X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file;h=cb99cabefa4aed0bb3e3d1daf59a2e2b4e500181;hb=2320da44a171273ec44c0adcaf991687a4780b6e;hp=b347a26c9b983f76aec2e9a7d0150f096dc9419b;hpb=7fa92ecd574c253ec98d7e9c028af83e044b14fe;p=jalview.git diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index b347a26..cb99cab 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file @@ -17,11 +17,11 @@ native_ui: ? # value for bootstrap support) # # Font family name: 'font_family': -# Example: 'font_family: Arial,Calibri,Helvetica' +# Example: 'font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica' # It is advisable to use more than one value for font_family (in # decreasing order of preference). Font family names have to be # comma separated (no spaces). Spaces in font names have to be -# replaced by underscores (e.g. 'Times_New_Roman'). +# replaced by underscores (e.g. 'Arial_Unicode_MS'). # # Font size: 'font_size': # Example: 'font_size: 10' @@ -32,22 +32,10 @@ native_ui: ? # # Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no' # -# Do/do not line up cladogram display: 'non_lined_up_cladogram': values: 'yes'/'no' -# # Cladogram display type: 'cladogram_type' -# Example: 'cladogram_type: ext_node_sum_dep' -# The three possible values are: non_lined_up -# ext_node_sum_dep -# total_node_sum_dep (for "uniform" branch lengths) -# -# Default size for graphics export and printing: 'graphics_export_x' and 'graphics_export_y': -# (Archaeopteryx tries to guess the locale, so setting these is not always necessary) -# Example: For A4 (portrait): -# 'graphics_export_x: 595' -# 'graphics_export_y: 845' -# For US Letter (portrait): -# 'graphics_export_x: 612' -# 'graphics_export_y: 792' +# Example: 'cladogram_type: non_lined_up' +# The three possible values are: lined_up +# non_lined_up # # Default line width for PDF export: 'pdf_export_line_wdith': # Example: 'pdf_export_line_width: 0.5' @@ -88,28 +76,30 @@ native_ui: ? # gradient # none # -# To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return' +# To determine what data field to return by clicking on "List Node Data": 'list_node_data_field' # Possible values: node_name # sequence_name # gene_name # sequence_acc -# sequence_mol_seq # sequence_mol_seq_fasta # sequence_symbol # taxonomy_scientific_name # taxonomy_code -# taxonomy_common_name +# domains +# domains_collapsed +# seq_annotations +# go_term_ids # user_selected # -# To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on' +# To determine where to return data selected by user clicking on "List Node Data": 'list_node_data_in' # Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of # classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE # Possible values: window (for output to window and buffer) # console (for output to console and buffer) # buffer_only (for output to buffer only) # -# To override label for menu item to return data of external nodes (default ""Return ..."): 'label_for_get_ext_descendents_data' -# Example: 'label_for_get_ext_descendents_data: Get_Node_Data' +# To override label for menu item to return data of external nodes (default "List Node Data"): 'list_node_data_custom_label' +# Example: 'list_node_data_custom_label: Get_Node_Data' # # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no' # @@ -129,6 +119,9 @@ native_ui: ? # To allow/not allow editing (cut, copy, and paste): allow_editing # Example: 'allow_editing: yes' # +# To allow/not allow thicker strokes for very small trees: allow_thick_strokes +# Example: 'allow_thick_strokes: yes' +# # NH/NHX/Nexus file parsing # ------------------------- # To replace underscores with spaces during NH/NHX/Nexus file parsing: @@ -157,23 +150,21 @@ native_ui: ? min_confidence_value: 0.0 -font_family: Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans -font_size: 10 +font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica +font_size: 11 font_size_min: 2 font_size_max: 20 antialias_screen: yes show_scale: yes -show_branch_length_values: no -cladogram_type: ext_node_sum_dep +cladogram_type: lined_up phylogeny_graphics_type: rectangular node_label_direction: horizontal show_default_node_shapes_internal: no show_default_node_shapes_external: no +show_node_shapes_for_nodes_with_vis_data: yes default_node_size: 4 default_node_shape: rectangle default_node_fill: solid -#graphics_export_x: 595 -#graphics_export_y: 792 pdf_export_line_width: 0.5 show_overview: yes overview_width: 120 @@ -182,18 +173,22 @@ overview_placement_type: upper_left color_labels_same_as_branch_length_values: no display_sequence_relations: no show_domain_labels: yes +line_up_renderable_data: yes +right_align_domain_architectures: no show_seq_annotation_ref_sources: yes branch_length_value_digits: 3 -confidence_value_digits: 3 +confidence_value_digits: 2 background_gradient: no allow_editing: yes -ext_descendents_data_to_return_on: window -ext_descendents_data_to_return: user_selected -#label_for_get_ext_descendents_data: Return_Node_Data +allow_thick_strokes: no +list_node_data_in: window +list_node_data_field: user_selected +list_node_data_custom_label: # NH/NHX/Nexus file parsing: internal_labels_are_confidence_values: no replace_underscores_in_nh_parsing: no taxonomy_extraction_in_nh_parsing: no +# phyloXML parsing: validate_against_phyloxml_xsd_schema: true @@ -211,6 +206,7 @@ validate_against_phyloxml_xsd_schema: true phylogram: display ? rollover: display yes +color_according_to_sequence: display no color_according_to_species: display no color_according_to_annotation: display no show_node_names: display yes @@ -220,14 +216,17 @@ show_seq_acc: display no show_gene_names: display yes show_taxonomy_code: display yes show_taxonomy_scientific_names: display yes +show_taxonomy_rank: display no show_taxonomy_common_names: display no show_taxonomy_images: display no show_annotations: display no write_confidence_values: display ? +write_branch_length_values: display no write_events: display ? use_visual_styles: display no width_branches: display no show_domain_architectures: display no +show_msa: display no show_binary_characters: display no show_binary_character_counts: display no display_internal_data: display yes @@ -243,9 +242,11 @@ show_vector_data: display no # Format: 'name: display/nodisplay' click_to: display_node_data display click_to: collapse_uncollapse display +click_to: uncollapse_all display click_to: reroot display click_to: subtree display click_to: swap display +click_to: order_subtree display click_to: sort_descendants display click_to: color_subtree display click_to: change_node_font display @@ -274,19 +275,20 @@ default_click_to: display_node_data display_color: background 0x000000 display_color: background_gradient_bottom 0x0000FF display_color: sequence 0xE6E6E6 -display_color: taxonomy 0xFFDCDC -display_color: confidence 0x38B0FF +display_color: taxonomy 0xB4B4B4 +display_color: confidence 0xB4B4B4 display_color: branch_length 0x8C8C8C display_color: branch 0xFFFFFF display_color: node_box 0xFFFFFF -display_color: collapsed 0xFFFF00 +display_color: collapsed 0xFFFFFF display_color: matching_a 0x00FF00 display_color: matching_b 0xFF0000 display_color: matching_a_and_b 0xFFFF00 display_color: duplication 0xFF0000 display_color: speciation 0x00FF00 display_color: duplication_or_specation 0xFFFF00 -display_color: domains 0x7B68EE +display_color: domain_label 0xE6E6E6 +display_color: domain_base 0x646464 display_color: binary_domain_combinations 0x4169FF display_color: annotation 0xADFF2F display_color: overview 0x828282 @@ -309,12 +311,13 @@ gui_menu_text_color: 0xFFFFFF gui_button_border_color: 0x000000 - -# Domain Structure Display Colors -# ------------------------------- -domain_structure_base_color: 0x202020 -domain_structure_font_color: 0x909090 - +# Vector Data Display Colors and Sizes +# ------------------------------------ +vector_data_min_color: 0x0000FF +vector_data_max_color: 0xFFFF00 +vector_data_mean_color: 0x000000 +vector_data_width: 120 +vector_data_height: 12 # Settings Specific for Archaeopteryx Applets (E and A) @@ -346,6 +349,13 @@ raxml_local: /bin/raxml +# Sequence colors +# --------------- +# Format: species_color: sequencename hexcolor +sequence_color: Tubulin-alpha 0xEE0000 +sequence_color: Tubulin-beta 0x00EE00 + + # Species colors # -------------- # Format: species_color: speciesname hexcolor @@ -357,7 +367,6 @@ species_color: CIOSA 0xFF2CAE species_color: BOVIN 0x5C3317 species_color: CANFA 0x8B2323 species_color: HUMAN 0xFF2400 -species_color: Homo_sapiens 0xFF2400 species_color: PANTR 0xCC2400 species_color: MOUSE 0xFF7F00 species_color: RAT 0xFFEF00 @@ -372,21 +381,23 @@ species_color: DANRE 0x0000BB species_color: TETNG 0x0000AA species_color: ORYLA 0x000088 species_color: GASAC 0x000066 -species_color: CAEEL 0xA0A0A0 +species_color: CAEEL 0x666699 species_color: CAEBR 0xB0B0B0 -species_color: DROME 0x706F00 -species_color: DROPS 0x504F00 +species_color: DROME 0x663366 +species_color: DROPS 0x996699 species_color: APIME 0x7A7700 species_color: AEDAE 0x8C5900 species_color: TRICA 0x918E00 -species_color: NEMVE 0xAABADD -species_color: HYDAT 0x7C9BCF +species_color: NEMVE 0x0066CC +species_color: HYDAT 0x3399FF +species_color: HYDVU 0x3399FF species_color: LUBBA 0xF7B5CB species_color: GEOCY 0xF5A0BD +species_color: AMPQE 0x009966 species_color: SUBDO 0xC790B9 species_color: MONBE 0xFC0FC0 -species_color: DICPU 0x23238E -species_color: DICDI 0x4D4DFF +species_color: DICPU 0xFFCC33 +species_color: DICDI 0xFFCC00 species_color: ENTHI 0x5959AB species_color: ARATH 0x00FF00 species_color: POPTR 0x006400 @@ -421,7 +432,7 @@ species_color: mammals 0xFF0000 species_color: Chordata 0x8470FF species_color: Echinodermata 0x6495ED species_color: Hemichordata 0x7EC0EE -species_color: Arthropoda 0x7AC5CD +species_color: Arthropoda 0x7AC5CD species_color: Nematoda 0x7171C6 species_color: Tardigrada 0x388E8E species_color: Annelida 0xC67171 @@ -448,9 +459,10 @@ species_color: Archaea 0x0000FF species_color: Eukaryota 0xFF0000 species_color: eukaryotes 0xFF0000 + + # Domain colors # ------------- - domain_color: Cofilin_ADF 0xFC0FC0 domain_color: TIR 0x900000 domain_color: NACHT 0x202020 @@ -463,15 +475,12 @@ domain_color: PAAD_DAPIN 0x9999CC domain_color: NB-ARC 0x500050 domain_color: WD40 0x888888 domain_color: RVT_1 0x999900 - domain_color: CBM_48 0xFF0000 domain_color: Alpha-amylase 0x0000FF domain_color: Alpha-amylase_C 0x0080FF - domain_color: CBM_48 0xFF0000 domain_color: Alpha-amylase 0x0000FF domain_color: Alpha-amylase_C 0x0080FF - domain_color: GDE_N 0x009000 domain_color: GDE_C 0x00FF00 domain_color: hGDE_N 0x990099 @@ -481,9 +490,9 @@ domain_color: hGDE_amylase 0x0000EE domain_color: hDGE_amylase 0x0000EE + # Annotation colors # ----------------- - annotation_color: dehydrogenase 0x0000FF annotation_color: kinase 0xFF00FF annotation_color: protease 0x009900