import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
-import org.forester.archaeopteryx.Options.NodeFill;
-import org.forester.archaeopteryx.Options.NodeShape;
import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.phylogeny.data.NodeVisualization;
+import org.forester.phylogeny.data.NodeVisualization.NodeFill;
+import org.forester.phylogeny.data.NodeVisualization.NodeShape;
import org.forester.util.ForesterUtil;
public final class Configuration {
- public enum UI {
- NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
- }
static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
private static final String WEB_LINK_KEY = "web_link";
private static final String DISPLAY_COLOR_KEY = "display_color";
private boolean _use_tabbed_display = false;
private boolean _hide_controls_and_menus = false;
private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
+ private File _mafft = null;
+ private File _clustalo = null;
+ private File _fastme = null;
+
private SortedMap<String, WebLink> _weblinks = null;
private SortedMap<String, Color> _display_colors = null;
private boolean _antialias_screen = true;
private boolean _abbreviate_scientific_names = false;
private boolean _color_labels_same_as_parent_branch = false;
private int _default_bootstrap_samples = -1;
- private NodeShape _default_node_shape = NodeShape.NONE;
+ private boolean _show_default_node_shapes = false;
+ 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_instead_of_labels = 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;
final static int color_according_to_species = 6;
final static int color_branches = 7;
final static int width_branches = 8;
- final static int show_domain_architectures = 9;
- final static int show_binary_characters = 10;
- final static int show_binary_character_counts = 11;
- final static int show_gene_names = 12;
- final static int show_sequence_acc = 13;
- final static int display_internal_data = 14;
- final static int dynamically_hide_data = 15;
- final static int show_taxonomy_scientific_names = 16;
- final static int show_taxonomy_common_names = 17;
- final static int color_according_to_annotation = 18;
- final static int show_property = 19;
+ final static int show_custom_node_shapes = 9;
+ final static int show_domain_architectures = 10;
+ final static int show_binary_characters = 11;
+ final static int show_binary_character_counts = 12;
+ final static int show_gene_names = 13;
+ final static int show_sequence_acc = 14;
+ final static int display_internal_data = 15;
+ final static int dynamically_hide_data = 16;
+ final static int show_taxonomy_scientific_names = 17;
+ final static int show_taxonomy_common_names = 18;
+ final static int color_according_to_annotation = 19;
final static int show_gene_symbols = 20;
final static int node_data_popup = 21;
final static int show_relation_confidence = 22;
final static int show_vector_data = 23;
final static int show_taxonomy_images = 24;
+ final static int show_properties = 25;
// ------------------
// Click-to options
// ------------------
final static int color_subtree = 5;
final static int open_seq_web = 6;
final static int open_tax_web = 7;
- final static int cut_subtree = 8;
- final static int copy_subtree = 9;
- final static int paste_subtree = 10;
- final static int delete_subtree_or_node = 11;
- final static int add_new_node = 12;
- final static int edit_node_data = 13;
- final static int blast = 14;
+ final static int blast = 8;
+ final static int cut_subtree = 9;
+ final static int copy_subtree = 10;
+ final static int paste_subtree = 11;
+ final static int delete_subtree_or_node = 12;
+ final static int add_new_node = 13;
+ final static int edit_node_data = 14;
+ final static int sort_descendents = 15;
// ---------------------------
// Display options for trees
// ---------------------------
String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
final static String display_options[][] = {
{ "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" }, { "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" },
+ { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" },
+ { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
+ { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
+ { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
+ { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
+ { "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" },
+ { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
{ "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
- { "Taxonomy Images", "display", "no" } };
+ { "Taxonomy Images", "display", "no" }, { "Properties", "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" },
- { "Open Sequence Web", "nodisplay" }, { "Open Taxonomy Web", "nodisplay" }, { "Cut Subtree", "display" },
- { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
- { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "display" } };
+ { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
+ { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
+ { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
+ { "Sort Descendants", "display" } };
// This option is selected in the dropdown
int default_clickto = Configuration.display_node_data;
// --------------
private static String DEFAULT_FONT_FAMILY = "";
static {
for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
- if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
+ if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
DEFAULT_FONT_FAMILY = font_name;
break;
}
}
}
- Configuration( final String cf, final boolean is_url, final boolean is_applet ) {
+ public Configuration() {
+ this( null, false, false, false );
+ }
+
+ public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) {
if ( ForesterUtil.isEmpty( cf ) ) {
config_filename = default_config_filename;
}
bf.close();
}
catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
- + config_filename + "]: " + e );
+ if ( verbose ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
+ + config_filename + "]: " + e );
+ }
}
}
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
- + config_filename + "]" );
+ if ( verbose ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
+ + config_filename + "]" );
+ }
}
}
}
}
}
- Color getGuiBackgroundColor() {
- return _gui_background_color;
- }
-
- Color getGuiCheckboxTextColor() {
- return _gui_checkbox_text_color;
- }
-
- Color getGuiCheckboxAndButtonActiveColor() {
- return _gui_checkbox_and_button_active_color;
- }
-
- Color getGuiButtonTextColor() {
- return _gui_button_text_color;
- }
-
- Color getGuiButtonBackgroundColor() {
- return _gui_button_background_color;
- }
-
- Color getGuiMenuBackgroundColor() {
- return _gui_menu_background_color;
- }
-
- Color getGuiMenuTextColor() {
- return _gui_menu_text_color;
- }
-
- Color getGuiButtonBorderColor() {
- return _gui_button_border_color;
- }
-
boolean displaySequenceRelations() {
return _display_sequence_relations;
}
else if ( name.equals( "swap" ) ) {
index = Configuration.swap;
}
+ else if ( name.equals( "sort_descendants" ) ) {
+ index = Configuration.sort_descendents;
+ }
else if ( name.equals( "display_sequences" ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
else if ( name.equals( "open_tax_web" ) ) {
index = Configuration.open_tax_web;
}
+ else if ( name.equals( "blast" ) ) {
+ index = Configuration.blast;
+ }
else if ( name.equals( "cut_subtree" ) ) {
index = Configuration.cut_subtree;
}
return clickto_options[ which ][ 0 ];
}
+ public int getDefaultBootstrapSamples() {
+ return _default_bootstrap_samples;
+ }
+
int getDefaultDisplayClicktoOption() {
return default_clickto;
}
+ public NodeFill getDefaultNodeFill() {
+ return _default_node_fill;
+ }
+
+ public NodeShape getDefaultNodeShape() {
+ return _default_node_shape;
+ }
+
+ public short getDefaultNodeShapeSize() {
+ return _default_node_shape_size;
+ }
+
SortedMap<String, Color> getDisplayColors() {
return _display_colors;
}
return _domain_colors;
}
+ public Color getDomainStructureBaseColor() {
+ return _domain_structure_base_color;
+ }
+
+ public Color getDomainStructureFontColor() {
+ return _domain_structure_font_color;
+ }
+
int getGraphicsExportX() {
return _graphics_export_x;
}
return _graphics_export_y;
}
- public int getDefaultBootstrapSamples() {
- return _default_bootstrap_samples;
+ Color getGuiBackgroundColor() {
+ return _gui_background_color;
+ }
+
+ Color getGuiButtonBackgroundColor() {
+ return _gui_button_background_color;
+ }
+
+ Color getGuiButtonBorderColor() {
+ return _gui_button_border_color;
+ }
+
+ Color getGuiButtonTextColor() {
+ return _gui_button_text_color;
+ }
+
+ Color getGuiCheckboxAndButtonActiveColor() {
+ return _gui_checkbox_and_button_active_color;
+ }
+
+ Color getGuiCheckboxTextColor() {
+ return _gui_checkbox_text_color;
+ }
+
+ Color getGuiMenuBackgroundColor() {
+ return _gui_menu_background_color;
+ }
+
+ Color getGuiMenuTextColor() {
+ return _gui_menu_text_color;
}
double getMinConfidenceValue() {
return _weblinks;
}
+ public boolean isAbbreviateScientificTaxonNames() {
+ return _abbreviate_scientific_names;
+ }
+
boolean isAntialiasScreen() {
return _antialias_screen;
}
return _background_color_gradient;
}
+ public boolean isColorLabelsSameAsParentBranch() {
+ return _color_labels_same_as_parent_branch;
+ }
+
/**
* Convenience method.
*
return _show_branch_length_values;
}
+ public boolean isShowDefaultNodeShapes() {
+ return _show_default_node_shapes;
+ }
+
+ public boolean isShowDomainLabels() {
+ return _show_domain_labels;
+ }
+
boolean isShowOverview() {
return _show_overview;
}
return _show_scale;
}
+ public boolean isTaxonomyColorizeNodeShapes() {
+ return _taxonomy_colorize_node_shapes;
+ }
+
final boolean isUseNativeUI() {
- if ( ( _ui == UI.UNKNOWN ) && Util.isMac() && Util.isJava15() ) {
+ if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
_ui = UI.NATIVE;
}
return _ui == UI.NATIVE;
final String[] fonts = font_str.split( ",+" );
for( String font : fonts ) {
font = font.replace( '_', ' ' ).trim();
- if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
+ if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
setBaseFontFamilyName( font );
break;
}
}
}
+ public void putDisplayColors( final String key, final Color color ) {
+ getDisplayColors().put( key, color );
+ }
+
/**
* read each line of config file, process non-comment lines
* @throws IOException
} while ( line != null );
}
+ public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
+ _abbreviate_scientific_names = abbreviate_scientific_names;
+ }
+
private void setAntialiasScreen( final boolean antialias_screen ) {
_antialias_screen = antialias_screen;
}
_background_color_gradient = background_color_gradient;
}
- private void setBaseFontFamilyName( final String base_font_family_name ) {
+ public void setBaseFontFamilyName( final String base_font_family_name ) {
_base_font_family_name = base_font_family_name;
}
- private void setBaseFontSize( final int base_font_size ) {
+ public void setBaseFontSize( final int base_font_size ) {
_base_font_size = base_font_size;
}
- private void setShowDomainLabels( final boolean show_domain_labels ) {
- _show_domain_labels = show_domain_labels;
+ private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
+ _cladogram_type = cladogram_type;
}
- private void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
- _abbreviate_scientific_names = abbreviate_scientific_names;
+ public void setColorizeBranches( final boolean b ) {
+ display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
}
- private void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
+ public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
_color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
}
- private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
- _cladogram_type = cladogram_type;
+ private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
+ _default_bootstrap_samples = default_bootstrap_samples;
+ }
+
+ public void setDefaultNodeFill( final NodeFill default_node_fill ) {
+ _default_node_fill = default_node_fill;
+ }
+
+ public void setDefaultNodeShape( final NodeShape default_node_shape ) {
+ _default_node_shape = default_node_shape;
+ }
+
+ public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
+ _default_node_shape_size = default_node_shape_size;
+ }
+
+ public void setDisplayAsPhylogram( final boolean b ) {
+ display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
}
- void setDisplayColors( final SortedMap<String, Color> display_colors ) {
+ public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
_display_colors = display_colors;
}
- private void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
+ public void setDisplayConfidenceValues( final boolean b ) {
+ display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayInternalData( final boolean b ) {
+ display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayNodeNames( final boolean b ) {
+ display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceAcc( final boolean b ) {
+ display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceNames( final boolean b ) {
+ display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
_display_sequence_relations = display_sequence_relations;
}
+ public void setDisplaySequenceSymbols( final boolean b ) {
+ display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyCode( final boolean b ) {
+ display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyCommonNames( final boolean b ) {
+ display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyImages( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyScientificNames( final boolean b ) {
+ display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDynamicallyHideData( final boolean b ) {
+ display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
+ }
+
private void setEditable( final boolean editable ) {
_editable = editable;
}
- private void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
+ public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
_nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
}
_graphics_export_y = graphics_export_y;
}
- private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
- _default_bootstrap_samples = default_bootstrap_samples;
- }
-
private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
_internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
}
_ui = UI.UNKNOWN;
}
}
+ else if ( key.equals( "path_to_mafft" ) ) {
+ setPathToMafft( new File( (String) st.nextElement() ) );
+ }
+ else if ( key.equals( "path_to_clustalo" ) ) {
+ setPathToClustalOmega( new File( (String) st.nextElement() ) );
+ }
+ else if ( key.equals( "path_to_fastme" ) ) {
+ setPathToFastME( new File( (String) st.nextElement() ) );
+ }
+ else if ( key.equals( "path_to_mafft" ) ) {
+ setPathToMafft( new File( (String) st.nextElement() ) );
+ }
else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
}
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_size" ) ) {
final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
setDefaultNodeShapeSize( i );
}
else if ( key.equals( "default_node_fill" ) ) {
final String fill_str = ( ( String ) st.nextElement() ).trim();
- if ( fill_str.equalsIgnoreCase( Options.NodeFill.NONE.toString() ) ) {
+ if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) {
setDefaultNodeFill( NodeFill.NONE );
}
- else if ( fill_str.equalsIgnoreCase( Options.NodeFill.GRADIENT.toString() ) ) {
+ else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
setDefaultNodeFill( NodeFill.GRADIENT );
}
- else if ( fill_str.equalsIgnoreCase( Options.NodeFill.SOLID.toString() ) ) {
+ else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
setDefaultNodeFill( NodeFill.SOLID );
}
else {
}
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( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
setDefaultNodeShape( NodeShape.CIRCLE );
}
- else if ( shape_str.equalsIgnoreCase( Options.NodeShape.RECTANGLE.toString() ) ) {
+ else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
setDefaultNodeShape( NodeShape.RECTANGLE );
}
else {
}
}
else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
- setTaxonomyColorizeNodeShapesInsteadOfLabels( parseBoolean( ( String ) st.nextElement() ) );
+ setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
// yet retrieved!
else if ( key.equals( "color_according_to_annotation" ) ) {
key_index = Configuration.color_according_to_annotation;
}
- else if ( key.equals( "show_property" ) ) {
- key_index = Configuration.show_property;
- }
else if ( key.equals( "show_vector_data" ) ) {
key_index = Configuration.show_vector_data;
}
+ else if ( key.equals( "show_properties" ) ) {
+ key_index = Configuration.show_properties;
+ }
else if ( key.equals( "show_relation_confidence" ) ) {
key_index = Configuration.show_relation_confidence;
}
+ else if ( key.equals( "show_custom_node_shapes" ) ) {
+ key_index = Configuration.show_custom_node_shapes;
+ }
// If we've found the key, set the values
if ( key_index >= 0 ) {
display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
"configuration key [function_color] is deprecated" );
}
else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
- getDisplayColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
+ putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( WEB_LINK_KEY ) ) {
if ( st.countTokens() == 3 ) {
}
}
- private void setMinConfidenceValue( final double min_confidence_value ) {
+ public void setMinConfidenceValue( final double min_confidence_value ) {
_min_confidence_value = min_confidence_value;
}
- void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
+ public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
_node_label_direction = node_label_direction;
}
- private void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) {
+ public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) {
this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values;
}
- private void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) {
+ public void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) {
this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values;
}
_ov_placement = ov_placement;
}
- void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
+ public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
_phylogeny_graphics_type = phylogeny_graphics_type;
}
- private void setPrintLineWidth( final float print_line_width ) {
+ public void setPrintLineWidth( final float print_line_width ) {
_print_line_width = print_line_width;
}
- private void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
+ public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
_nh_parsing_replace_underscores = nh_parsing_replace_underscores;
}
- private void setShowBranchLengthValues( final boolean show_branch_length_values ) {
+ public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
_show_branch_length_values = show_branch_length_values;
}
- private void setShowOverview( final boolean show_overview ) {
- _show_overview = show_overview;
+ public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
+ _show_default_node_shapes = show_default_node_shapes;
}
- private void setShowScale( final boolean show_scale ) {
- _show_scale = show_scale;
+ public void setShowDomainLabels( final boolean show_domain_labels ) {
+ _show_domain_labels = show_domain_labels;
}
- private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
- _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
+ private void setShowOverview( final boolean show_overview ) {
+ _show_overview = show_overview;
}
- void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
- _weblinks = weblinks;
+ public void setShowScale( final boolean show_scale ) {
+ _show_scale = show_scale;
}
- static String getDefaultFontFamilyName() {
- return DEFAULT_FONT_FAMILY;
+ public void setTaxonomyColorize( final boolean b ) {
+ display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
}
- static enum TRIPLET {
- TRUE, FALSE, UNKNOWN
+ public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
+ _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
}
- public Color getDomainStructureFontColor() {
- return _domain_structure_font_color;
+ public void setUseBranchesWidths( final boolean b ) {
+ display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
}
- public Color getDomainStructureBaseColor() {
- return _domain_structure_base_color;
+ private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
+ _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
}
- public boolean isColorLabelsSameAsParentBranch() {
- return _color_labels_same_as_parent_branch;
+ void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
+ _weblinks = weblinks;
}
- public boolean isShowDomainLabels() {
- return _show_domain_labels;
+ static String getDefaultFontFamilyName() {
+ return DEFAULT_FONT_FAMILY;
}
- public boolean isAbbreviateScientificTaxonNames() {
- return _abbreviate_scientific_names;
+
+ public File getPathToMafft() {
+ return _mafft;
}
- public NodeShape getDefaultNodeShape() {
- return _default_node_shape;
- }
+
- private void setDefaultNodeShape( final NodeShape default_node_shape ) {
- _default_node_shape = default_node_shape;
+ public File getPathToClustalOmega() {
+ return _clustalo;
}
- private void setDefaultNodeFill( final NodeFill default_node_fill ) {
- _default_node_fill = default_node_fill;
+
+ public File getPathToFastME() {
+ return _fastme;
}
-
- public NodeFill getDefaultNodeFill() {
- return _default_node_fill;
+
+
+ public void setPathToMafft( final File mafft ) {
+ _mafft = mafft;
}
- private void setDefaultNodeShapeSize( final short default_node_shape_size ) {
- _default_node_shape_size = default_node_shape_size;
+
+
+ public void setPathToClustalOmega( final File clustalo ) {
+ _clustalo = clustalo ;
}
- public short getDefaultNodeShapeSize() {
- return _default_node_shape_size;
+
+ public void setPathToFastME( final File fastme ) {
+ _fastme = fastme;
}
- private void setTaxonomyColorizeNodeShapesInsteadOfLabels( final boolean taxonomy_colorize_node_shapes_instead_of_labels ) {
- _taxonomy_colorize_node_shapes_instead_of_labels = taxonomy_colorize_node_shapes_instead_of_labels;
+ static enum TRIPLET {
+ TRUE, FALSE, UNKNOWN
}
- public boolean isTaxonomyColorizeNodeShapesInsteadOfLabels() {
- return _taxonomy_colorize_node_shapes_instead_of_labels;
+ public enum UI {
+ NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
}
}
git://source.jalview.org / jalview.git / blobdiff