2c > x2a ) {
- x2c = x2a;
- }
- drawLine( x1, y1, x2c, y2, g );
+ else {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ float x2c = x1 + EURO_D;
+ if ( x2c > x2a ) {
+ x2c = x2a;
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- if ( y2 > y1 ) {
- y2_r = y2 - ROUNDED_D;
- if ( y2_r < y1 ) {
- y2_r = y1;
- }
- drawLine( x1, y1, x1, y2_r, g );
- }
- else {
- y2_r = y2 + ROUNDED_D;
- if ( y2_r > y1 ) {
- y2_r = y1;
- }
- drawLine( x1, y1, x1, y2_r, g );
+ drawLine( x1, y1, x2c, y2, g );
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ if ( y2 > y1 ) {
+ y2_r = y2 - ROUNDED_D;
+ if ( y2_r < y1 ) {
+ y2_r = y1;
}
+ drawLine( x1, y1, x1, y2_r, g );
}
else {
- drawLine( x1, y1, x1, y2, g );
+ y2_r = y2 + ROUNDED_D;
+ if ( y2_r > y1 ) {
+ y2_r = y1;
+ }
+ drawLine( x1, y1, x1, y2_r, g );
}
}
+ else {
+ drawLine( x1, y1, x1, y2, g );
+ }
}
+ //}
}
// draw the horizontal line
if ( !to_graphics_file && !to_pdf
return;
}
float x1_r = 0;
- if ( draw_horizontal ) {
- if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x1_r = x1a + ROUNDED_D;
- if ( x1_r < x2a ) {
- drawLine( x1_r, y2, x2a, y2, g );
- }
+ // if ( draw_horizontal ) {
+ if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x1_r = x1a + ROUNDED_D;
+ if ( x1_r < x2a ) {
+ drawLine( x1_r, y2, x2a, y2, g );
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- final float x1c = x1a + EURO_D;
- if ( x1c < x2a ) {
- drawLine( x1c, y2, x2a, y2, g );
- }
- }
- else {
- drawLine( x1a, y2, x2a, y2, g );
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ final float x1c = x1a + EURO_D;
+ if ( x1c < x2a ) {
+ drawLine( x1c, y2, x2a, y2, g );
}
}
else {
- final double w = PhylogenyMethods.getBranchWidthValue( node );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x1_r = x1a + ROUNDED_D;
- if ( x1_r < x2a ) {
- drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
- }
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- final float x1c = x1a + EURO_D;
- if ( x1c < x2a ) {
- drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
- }
+ drawLine( x1a, y2, x2a, y2, g );
+ }
+ }
+ else {
+ final double w = PhylogenyMethods.getBranchWidthValue( node );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x1_r = x1a + ROUNDED_D;
+ if ( x1_r < x2a ) {
+ drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
}
- else {
- drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ final float x1c = x1a + EURO_D;
+ if ( x1c < x2a ) {
+ drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
}
}
+ else {
+ drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+ }
}
+ //}
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
if ( x1_r > x2a ) {
x1_r = x2a;
paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
}
else {
+ Color outline_color = null;
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
+ outline_color = Color.BLACK;
}
else if ( getControlPanel().isEvents() && Util.isHasAssignedEvent( node ) ) {
final Event event = node.getNodeData().getEvent();
if ( event.isDuplication() ) {
- g.setColor( getTreeColorSet().getDuplicationBoxColor() );
+ outline_color = getTreeColorSet().getDuplicationBoxColor();
}
else if ( event.isSpeciation() ) {
- g.setColor( getTreeColorSet().getSpecBoxColor() );
+ outline_color = getTreeColorSet().getSpecBoxColor();
}
else if ( event.isSpeciationOrDuplication() ) {
- g.setColor( getTreeColorSet().getDuplicationOrSpeciationColor() );
+ outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
}
}
+ else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
+ outline_color = getTaxonomyBasedColor( node );
+ }
else {
- assignGraphicsForNodeBoxWithColorForParentBranch( node, g );
+ outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
}
- if ( ( ( getOptions().getDefaultNodeShape() != Options.NodeShape.NONE ) && !to_pdf && !to_graphics_file )
+ if ( ( ( getOptions().isShowDefaultNodeShapes() ) /*&& !to_pdf && !to_graphics_file*/)
|| ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
if ( to_pdf || to_graphics_file ) {
if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) {
_box_size,
_box_size,
g,
- Color.BLACK,
- g.getColor(),
- g.getColor() );
+ outline_color,
+ getBackground(),
+ outline_color );
}
}
else {
_box_size,
_box_size,
g,
- Color.BLACK,
- g.getColor(),
- g.getColor() );
+ outline_color,
+ getBackground(),
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ drawOvalGradient( x - _half_box_size,
+ y - _half_box_size,
+ _box_size,
+ _box_size,
+ g,
+ getBackground(),
+ getBackground(),
+ outline_color );
}
else if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
+ g.setColor( outline_color );
drawOvalFilled( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g );
}
}
_box_size,
_box_size,
g,
- Color.BLACK,
- g.getColor(),
- g.getColor() );
+ outline_color,
+ getBackground(),
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ drawRectGradient( x - _half_box_size,
+ y - _half_box_size,
+ _box_size,
+ _box_size,
+ g,
+ getBackground(),
+ getBackground(),
+ outline_color );
}
else if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
+ g.setColor( outline_color );
drawRectFilled( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g );
}
}
git://source.jalview.org / jalview.git / commitdiff