X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file;h=1c417bb271726006ce1cbcef10f1903500abe27b;hb=dd8e6f3ab54507a5e4f1e66b3270eb6946cee5d7;hp=645d6714c82ead8b851c903a518e66cc1b7b62f7;hpb=f47c40112b8f637cf6559f84bdb5222b289c8355;p=jalview.git diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index 645d671..1c417bb 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file @@ -15,23 +15,31 @@ native_ui: ? # Minimal confidence value to be displayed: 'min_confidence_value': # Example: 'min_confidence_value: 50.0' (a commonly used # value for bootstrap support) +# # Font family name: 'font_family': # Example: 'font_family: Arial,Calibri,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'). +# # Font size: 'font_size': # Example: 'font_size: 10' +# # Screen antialias: 'antialias_screen': values: 'yes'/'no' +# # Show Scale: 'show_scale': values: 'yes'/'no' +# # 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): @@ -40,9 +48,12 @@ native_ui: ? # For US Letter (portrait): # 'graphics_export_x: 612' # 'graphics_export_y: 792' +# # Default line width for PDF export: 'pdf_export_line_wdith': # Example: 'pdf_export_line_width: 0.5' +# # Show overview: 'show_overview': values: 'yes'/'no' +# # Phylogeny graphics type: 'phylogeny_graphics_type': # Example: 'phylogeny_graphics_type: euro_style' # The eight possible values are: rectangular @@ -53,18 +64,24 @@ native_ui: ? # convex # unrooted # circular +# # Node label direction for circular and unrooted type: 'node_label_direction': # Example: 'node_label_direction: horizontal' # The two possible values are: horizontal # radial +# # Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no' +# # Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no' +# # Default node shape size: 'default_node_size' # Example: 'default_node_size: 6' +# # Default node shape type: 'default_node_shape' # Example: 'default_node_shape: ' # Possible values: circle # rectangle +# # Default node shape fill: 'default_node_fill' # Example: 'default_node_fill: ' # Possible values: solid @@ -74,12 +91,14 @@ native_ui: ? # To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return' # 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 # user_selected # # To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on' @@ -93,12 +112,20 @@ native_ui: ? # Example: 'label_for_get_ext_descendents_data: Get_Node_Data' # # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no' +# # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no' +# # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no' +# +# Do/not show reference sources for sequence annotation: 'show_seq_annotation_ref_sources': values: 'yes'/'no' +# # Number of fraction digits for branch length values: 'branch_length_value_digits' +# # Number of fraction digits for confidence values: 'confidence_value_digits' +# # To turn on/off background color gradient: background_gradient # Example: 'background_gradient: yes' +# # To allow/not allow editing (cut, copy, and paste): allow_editing # Example: 'allow_editing: yes' # @@ -107,15 +134,17 @@ native_ui: ? # To replace underscores with spaces during NH/NHX/Nexus file parsing: # 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no' # -# To extract UniProt taxonomy codes (e.g. CAEEL) from node names during NH/NHX/Nexus file parsing: -# 'taxonomy_extraction_in_nh_parsing', -# possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), 'no' +# To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names) +# from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing' +# possible values are: +# 'no' +# 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453) +# 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090) +# 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis) # # Internal node labels are confidence values during NH/NHX/Nexus file parsing: # 'internal_labels_are_confidence_values', possible values are 'yes', 'no' - - - +# # phyloXML parsing # ---------------- # To ensure compatibility with all current and future @@ -126,9 +155,6 @@ native_ui: ? # with: # 'validate_against_phyloxml_xsd_schema: true' -validate_against_phyloxml_xsd_schema: true - - min_confidence_value: 0.0 font_family: Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans @@ -146,7 +172,6 @@ show_default_node_shapes_external: no default_node_size: 4 default_node_shape: rectangle default_node_fill: solid -taxonomy_colorize_node_shapes: no #graphics_export_x: 595 #graphics_export_y: 792 pdf_export_line_width: 0.5 @@ -157,17 +182,19 @@ overview_placement_type: upper_left color_labels_same_as_branch_length_values: no display_sequence_relations: no show_domain_labels: yes +show_seq_annotation_ref_sources: yes branch_length_value_digits: 3 confidence_value_digits: 3 background_gradient: no allow_editing: yes ext_descendents_data_to_return_on: window -ext_descendents_data_to_return: sequence_mol_seq_fasta -#label_for_get_ext_descendents_data: Get_Node_Data +ext_descendents_data_to_return: user_selected +#label_for_get_ext_descendents_data: Return_Node_Data # NH/NHX/Nexus file parsing: internal_labels_are_confidence_values: no replace_underscores_in_nh_parsing: no -taxonomy_extraction_in_nh_parsing: yes +taxonomy_extraction_in_nh_parsing: no +validate_against_phyloxml_xsd_schema: true # Checkbox Display Selection @@ -184,20 +211,22 @@ taxonomy_extraction_in_nh_parsing: yes phylogram: display ? rollover: display yes -color_according_to_species: 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 +show_seq_names: display yes +show_seq_symbols: display yes +show_seq_acc: display no show_gene_names: display yes -show_gene_symbols: display yes -show_sequence_acc: display no show_taxonomy_code: display yes show_taxonomy_scientific_names: display yes show_taxonomy_common_names: display no -show_taxonomy_images: display yes +show_taxonomy_images: display no show_annotations: display no write_confidence_values: display ? write_events: display ? -color_branches: display no +use_visual_styles: display no width_branches: display no show_domain_architectures: display no show_binary_characters: display no @@ -220,7 +249,10 @@ click_to: subtree display click_to: swap display click_to: sort_descendants display click_to: color_subtree display +click_to: change_node_font display +click_to: color_node_font display click_to: open_seq_web display +click_to: open_pdb_web display click_to: open_tax_web display click_to: blast display click_to: cut_subtree display @@ -242,14 +274,16 @@ default_click_to: display_node_data display_color: background 0x000000 display_color: background_gradient_bottom 0x0000FF -display_color: sequence 0xDCDCDC +display_color: sequence 0xE6E6E6 display_color: taxonomy 0xB4B4B4 -display_color: confidence 0x38B0DE +display_color: confidence 0x38B0FF display_color: branch_length 0x8C8C8C display_color: branch 0xFFFFFF display_color: node_box 0xFFFFFF -display_color: collapsed 0xFFFF00 -display_color: matching_nodes 0x00FF00 +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 @@ -313,6 +347,13 @@ 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 @@ -415,27 +456,40 @@ 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 -domain_color: CARD 0xFF0000 -domain_color: Peptidase_C14 0x00FF00 -domain_color: Death 0x0000FF -domain_color: DED 0x00FFFF -domain_color: BIR 0xCCFF33 -domain_color: PAAD_DAPIN 0x9999CC -domain_color: NB-ARC 0x500050 -domain_color: WD40 0x888888 -domain_color: RVT_1 0x999900 +domain_color: Cofilin_ADF 0xFC0FC0 +domain_color: TIR 0x900000 +domain_color: NACHT 0x202020 +domain_color: CARD 0xFF0000 +domain_color: Peptidase_C14 0x00FF00 +domain_color: Death 0x0000FF +domain_color: DED 0x00FFFF +domain_color: BIR 0xCCFF33 +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 +domain_color: GDE_N_bis 0x007000 +domain_color: hGDE_central 0xFF8000 +domain_color: hGDE_amylase 0x0000EE +domain_color: hDGE_amylase 0x0000EE # Annotation colors # ----------------- - annotation_color: dehydrogenase 0x0000FF annotation_color: kinase 0xFF00FF annotation_color: protease 0x009900