- 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 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 isColorByTaxonomicGroup() {
+ return false;
+ }
+
+ public boolean isColorLabelsSameAsParentBranch() {
+ return _color_labels_same_as_parent_branch;
+ }
+
+ public boolean isMidpointReroot() {
+ return _midpoint_root;
+ }
+
+ 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;
+ }
+
+ 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;
+ }
+
+ 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_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";
+ }
+
+ public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;