public final class Configuration {
+ public enum EXT_NODE_DATA_RETURN_ON {
+ BUFFER_ONLY, CONSOLE, WINODW;
+ }
+
+ static enum TRIPLET {
+ FALSE, TRUE, UNKNOWN
+ }
+
+ public enum UI {
+ CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
+ }
final static String clickto_options[][] = {
{ "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
{ "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "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" } };
+ private final static String DEFAULT_SPECIES_COLORS[][] = {
+ { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
+ { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
+ { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
+ { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
+ { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
+ { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
+ { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
+ { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
+ { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
+ { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
+ { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
+ { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
+ { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
+ { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
+ { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
+ { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
+ { "PORGI", "0x918E00" } };
final static int display_node_data = 0;
final static int collapse_uncollapse = 1;
final static int reroot = 2;
}
}
+ static String getDefaultFontFamilyName() {
+ return DEFAULT_FONT_FAMILY;
+ }
+
public Configuration() {
this( null, false, false, false );
}
}
}
+ 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;
+ }
+
public String getBaseFontFamilyName() {
return _base_font_family_name;
}
+ int getBaseFontSize() {
+ return _base_font_size;
+ }
+
+ CLADOGRAM_TYPE getCladogramType() {
+ return _cladogram_type;
+ }
+
+ 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_pdb_web" ) ) {
+ index = Configuration.open_pdb_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( "change_node_font" ) ) {
+ index = Configuration.change_node_font;
+ }
+ else if ( name.equals( "color_node_font" ) ) {
+ index = Configuration.color_node_font;
+ }
+ else if ( name.equals( "color_subtree" ) ) {
+ index = Configuration.color_subtree;
+ }
+ return index;
+ }
+
+ int getClickToOptionsCount() {
+ return clickto_options.length;
+ }
+
+ String getClickToTitle( final int which ) {
+ return clickto_options[ which ][ 0 ];
+ }
+
public int getDefaultBootstrapSamples() {
return _default_bootstrap_samples;
}
+ int getDefaultDisplayClicktoOption() {
+ return default_clickto;
+ }
+
public NodeFill getDefaultNodeFill() {
return _default_node_fill;
}
return _default_node_shape_size;
}
+ 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;
+ }
+
public NODE_DATA getExtDescNodeDataToReturn() {
return _ext_desc_data_to_return;
}
return _frame_y_size;
}
- public String getLabelForGetExtDescendentsData() {
- return _label_for_get_ext_descendents_data;
+ int getGraphicsExportX() {
+ return _graphics_export_x;
}
- public File getPathToLocalFastme() {
- return _path_to_local_fastme;
+ int getGraphicsExportY() {
+ return _graphics_export_y;
}
- public File getPathToLocalMafft() {
- return _path_to_local_mafft;
+ Color getGuiBackgroundColor() {
+ return _gui_background_color;
}
- public File getPathToLocalRaxml() {
- return _path_to_local_raxml;
+ Color getGuiButtonBackgroundColor() {
+ return _gui_button_background_color;
}
- public boolean isAbbreviateScientificTaxonNames() {
- return _abbreviate_scientific_names;
+ Color getGuiButtonBorderColor() {
+ return _gui_button_border_color;
}
- public boolean isBackgroundColorGradient() {
- return _background_color_gradient;
+ Color getGuiButtonTextColor() {
+ return _gui_button_text_color;
}
- public boolean isColorByTaxonomicGroup() {
- return false;
+ Color getGuiCheckboxAndButtonActiveColor() {
+ return _gui_checkbox_and_button_active_color;
}
- public boolean isColorLabelsSameAsParentBranch() {
- return _color_labels_same_as_parent_branch;
+ Color getGuiCheckboxTextColor() {
+ return _gui_checkbox_text_color;
}
- public boolean isMidpointReroot() {
- return _midpoint_root;
+ Color getGuiMenuBackgroundColor() {
+ return _gui_menu_background_color;
}
- public boolean isShowAnnotationRefSource() {
- return _show_annotation_ref_source;
+ Color getGuiMenuTextColor() {
+ return _gui_menu_text_color;
}
- public boolean isShowDefaultNodeShapesExternal() {
- return _show_default_node_shapes_external;
+ public String getLabelForGetExtDescendentsData() {
+ return _label_for_get_ext_descendents_data;
}
- public boolean isShowDefaultNodeShapesInternal() {
- return _show_default_node_shapes_internal;
+ int getMaxBaseFontSize() {
+ return _max_base_font_size;
}
- public boolean isShowDomainLabels() {
- return _show_domain_labels;
+ int getMinBaseFontSize() {
+ return _min_base_font_size;
}
- public void putDisplayColors( final String key, final Color color ) {
- getDisplayColors().put( key, color );
+ double getMinConfidenceValue() {
+ return _min_confidence_value;
}
- public void setAddTaxonomyImagesCB( final boolean b ) {
- display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
+ NODE_LABEL_DIRECTION getNodeLabelDirection() {
+ return _node_label_direction;
}
- public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
- _abbreviate_scientific_names = abbreviate_scientific_names;
+ short getNumberOfDigitsAfterCommaForBranchLengthValues() {
+ return _number_of_digits_after_comma_for_branch_length_values;
}
- public void setBackgroundColorGradient( final boolean background_color_gradient ) {
- _background_color_gradient = background_color_gradient;
+ short getNumberOfDigitsAfterCommaForConfidenceValues() {
+ return _number_of_digits_after_comma_for_confidence_values;
}
- public void setBaseFontFamilyName( final String base_font_family_name ) {
- _base_font_family_name = base_font_family_name;
+ short getOvMaxHeight() {
+ return _ov_max_height;
}
- public void setBaseFontSize( final int base_font_size ) {
- _base_font_size = base_font_size;
+ short getOvMaxWidth() {
+ return _ov_max_width;
}
- public void setColorizeBranches( final boolean b ) {
- display_options[ use_style ][ 2 ] = b ? "yes" : "no";
+ OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
+ return _ov_placement;
}
- 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 setUseStyle( final boolean b ) {
- display_options[ use_style ][ 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_seq_names ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayGeneNames( 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_seq_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 setMidpointReroot( final boolean midpoint_root ) {
- _midpoint_root = midpoint_root;
- }
-
- 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 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;
- }
-
- boolean displaySequenceRelations() {
- return _display_sequence_relations;
+ public File getPathToLocalFastme() {
+ return _path_to_local_fastme;
}
- boolean doCheckOption( final int which ) {
- return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
- || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
+ public File getPathToLocalMafft() {
+ return _path_to_local_mafft;
}
- boolean doDisplayClickToOption( final int which ) {
- return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ public File getPathToLocalRaxml() {
+ return _path_to_local_raxml;
}
- boolean doDisplayOption( final int which ) {
- return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
+ return _phylogeny_graphics_type;
}
- /**
- * 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( "?" );
+ float getPrintLineWidth() {
+ return _print_line_width;
}
- Map<String, Color> getAnnotationColors() {
- if ( _annotation_colors == null ) {
- _annotation_colors = new Hashtable<String, Color>();
+ Hashtable<String, Color> getSequenceColors() {
+ if ( _sequence_colors == null ) {
+ _sequence_colors = new Hashtable<String, Color>();
}
- return _annotation_colors;
- }
-
- int getBaseFontSize() {
- return _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 ];
+ return _sequence_colors;
}
- Map<String, Color> getDomainColors() {
- if ( _domain_colors == null ) {
- _domain_colors = new Hashtable<String, Color>();
+ Hashtable<String, Color> getSpeciesColors() {
+ if ( _species_colors == null ) {
+ initSpeciesColors();
}
- 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;
- }
-
- int getMaxBaseFontSize() {
- return _max_base_font_size;
- }
-
- int getMinBaseFontSize() {
- return _min_base_font_size;
- }
-
- 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;
+ return _species_colors;
}
- short getOvMaxHeight() {
- return _ov_max_height;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
- short getOvMaxWidth() {
- return _ov_max_width;
+ public double getVectorDataHeight() {
+ return _vector_data_height;
}
- OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
- return _ov_placement;
+ public Color getVectorDataMaxColor() {
+ return _vector_data_max_color;
}
- PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
- return _phylogeny_graphics_type;
+ public Color getVectorDataMeanColor() {
+ return _vector_data_mean_color;
}
- float getPrintLineWidth() {
- return _print_line_width;
+ public Color getVectorDataMinColor() {
+ return _vector_data_min_color;
}
- Hashtable<String, Color> getSpeciesColors() {
- if ( _species_colors == null ) {
- _species_colors = new Hashtable<String, Color>();
- }
- return _species_colors;
+ public int getVectorDataWidth() {
+ return _vector_data_width;
}
- Hashtable<String, Color> getSequenceColors() {
- if ( _sequence_colors == null ) {
- _sequence_colors = new Hashtable<String, Color>();
+ private final void initSpeciesColors() {
+ _species_colors = new Hashtable<String, Color>();
+ for( final String[] s : DEFAULT_SPECIES_COLORS ) {
+ _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) );
}
- return _sequence_colors;
}
- final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
- return _taxonomy_extraction;
+ public boolean isAbbreviateScientificTaxonNames() {
+ return _abbreviate_scientific_names;
}
boolean isAntialiasScreen() {
return _antialias_screen;
}
+ public boolean isBackgroundColorGradient() {
+ return _background_color_gradient;
+ }
+
+ public boolean isColorByTaxonomicGroup() {
+ return false;
+ }
+
+ public boolean isColorLabelsSameAsParentBranch() {
+ return _color_labels_same_as_parent_branch;
+ }
+
/**
* Convenience method.
*
return _internal_number_are_confidence_for_nh_parsing;
}
- boolean isReplaceUnderscoresInNhParsing() {
- return _nh_parsing_replace_underscores;
- }
-
- boolean isShowOverview() {
- return _show_overview;
- }
-
- boolean isShowScale() {
- return _show_scale;
- }
-
- final boolean isUseNativeUI() {
- if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
- _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;
- }
-
- final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
- _taxonomy_extraction = taxonomy_extraction;
+ final public boolean isLineUpRendarableNodeData() {
+ return _line_up_renderable_node_data;
}
- 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_pdb_web" ) ) {
- index = Configuration.open_pdb_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( "change_node_font" ) ) {
- index = Configuration.change_node_font;
- }
- else if ( name.equals( "color_node_font" ) ) {
- index = Configuration.color_node_font;
- }
- else if ( name.equals( "color_subtree" ) ) {
- index = Configuration.color_subtree;
+ public boolean isMidpointReroot() {
+ return _midpoint_root;
+ }
+
+ boolean isReplaceUnderscoresInNhParsing() {
+ return _nh_parsing_replace_underscores;
+ }
+
+ final public boolean isRightLineUpDomains() {
+ return _right_align_domains;
+ }
+
+ public boolean isShowAnnotationRefSource() {
+ return _show_annotation_ref_source;
+ }
+
+ 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;
+ }
+
+ boolean isShowOverview() {
+ return _show_overview;
+ }
+
+ boolean isShowScale() {
+ return _show_scale;
+ }
+
+ final boolean isUseNativeUI() {
+ if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
+ _ui = UI.NATIVE;
}
- return index;
+ return _ui == UI.NATIVE;
+ }
+
+ /**
+ * Only used by ArchaeoptryxE.
+ *
+ */
+ boolean isUseTabbedDisplay() {
+ return _use_tabbed_display;
+ }
+
+ boolean isValidatePhyloXmlAgainstSchema() {
+ return _validate_against_phyloxml_xsd_schema;
}
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;
+ }
+
+ public void setAddTaxonomyImagesCB( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
+ }
+
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[ use_style ][ 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;
}
+ 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 setDisplayGeneNames( final boolean b ) {
+ display_options[ show_gene_names ][ 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_seq_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_seq_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;
}
+ public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;
+ }
+
private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
_ext_node_data_return_on = ext_node_data_return_on;
}
+ 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;
+ }
+
private void setGraphicsExportX( final int graphics_export_x ) {
_graphics_export_x = graphics_export_x;
}
_label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
}
+ final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
+ _line_up_renderable_node_data = line_up_renderable_node_data;
+ }
+
private void setMaxBaseFontSize( final int max_base_font_size ) {
_max_base_font_size = max_base_font_size;
}
+ public void setMidpointReroot( final boolean midpoint_root ) {
+ _midpoint_root = midpoint_root;
+ }
+
private void setMinBaseFontSize( final int min_base_font_size ) {
_min_base_font_size = min_base_font_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;
+ }
+
private void setOvMaxHeight( final short ov_max_height ) {
_ov_max_height = ov_max_height;
}
_path_to_local_raxml = path_to_local_raxml;
}
- private void setShowAnnotationRefSource( final boolean b ) {
- _show_annotation_ref_source = b;
- }
-
- private void setShowOverview( final boolean show_overview ) {
- _show_overview = show_overview;
- }
-
- private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
- _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
- }
-
- static String getDefaultFontFamilyName() {
- return DEFAULT_FONT_FAMILY;
+ public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
+ _phylogeny_graphics_type = phylogeny_graphics_type;
}
- public enum EXT_NODE_DATA_RETURN_ON {
- BUFFER_ONLY, CONSOLE, WINODW;
+ public void setPrintLineWidth( final float print_line_width ) {
+ _print_line_width = print_line_width;
}
- public enum UI {
- CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
+ public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
+ _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
}
- static enum TRIPLET {
- FALSE, TRUE, UNKNOWN
+ final public void setRightLineUpDomains( final boolean right_align_domains ) {
+ _right_align_domains = right_align_domains;
}
- public Color getVectorDataMinColor() {
- return _vector_data_min_color;
+ private void setShowAnnotationRefSource( final boolean b ) {
+ _show_annotation_ref_source = b;
}
- public Color getVectorDataMaxColor() {
- return _vector_data_max_color;
+ public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+ _show_default_node_shapes_external = show_default_node_shapes_external;
}
- public Color getVectorDataMeanColor() {
- return _vector_data_mean_color;
+ public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+ _show_default_node_shapes_internal = show_default_node_shapes_internal;
}
- public double getVectorDataHeight() {
- return _vector_data_height;
+ public void setShowDomainLabels( final boolean show_domain_labels ) {
+ _show_domain_labels = show_domain_labels;
}
- public int getVectorDataWidth() {
- return _vector_data_width;
+ private void setShowOverview( final boolean show_overview ) {
+ _show_overview = show_overview;
}
- final public boolean isLineUpRendarableNodeData() {
- return _line_up_renderable_node_data;
+ public void setShowScale( final boolean show_scale ) {
+ _show_scale = show_scale;
}
- final public boolean isRightLineUpDomains() {
- return _right_align_domains;
+ final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
}
- final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
- _line_up_renderable_node_data = line_up_renderable_node_data;
+ public void setUseStyle( final boolean b ) {
+ display_options[ use_style ][ 2 ] = b ? "yes" : "no";
}
- final public void setRightLineUpDomains( final boolean right_align_domains ) {
- _right_align_domains = right_align_domains;
+ private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
+ _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
}
}
git://source.jalview.org / jalview.git / commitdiff