// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
-import java.net.MalformedURLException;
import java.net.URL;
import java.util.Arrays;
import java.util.Hashtable;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.phylogeny.data.NodeData.NODE_DATA;
+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 {
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 static final int DEPRECATED = -2;
- private TRIPLET _native_ui = TRIPLET.FALSE;
+ private UI _ui = UI.UNKNOWN;
private boolean _use_tabbed_display = false;
private boolean _hide_controls_and_menus = false;
private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
- private SortedMap<String, WebLink> _weblinks = null;
private SortedMap<String, Color> _display_colors = null;
private boolean _antialias_screen = true;
private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
private String _base_font_family_name = "";
private int _base_font_size = -1;
+ private int _min_base_font_size = 2;
+ private int _max_base_font_size = 20;
private int _graphics_export_x = -1;
private int _graphics_export_y = -1;
private short _ov_max_width = 80;
private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
private boolean _editable = true;
private boolean _nh_parsing_replace_underscores = false;
- private boolean _nh_parsing_extract_pfam_taxonomy_codes = false;
+ private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT;
private boolean _internal_number_are_confidence_for_nh_parsing = false;
private boolean _display_sequence_relations = false;
private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
private boolean _show_domain_labels = true;
private boolean _abbreviate_scientific_names = false;
private boolean _color_labels_same_as_parent_branch = false;
+ private boolean _show_default_node_shapes_internal = false;
+ private boolean _show_default_node_shapes_external = false;
+ private NodeShape _default_node_shape = NodeShape.RECTANGLE;
+ private NodeFill _default_node_fill = NodeFill.SOLID;
+ private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
+ private boolean _taxonomy_colorize_node_shapes = false;
private int _default_bootstrap_samples = -1;
+ private File _path_to_local_mafft = null;
+ private File _path_to_local_fastme = null;
+ private File _path_to_local_raxml = null;
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;
+ final static int get_ext_desc_data = 16;
+ final static int select_nodes = 17;
// ---------------------------
// 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" },
+ { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
+ { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" },
+ { "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", "no" }, { "Prot/Gene Acc", "display", "no" },
+ { "Seq Name", "display", "yes" }, { "Seq 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" } };
+ { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
+ { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
+ { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
+ { "Properties", "nodisplay", "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" }, { "Return", "display" }, { "Select Node(s)", "display" } };
// This option is selected in the dropdown
int default_clickto = Configuration.display_node_data;
// --------------
private static Hashtable<String, Color> _annotation_colors;
boolean verbose = Constants.VERBOSE_DEFAULT;
private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
- private TRIPLET _use_native_ui;
private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
+ private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
+ private String _label_for_get_ext_descendents_data = "";
+ private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
+ private int _frame_x_size;
+ private int _frame_y_size;
+ private boolean _midpoint_root = false;
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;
}
else {
config_filename = cf;
}
- setWebLinks( new TreeMap<String, WebLink>() );
setDisplayColors( new TreeMap<String, Color>() );
config_filename = config_filename.trim();
URL u = null;
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 + "]" );
+ }
}
}
}
- private void createWebLink( final String url_str, final String desc, final String source_identifier ) {
- WebLink weblink = null;
- boolean ex = false;
- try {
- weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() );
- }
- catch ( final MalformedURLException e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" );
- ex = true;
- }
- if ( !ex && ( weblink != null ) ) {
- getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink );
- }
+ public String getBaseFontFamilyName() {
+ return _base_font_family_name;
}
- Color getGuiBackgroundColor() {
- return _gui_background_color;
+ public int getDefaultBootstrapSamples() {
+ return _default_bootstrap_samples;
}
- Color getGuiCheckboxTextColor() {
- return _gui_checkbox_text_color;
+ public NodeFill getDefaultNodeFill() {
+ return _default_node_fill;
}
- Color getGuiCheckboxAndButtonActiveColor() {
- return _gui_checkbox_and_button_active_color;
+ public NodeShape getDefaultNodeShape() {
+ return _default_node_shape;
}
- Color getGuiButtonTextColor() {
- return _gui_button_text_color;
+ public short getDefaultNodeShapeSize() {
+ return _default_node_shape_size;
}
- Color getGuiButtonBackgroundColor() {
- return _gui_button_background_color;
+ public Color getDomainStructureBaseColor() {
+ return _domain_structure_base_color;
}
- Color getGuiMenuBackgroundColor() {
- return _gui_menu_background_color;
+ public Color getDomainStructureFontColor() {
+ return _domain_structure_font_color;
}
- Color getGuiMenuTextColor() {
- return _gui_menu_text_color;
+ public NODE_DATA getExtDescNodeDataToReturn() {
+ return _ext_desc_data_to_return;
}
- Color getGuiButtonBorderColor() {
- return _gui_button_border_color;
+ public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
+ return _ext_node_data_return_on;
+ }
+
+ public int getFrameXSize() {
+ return _frame_x_size;
+ }
+
+ public int getFrameYSize() {
+ return _frame_y_size;
+ }
+
+ public String getLabelForGetExtDescendentsData() {
+ return _label_for_get_ext_descendents_data;
+ }
+
+ public File getPathToLocalFastme() {
+ return _path_to_local_fastme;
+ }
+
+ public File getpathToLocalMafft() {
+ return _path_to_local_mafft;
+ }
+
+ public File getPathToLocalRaxml() {
+ return _path_to_local_raxml;
+ }
+
+ public boolean isAbbreviateScientificTaxonNames() {
+ return _abbreviate_scientific_names;
+ }
+
+ public boolean isBackgroundColorGradient() {
+ return _background_color_gradient;
+ }
+
+ public boolean isColorLabelsSameAsParentBranch() {
+ return _color_labels_same_as_parent_branch;
+ }
+
+ public boolean isShowDefaultNodeShapesExternal() {
+ return _show_default_node_shapes_external;
+ }
+
+ public boolean isShowDefaultNodeShapesInternal() {
+ return _show_default_node_shapes_internal;
+ }
+
+ public boolean isShowDomainLabels() {
+ return _show_domain_labels;
+ }
+
+ public boolean isTaxonomyColorizeNodeShapes() {
+ return _taxonomy_colorize_node_shapes;
+ }
+
+ public void putDisplayColors( final String key, final Color color ) {
+ getDisplayColors().put( key, color );
+ }
+
+ public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
+ _abbreviate_scientific_names = abbreviate_scientific_names;
+ }
+
+ public void setBackgroundColorGradient( final boolean background_color_gradient ) {
+ _background_color_gradient = background_color_gradient;
+ }
+
+ public void setBaseFontFamilyName( final String base_font_family_name ) {
+ _base_font_family_name = base_font_family_name;
+ }
+
+ public void setBaseFontSize( final int base_font_size ) {
+ _base_font_size = base_font_size;
+ }
+
+ private void setMaxBaseFontSize( final int max_base_font_size ) {
+ _max_base_font_size = max_base_font_size;
+ }
+
+ private void setMinBaseFontSize( final int min_base_font_size ) {
+ _min_base_font_size = min_base_font_size;
+ }
+
+ public void setColorizeBranches( final boolean b ) {
+ display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
+ _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
+ }
+
+ 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";
+ }
+
+ public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
+ _display_colors = display_colors;
+ }
+
+ 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";
+ }
+
+ public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;
+ }
+
+ public void setFrameXSize( final int frame_x_size ) {
+ _frame_x_size = frame_x_size;
+ }
+
+ public void setFrameYSize( final int frame_y_size ) {
+ _frame_y_size = frame_y_size;
+ }
+
+ public void setMinConfidenceValue( final double min_confidence_value ) {
+ _min_confidence_value = min_confidence_value;
+ }
+
+ public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
+ _node_label_direction = node_label_direction;
+ }
+
+ public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
+ _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
+ }
+
+ public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
+ _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
+ }
+
+ public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
+ _phylogeny_graphics_type = phylogeny_graphics_type;
+ }
+
+ public void setPrintLineWidth( final float print_line_width ) {
+ _print_line_width = print_line_width;
+ }
+
+ public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
+ _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
+ }
+
+ public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
+ _show_branch_length_values = show_branch_length_values;
+ }
+
+ public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+ _show_default_node_shapes_external = show_default_node_shapes_external;
+ }
+
+ public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+ _show_default_node_shapes_internal = show_default_node_shapes_internal;
+ }
+
+ public void setShowDomainLabels( final boolean show_domain_labels ) {
+ _show_domain_labels = show_domain_labels;
+ }
+
+ public void setShowScale( final boolean show_scale ) {
+ _show_scale = show_scale;
+ }
+
+ public void setTaxonomyColorize( final boolean b ) {
+ display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
+ _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
+ }
+
+ public void setUseBranchesWidths( final boolean b ) {
+ display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
}
boolean displaySequenceRelations() {
return _annotation_colors;
}
- public String getBaseFontFamilyName() {
- return _base_font_family_name;
- }
-
int getBaseFontSize() {
return _base_font_size;
}
- CLADOGRAM_TYPE getCladogramType() {
- return _cladogram_type;
+ int getMinBaseFontSize() {
+ return _min_base_font_size;
}
- private int getClickToIndex( final String name ) {
- int index = -1;
- if ( name.equals( "edit_info" ) ) {
- index = Configuration.display_node_data;
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [edit_info] is deprecated, use [display node data] instead" );
- }
- else if ( name.equals( "display_node_data" ) ) {
- index = Configuration.display_node_data;
- }
- else if ( name.equals( "collapse_uncollapse" ) ) {
- index = Configuration.collapse_uncollapse;
- }
- else if ( name.equals( "reroot" ) ) {
- index = Configuration.reroot;
- }
- else if ( name.equals( "subtree" ) ) {
- index = Configuration.subtree;
- }
- else if ( name.equals( "swap" ) ) {
- index = Configuration.swap;
- }
- else if ( name.equals( "display_sequences" ) ) {
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "open_seq_web" ) ) {
- index = Configuration.open_seq_web;
- }
- else if ( name.equals( "open_tax_web" ) ) {
- index = Configuration.open_tax_web;
- }
- else if ( name.equals( "cut_subtree" ) ) {
- index = Configuration.cut_subtree;
- }
- else if ( name.equals( "copy_subtree" ) ) {
- index = Configuration.copy_subtree;
- }
- else if ( name.equals( "paste_subtree" ) ) {
- index = Configuration.paste_subtree;
- }
- else if ( name.equals( "delete" ) ) {
- index = Configuration.delete_subtree_or_node;
- }
- else if ( name.equals( "add_new_node" ) ) {
- index = Configuration.add_new_node;
- }
- else if ( name.equals( "edit_node_data" ) ) {
- index = Configuration.edit_node_data;
- }
- else if ( name.equals( "display_node_popup" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [display_node_popup] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "custom_option" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "color_subtree" ) ) {
- index = Configuration.color_subtree;
- }
- else if ( name.equals( "go_to_swiss_prot" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
- return DEPRECATED;
- }
- return index;
+ int getMaxBaseFontSize() {
+ return _max_base_font_size;
+ }
+
+ CLADOGRAM_TYPE getCladogramType() {
+ return _cladogram_type;
}
int getClickToOptionsCount() {
return _domain_colors;
}
- int getGraphicsExportX() {
- return _graphics_export_x;
+ int getGraphicsExportX() {
+ return _graphics_export_x;
+ }
+
+ int getGraphicsExportY() {
+ return _graphics_export_y;
+ }
+
+ 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;
}
- int getGraphicsExportY() {
- return _graphics_export_y;
+ Color getGuiMenuBackgroundColor() {
+ return _gui_menu_background_color;
}
- int getDefaultBootstrapSamples() {
- return _default_bootstrap_samples;
+ Color getGuiMenuTextColor() {
+ return _gui_menu_text_color;
}
double getMinConfidenceValue() {
return _species_colors;
}
- TreeColorSet getTreeColorSet() {
- return null;
- }
-
- TreeFontSet getTreeFontSet() {
- return null;
- }
-
- WebLink getWebLink( final String source ) {
- return getWebLinks().get( source );
- }
-
- Map<String, WebLink> getWebLinks() {
- return _weblinks;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
boolean isAntialiasScreen() {
+ if ( AptxUtil.isMac() ) {
+ // Apple Macintosh graphics are slow, turn off anti-alias.
+ return false;
+ }
return _antialias_screen;
}
- public boolean isBackgroundColorGradient() {
- return _background_color_gradient;
- }
-
/**
* Convenience method.
*
return _editable;
}
- boolean isExtractPfamTaxonomyCodesInNhParsing() {
- return _nh_parsing_extract_pfam_taxonomy_codes;
- }
-
- boolean isHasWebLink( final String source ) {
- return getWebLinks().containsKey( source );
- }
-
/**
* Only used by ArchaeoptryxE.
*
}
final boolean isUseNativeUI() {
- if ( ( _use_native_ui == null ) || ( _use_native_ui == TRIPLET.UNKNOWN ) ) {
- if ( ( _native_ui == TRIPLET.UNKNOWN ) && Util.isMac() && Util.isJava15() ) {
- _use_native_ui = TRIPLET.TRUE;
- }
- else if ( _native_ui == TRIPLET.TRUE ) {
- _use_native_ui = TRIPLET.TRUE;
- }
- else {
- _use_native_ui = TRIPLET.FALSE;
- }
+ if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) {
+ _ui = UI.NATIVE;
}
- return _use_native_ui == TRIPLET.TRUE;
+ return _ui == UI.NATIVE;
}
/**
return _validate_against_phyloxml_xsd_schema;
}
+ final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
+ }
+
+ private int getClickToIndex( final String name ) {
+ int index = -1;
+ if ( name.equals( "edit_info" ) ) {
+ index = Configuration.display_node_data;
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [edit_info] is deprecated, use [display node data] instead" );
+ }
+ else if ( name.equals( "display_node_data" ) ) {
+ index = Configuration.display_node_data;
+ }
+ else if ( name.equals( "collapse_uncollapse" ) ) {
+ index = Configuration.collapse_uncollapse;
+ }
+ else if ( name.equals( "reroot" ) ) {
+ index = Configuration.reroot;
+ }
+ else if ( name.equals( "subtree" ) ) {
+ index = Configuration.subtree;
+ }
+ else if ( name.equals( "swap" ) ) {
+ index = Configuration.swap;
+ }
+ else if ( name.equals( "sort_descendants" ) ) {
+ index = Configuration.sort_descendents;
+ }
+ else if ( name.equals( "get_ext_descendents_data" ) ) {
+ index = Configuration.get_ext_desc_data;
+ }
+ else if ( name.equals( "display_sequences" ) ) {
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "open_seq_web" ) ) {
+ index = Configuration.open_seq_web;
+ }
+ 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;
+ }
+ else if ( name.equals( "copy_subtree" ) ) {
+ index = Configuration.copy_subtree;
+ }
+ else if ( name.equals( "paste_subtree" ) ) {
+ index = Configuration.paste_subtree;
+ }
+ else if ( name.equals( "delete" ) ) {
+ index = Configuration.delete_subtree_or_node;
+ }
+ else if ( name.equals( "add_new_node" ) ) {
+ index = Configuration.add_new_node;
+ }
+ else if ( name.equals( "edit_node_data" ) ) {
+ index = Configuration.edit_node_data;
+ }
+ else if ( name.equals( "select_nodes" ) ) {
+ index = Configuration.select_nodes;
+ }
+ else if ( name.equals( "display_node_popup" ) ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME,
+ "configuration key [display_node_popup] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "custom_option" ) ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "color_subtree" ) ) {
+ index = Configuration.color_subtree;
+ }
+ return index;
+ }
+
private boolean parseBoolean( final String str ) {
final String my_str = str.trim().toLowerCase();
if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
private double parseDouble( final String str ) {
double d = 0.0;
try {
- d = Double.parseDouble( str );
+ d = Double.parseDouble( str.trim() );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
private float parseFloat( final String str ) {
float f = 0.0f;
try {
- f = Float.parseFloat( str );
+ f = Float.parseFloat( str.trim() );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
private int parseInt( final String str ) {
int i = -1;
try {
- i = Integer.parseInt( str );
+ i = Integer.parseInt( str.trim() );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
private short parseShort( final String str ) {
short i = -1;
try {
- i = Short.parseShort( str );
+ i = Short.parseShort( str.trim() );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
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;
}
_antialias_screen = antialias_screen;
}
- public void setBackgroundColorGradient( final boolean background_color_gradient ) {
- _background_color_gradient = background_color_gradient;
- }
-
- private void setBaseFontFamilyName( final String base_font_family_name ) {
- _base_font_family_name = base_font_family_name;
- }
-
- private 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 setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
- _abbreviate_scientific_names = abbreviate_scientific_names;
- }
-
- private 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;
}
- void setDisplayColors( final SortedMap<String, Color> display_colors ) {
- _display_colors = display_colors;
- }
-
- private void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
- _display_sequence_relations = display_sequence_relations;
+ private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
+ _default_bootstrap_samples = default_bootstrap_samples;
}
private void setEditable( final boolean editable ) {
_editable = editable;
}
- private void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
- _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
+ private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
+ _ext_node_data_return_on = ext_node_data_return_on;
}
private void setGraphicsExportX( final int graphics_export_x ) {
_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;
}
* Set a key-value(s) tuple
*/
private void setKeyValue( final StringTokenizer st ) {
- String key = ( String ) st.nextElement();
- key = key.replace( ':', ' ' );
- key = key.trim();
- key = key.toLowerCase();
+ final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
+ if ( !st.hasMoreElements() ) {
+ return;
+ }
// Handle single value settings first:
if ( key.equals( "default_click_to" ) ) {
final String clickto_name = ( String ) st.nextElement();
else if ( key.equals( "native_ui" ) ) {
final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
- _native_ui = TRIPLET.TRUE;
+ _ui = UI.NATIVE;
}
else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
- _native_ui = TRIPLET.FALSE;
+ _ui = UI.CROSSPLATFORM;
}
else if ( my_str.equals( "?" ) ) {
- _native_ui = TRIPLET.UNKNOWN;
+ _ui = UI.UNKNOWN;
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
+ "]" );
- _native_ui = TRIPLET.FALSE;
+ _ui = UI.UNKNOWN;
}
}
else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
else if ( key.equals( "font_size" ) ) {
final String size_str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( size_str );
- setBaseFontSize( i );
+ if ( i > 0 ) {
+ setBaseFontSize( i );
+ }
+ }
+ else if ( key.equals( "font_size_min" ) ) {
+ final String size_str = ( ( String ) st.nextElement() ).trim();
+ final int i = parseInt( size_str );
+ if ( i > 0 ) {
+ setMinBaseFontSize( i );
+ }
+ }
+ else if ( key.equals( "font_size_max" ) ) {
+ final String size_str = ( ( String ) st.nextElement() ).trim();
+ final int i = parseInt( size_str );
+ if ( i > 1 ) {
+ setMaxBaseFontSize( i );
+ }
}
else if ( key.equals( "graphics_export_x" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( str );
- setGraphicsExportX( i );
+ if ( i > 0 ) {
+ setGraphicsExportX( i );
+ }
}
else if ( key.equals( "graphics_export_y" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( str );
- setGraphicsExportY( i );
+ if ( i > 0 ) {
+ setGraphicsExportY( i );
+ }
}
else if ( key.equals( "pdf_export_line_width" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
"value for [pdf_export_line_width] cannot be zero or negative" );
}
}
+ else if ( key.equals( "window_initial_size_x" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ final int i = parseInt( str );
+ if ( i > 0 ) {
+ setFrameXSize( i );
+ }
+ }
+ else if ( key.equals( "window_initial_size_y" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ final int i = parseInt( str );
+ if ( i > 0 ) {
+ setFrameYSize( i );
+ }
+ }
else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( str );
"value for [default_number_of_bootstrap_resamples] cannot be negative" );
}
}
+ else if ( key.equals( "mafft_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalMafft( new File( str ) );
+ }
+ }
+ else if ( key.equals( "fastme_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalFastme( new File( str ) );
+ }
+ }
+ else if ( key.equals( "raxml_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalRaxml( new File( str ) );
+ }
+ }
else if ( key.equals( "show_scale" ) ) {
setShowScale( parseBoolean( ( String ) st.nextElement() ) );
}
_use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
}
else if ( key.equals( "overview_width" ) ) {
- final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
+ final short i = parseShort( ( ( String ) st.nextElement() ) );
setOvMaxWidth( i );
}
else if ( key.equals( "overview_height" ) ) {
- final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
+ final short i = parseShort( ( ( String ) st.nextElement() ) );
setOvMaxHeight( i );
}
else if ( key.equals( "overview_placement_type" ) ) {
}
else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
final boolean r = parseBoolean( ( String ) st.nextElement() );
- if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) {
+ if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"attempt to extract taxonomies and replace underscores at the same time" );
setReplaceUnderscoresInNhParsing( r );
}
}
- else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
- final boolean e = parseBoolean( ( String ) st.nextElement() );
- if ( e && isReplaceUnderscoresInNhParsing() ) {
+ else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
+ final String s = ( String ) st.nextElement();
+ if ( s.equalsIgnoreCase( "no" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
+ }
+ else if ( s.equalsIgnoreCase( "yes" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ }
+ else if ( s.equalsIgnoreCase( "pfam" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ }
+ else {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME,
+ "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
+ }
+ if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"attempt to extract taxonomies and replace underscores at the same time" );
}
- else {
- setExtractPfamTaxonomyCodesInNhParsing( e );
- }
}
else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
setInternalNumberAreConfidenceForNhParsing( 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" ) ) {
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
+ final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
+ setShowDefaultNodeShapesInternal( b );
+ setShowDefaultNodeShapesExternal( b );
+ }
+ else if ( key.equals( "show_default_node_shapes_internal" ) ) {
+ setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+ }
+ else if ( key.equals( "show_default_node_shapes_external" ) ) {
+ setShowDefaultNodeShapesExternal( 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( NodeVisualization.NodeFill.NONE.toString() ) ) {
+ setDefaultNodeFill( NodeFill.NONE );
+ }
+ else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) {
+ setDefaultNodeFill( NodeFill.GRADIENT );
+ }
+ else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) {
+ setDefaultNodeFill( NodeFill.SOLID );
+ }
+ else {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
+ + "] for [default_node_fill]" );
+ }
+ }
+ else if ( key.equals( "default_node_shape" ) ) {
+ final String shape_str = ( ( String ) st.nextElement() ).trim();
+ if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) {
+ setDefaultNodeShape( NodeShape.CIRCLE );
+ }
+ else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) {
+ setDefaultNodeShape( NodeShape.RECTANGLE );
+ }
+ else {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
+ + "] for [default_node_shape]" );
+ }
+ }
+ else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
+ setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
+ }
+ else if ( key.equals( "midpoint_reroot" ) ) {
+ setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
+ }
+ else if ( key.equals( "ext_descendents_data_to_return" ) ) {
+ final String s = ( ( String ) st.nextElement() ).trim();
+ if ( s.equalsIgnoreCase( "node_name" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
+ }
+ else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
+ }
+ else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
+ }
+ else if ( s.equalsIgnoreCase( "user_selected" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
+ }
+ else {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
+ + "] for [ext_descendents_data_to_return]" );
+ }
+ }
+ else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
+ final String s = ( ( String ) st.nextElement() ).trim();
+ if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
+ + "] for [label_for_get_ext_descendents_data]" );
+ }
+ else {
+ setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
+ }
+ }
+ else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
+ final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
+ if ( s.equals( "console" ) ) {
+ setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
+ }
+ else if ( s.equals( "window" ) ) {
+ setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
+ }
+ else if ( s.equals( "buffer_only" ) ) {
+ setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
+ }
+ else {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
+ + "] for [ext_descendents_data_to_return_on]" );
+ }
+ }
else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
// yet retrieved!
int key_index = -1;
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() ) );
- }
- else if ( key.equals( WEB_LINK_KEY ) ) {
- if ( st.countTokens() == 3 ) {
- createWebLink( ( String ) st.nextElement(),
- ( String ) st.nextElement(),
- ( String ) st.nextElement() );
- }
- else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "illegal format in configuration file for key [" + key + "]" );
- }
+ putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
}
}
- private void setMinConfidenceValue( final double min_confidence_value ) {
- _min_confidence_value = min_confidence_value;
- }
-
- 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 ) {
- 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 ) {
- this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values;
+ private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
+ _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
}
private void setOvMaxHeight( final short ov_max_height ) {
_ov_placement = ov_placement;
}
- void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
- _phylogeny_graphics_type = phylogeny_graphics_type;
- }
-
- private void setPrintLineWidth( final float print_line_width ) {
- _print_line_width = print_line_width;
+ private void setPathToLocalFastme( final File path_to_local_fastme ) {
+ _path_to_local_fastme = path_to_local_fastme;
}
- private void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
- _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
+ private void setPathToLocalMafft( final File path_to_local_mafft ) {
+ _path_to_local_mafft = path_to_local_mafft;
}
- private void setShowBranchLengthValues( final boolean show_branch_length_values ) {
- _show_branch_length_values = show_branch_length_values;
+ private void setPathToLocalRaxml( final File path_to_local_raxml ) {
+ _path_to_local_raxml = path_to_local_raxml;
}
private void setShowOverview( final boolean show_overview ) {
_show_overview = show_overview;
}
- private void setShowScale( final boolean show_scale ) {
- _show_scale = show_scale;
- }
-
private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
_validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
}
- void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
- _weblinks = weblinks;
- }
-
static String getDefaultFontFamilyName() {
return DEFAULT_FONT_FAMILY;
}
- static enum TRIPLET {
- TRUE, FALSE, UNKNOWN
- }
-
- public Color getDomainStructureFontColor() {
- return _domain_structure_font_color;
+ public enum EXT_NODE_DATA_RETURN_ON {
+ CONSOLE, WINODW, BUFFER_ONLY;
}
- public Color getDomainStructureBaseColor() {
- return _domain_structure_base_color;
+ public enum UI {
+ NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
}
- public boolean isColorLabelsSameAsParentBranch() {
- return _color_labels_same_as_parent_branch;
+ static enum TRIPLET {
+ TRUE, FALSE, UNKNOWN
}
- public boolean isShowDomainLabels() {
- return _show_domain_labels;
+ public boolean isMidpointReroot() {
+ return _midpoint_root;
}
- public boolean isAbbreviateScientificTaxonNames() {
- return _abbreviate_scientific_names;
+ public void setMidpointReroot( final boolean midpoint_root ) {
+ _midpoint_root = midpoint_root;
}
}
git://source.jalview.org / jalview.git / blobdiff