// 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;
public final class Configuration {
- public enum EXT_NODE_DATA_RETURN_ON {
- CONSOLE, WINODW, BUFFER_ONLY;
- }
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 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 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 = false;
+ private boolean _show_default_node_shapes_internal = false;
+ private boolean _show_default_node_shapes_external = 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 File _path_to_local_mafft = null;
private File _path_to_local_fastme = null;
private File _path_to_local_raxml = null;
- private File _path_to_local_clustalo = null;
final static int display_as_phylogram = 0;
final static int show_node_names = 1;
final static int show_tax_code = 2;
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 Values", "display", "?" }, { "Event", "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", "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" }, { "Properties", "display", "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" },
+ { "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" }, { "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" },
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 static String DEFAULT_FONT_FAMILY = "";
static {
for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
}
}
- 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 );
- }
- }
-
- boolean displaySequenceRelations() {
- return _display_sequence_relations;
+ public String getBaseFontFamilyName() {
+ return _base_font_family_name;
}
- boolean doCheckOption( final int which ) {
- return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
- || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
+ public int getDefaultBootstrapSamples() {
+ return _default_bootstrap_samples;
}
- boolean doDisplayClickToOption( final int which ) {
- return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ public NodeFill getDefaultNodeFill() {
+ return _default_node_fill;
}
- boolean doDisplayOption( final int which ) {
- return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ public NodeShape getDefaultNodeShape() {
+ return _default_node_shape;
}
- /**
- * Will attempt to use the phylogeny to determine whether to check
- * this or not (e.g. phylogram)
- *
- */
- boolean doGuessCheckOption( final int which ) {
- return display_options[ which ][ 2 ].equals( "?" );
+ public short getDefaultNodeShapeSize() {
+ return _default_node_shape_size;
}
- Map<String, Color> getAnnotationColors() {
- if ( _annotation_colors == null ) {
- _annotation_colors = new Hashtable<String, Color>();
- }
- return _annotation_colors;
+ public Color getDomainStructureBaseColor() {
+ return _domain_structure_base_color;
}
- public String getBaseFontFamilyName() {
- return _base_font_family_name;
+ public Color getDomainStructureFontColor() {
+ return _domain_structure_font_color;
}
- int getBaseFontSize() {
- return _base_font_size;
+ public NODE_DATA getExtDescNodeDataToReturn() {
+ return _ext_desc_data_to_return;
}
- CLADOGRAM_TYPE getCladogramType() {
- return _cladogram_type;
+ public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
+ return _ext_node_data_return_on;
}
- 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;
- }
- 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;
+ public int getFrameXSize() {
+ return _frame_x_size;
}
- int getClickToOptionsCount() {
- return clickto_options.length;
+ public int getFrameYSize() {
+ return _frame_y_size;
}
- String getClickToTitle( final int which ) {
- return clickto_options[ which ][ 0 ];
+ public String getLabelForGetExtDescendentsData() {
+ return _label_for_get_ext_descendents_data;
}
- public int getDefaultBootstrapSamples() {
- return _default_bootstrap_samples;
+ public File getPathToLocalFastme() {
+ return _path_to_local_fastme;
}
public File getpathToLocalMafft() {
return _path_to_local_mafft;
}
- public File getPathToLocalFastme() {
- return _path_to_local_fastme;
- }
-
public File getPathToLocalRaxml() {
return _path_to_local_raxml;
}
- int getDefaultDisplayClicktoOption() {
- return default_clickto;
+ public boolean isAbbreviateScientificTaxonNames() {
+ return _abbreviate_scientific_names;
}
- public NodeFill getDefaultNodeFill() {
- return _default_node_fill;
+ public boolean isBackgroundColorGradient() {
+ return _background_color_gradient;
}
- public NodeShape getDefaultNodeShape() {
- return _default_node_shape;
+ public boolean isColorLabelsSameAsParentBranch() {
+ return _color_labels_same_as_parent_branch;
}
- public short getDefaultNodeShapeSize() {
- return _default_node_shape_size;
+ public boolean isShowDefaultNodeShapesExternal() {
+ return _show_default_node_shapes_external;
}
- SortedMap<String, Color> getDisplayColors() {
- return _display_colors;
+ public boolean isShowDefaultNodeShapesInternal() {
+ return _show_default_node_shapes_internal;
}
- String getDisplayTitle( final int which ) {
- return display_options[ which ][ 0 ];
+ public boolean isShowDomainLabels() {
+ return _show_domain_labels;
}
- Map<String, Color> getDomainColors() {
- if ( _domain_colors == null ) {
- _domain_colors = new Hashtable<String, Color>();
- }
- return _domain_colors;
+ public boolean isTaxonomyColorizeNodeShapes() {
+ return _taxonomy_colorize_node_shapes;
}
- public Color getDomainStructureBaseColor() {
- return _domain_structure_base_color;
+ public void putDisplayColors( final String key, final Color color ) {
+ getDisplayColors().put( key, color );
}
- public Color getDomainStructureFontColor() {
- return _domain_structure_font_color;
+ public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
+ _abbreviate_scientific_names = abbreviate_scientific_names;
}
- int getGraphicsExportX() {
- return _graphics_export_x;
+ public void setBackgroundColorGradient( final boolean background_color_gradient ) {
+ _background_color_gradient = background_color_gradient;
}
- int getGraphicsExportY() {
- return _graphics_export_y;
+ public void setBaseFontFamilyName( final String base_font_family_name ) {
+ _base_font_family_name = base_font_family_name;
}
- Color getGuiBackgroundColor() {
- return _gui_background_color;
+ public void setBaseFontSize( final int base_font_size ) {
+ _base_font_size = base_font_size;
}
- Color getGuiButtonBackgroundColor() {
- return _gui_button_background_color;
+ private void setMaxBaseFontSize( final int max_base_font_size ) {
+ _max_base_font_size = max_base_font_size;
}
- Color getGuiButtonBorderColor() {
- return _gui_button_border_color;
+ private void setMinBaseFontSize( final int min_base_font_size ) {
+ _min_base_font_size = min_base_font_size;
}
- Color getGuiButtonTextColor() {
- return _gui_button_text_color;
+ public void setColorizeBranches( final boolean b ) {
+ display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
}
- Color getGuiCheckboxAndButtonActiveColor() {
- return _gui_checkbox_and_button_active_color;
+ public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
+ _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
}
- Color getGuiCheckboxTextColor() {
- return _gui_checkbox_text_color;
+ public void setDefaultNodeFill( final NodeFill default_node_fill ) {
+ _default_node_fill = default_node_fill;
}
- Color getGuiMenuBackgroundColor() {
- return _gui_menu_background_color;
+ public void setDefaultNodeShape( final NodeShape default_node_shape ) {
+ _default_node_shape = default_node_shape;
}
- Color getGuiMenuTextColor() {
- return _gui_menu_text_color;
+ public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
+ _default_node_shape_size = default_node_shape_size;
}
- double getMinConfidenceValue() {
- return _min_confidence_value;
+ public void setDisplayAsPhylogram( final boolean b ) {
+ display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
}
- NODE_LABEL_DIRECTION getNodeLabelDirection() {
- return _node_label_direction;
+ public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
+ _display_colors = display_colors;
}
- short getNumberOfDigitsAfterCommaForBranchLengthValues() {
- return _number_of_digits_after_comma_for_branch_length_values;
+ public void setDisplayConfidenceValues( final boolean b ) {
+ display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
}
- short getNumberOfDigitsAfterCommaForConfidenceValues() {
- return _number_of_digits_after_comma_for_confidence_values;
+ public void setDisplayInternalData( final boolean b ) {
+ display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
}
- short getOvMaxHeight() {
- return _ov_max_height;
+ public void setDisplayNodeNames( final boolean b ) {
+ display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
}
- short getOvMaxWidth() {
- return _ov_max_width;
+ public void setDisplaySequenceAcc( final boolean b ) {
+ display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
}
- OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
- return _ov_placement;
- }
+ 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 _display_sequence_relations;
+ }
+
+ boolean doCheckOption( final int which ) {
+ return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
+ || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
+ }
+
+ boolean doDisplayClickToOption( final int which ) {
+ return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ }
+
+ boolean doDisplayOption( final int which ) {
+ return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ }
+
+ /**
+ * Will attempt to use the phylogeny to determine whether to check
+ * this or not (e.g. phylogram)
+ *
+ */
+ boolean doGuessCheckOption( final int which ) {
+ return display_options[ which ][ 2 ].equals( "?" );
+ }
+
+ Map<String, Color> getAnnotationColors() {
+ if ( _annotation_colors == null ) {
+ _annotation_colors = new Hashtable<String, Color>();
+ }
+ return _annotation_colors;
+ }
+
+ int getBaseFontSize() {
+ return _base_font_size;
+ }
+
+ int getMinBaseFontSize() {
+ return _min_base_font_size;
+ }
+
+ int getMaxBaseFontSize() {
+ return _max_base_font_size;
+ }
+
+ CLADOGRAM_TYPE getCladogramType() {
+ return _cladogram_type;
+ }
+
+ int getClickToOptionsCount() {
+ return clickto_options.length;
+ }
+
+ String getClickToTitle( final int which ) {
+ return clickto_options[ which ][ 0 ];
+ }
+
+ int getDefaultDisplayClicktoOption() {
+ return default_clickto;
+ }
+
+ SortedMap<String, Color> getDisplayColors() {
+ return _display_colors;
+ }
+
+ String getDisplayTitle( final int which ) {
+ return display_options[ which ][ 0 ];
+ }
+
+ Map<String, Color> getDomainColors() {
+ if ( _domain_colors == null ) {
+ _domain_colors = new Hashtable<String, Color>();
+ }
+ return _domain_colors;
+ }
+
+ 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;
+ }
+
+ Color getGuiMenuBackgroundColor() {
+ return _gui_menu_background_color;
+ }
+
+ Color getGuiMenuTextColor() {
+ return _gui_menu_text_color;
+ }
+
+ double getMinConfidenceValue() {
+ return _min_confidence_value;
+ }
+
+ NODE_LABEL_DIRECTION getNodeLabelDirection() {
+ return _node_label_direction;
+ }
+
+ short getNumberOfDigitsAfterCommaForBranchLengthValues() {
+ return _number_of_digits_after_comma_for_branch_length_values;
+ }
+
+ short getNumberOfDigitsAfterCommaForConfidenceValues() {
+ return _number_of_digits_after_comma_for_confidence_values;
+ }
+
+ short getOvMaxHeight() {
+ return _ov_max_height;
+ }
+
+ short getOvMaxWidth() {
+ return _ov_max_width;
+ }
+
+ OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
+ return _ov_placement;
+ }
PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
return _phylogeny_graphics_type;
return _species_colors;
}
- TreeColorSet getTreeColorSet() {
- return null;
- }
-
- TreeFontSet getTreeFontSet() {
- return null;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
WebLink getWebLink( final String source ) {
return _weblinks;
}
- public boolean isAbbreviateScientificTaxonNames() {
- return _abbreviate_scientific_names;
- }
-
boolean isAntialiasScreen() {
return _antialias_screen;
}
- public boolean isBackgroundColorGradient() {
- return _background_color_gradient;
- }
-
- public boolean isColorLabelsSameAsParentBranch() {
- return _color_labels_same_as_parent_branch;
- }
-
/**
* Convenience method.
*
return _editable;
}
- final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
- return _taxonomy_extraction;
- }
-
boolean isHasWebLink( final String source ) {
return getWebLinks().containsKey( source );
}
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 ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
_ui = UI.NATIVE;
}
- return _ui == UI.NATIVE;
- }
-
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isUseTabbedDisplay() {
- return _use_tabbed_display;
- }
-
- boolean isValidatePhyloXmlAgainstSchema() {
- return _validate_against_phyloxml_xsd_schema;
+ return _ui == UI.NATIVE;
+ }
+
+ /**
+ * Only used by ArchaeoptryxE.
+ *
+ */
+ boolean isUseTabbedDisplay() {
+ return _use_tabbed_display;
+ }
+
+ boolean isValidatePhyloXmlAgainstSchema() {
+ return _validate_against_phyloxml_xsd_schema;
+ }
+
+ final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
+ }
+
+ void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
+ _weblinks = weblinks;
+ }
+
+ 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 );
+ }
+ }
+
+ 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;
+ }
+ 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;
}
private boolean parseBoolean( final String str ) {
}
}
- 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;
}
- 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 setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
_cladogram_type = cladogram_type;
}
- 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;
- }
-
private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
_default_bootstrap_samples = default_bootstrap_samples;
}
- private void setPathToLocalMafft( final File path_to_local_mafft ) {
- _path_to_local_mafft = path_to_local_mafft;
- }
-
- private void setPathToLocalFastme( final File path_to_local_fastme ) {
- _path_to_local_fastme = path_to_local_fastme;
- }
-
- private void setPathToLocalRaxml( final File path_to_local_raxml ) {
- _path_to_local_raxml = path_to_local_raxml;
- }
-
- public File getPathToLocalClustalOmega() {
- return _path_to_local_clustalo;
- }
-
- public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
- _path_to_local_clustalo = path_to_local_clustalo;
- }
-
- 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";
- }
-
private void setEditable( final boolean editable ) {
_editable = editable;
}
- final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
- _taxonomy_extraction = taxonomy_extraction;
+ 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 ) {
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( "clustalo_local" ) ) {
- final String str = ( ( String ) st.nextElement() ).trim();
- if ( !ForesterUtil.isEmpty( str ) ) {
- setPathToLocalClustalOmega( new File( str ) );
- }
- }
else if ( key.equals( "mafft_local" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
if ( !ForesterUtil.isEmpty( str ) ) {
_domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "show_default_node_shapes" ) ) {
- setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+ 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() );
_label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
}
- public String getLabelForGetExtDescendentsData() {
- return _label_for_get_ext_descendents_data;
- }
-
- 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;
- }
-
private void setOvMaxHeight( final short ov_max_height ) {
_ov_max_height = ov_max_height;
}
_ov_placement = ov_placement;
}
- 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;
+ private void setPathToLocalFastme( final File path_to_local_fastme ) {
+ _path_to_local_fastme = path_to_local_fastme;
}
- public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
- _show_default_node_shapes = show_default_node_shapes;
+ private void setPathToLocalMafft( final File path_to_local_mafft ) {
+ _path_to_local_mafft = path_to_local_mafft;
}
- public void setShowDomainLabels( final boolean show_domain_labels ) {
- _show_domain_labels = show_domain_labels;
+ 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;
}
- 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";
- }
-
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 enum EXT_NODE_DATA_RETURN_ON {
+ CONSOLE, WINODW, BUFFER_ONLY;
}
public enum UI {
NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
}
- public NODE_DATA getExtDescNodeDataToReturn() {
- return _ext_desc_data_to_return;
- }
-
- public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
- _ext_desc_data_to_return = ext_desc_data_to_return;
- }
-
- public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
- return _ext_node_data_return_on;
- }
-
- private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
- _ext_node_data_return_on = ext_node_data_return_on;
+ static enum TRIPLET {
+ TRUE, FALSE, UNKNOWN
}
}
git://source.jalview.org / jalview.git / blobdiff