X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file;h=47e84d0803df5356a305aa749310f73386e7ab2e;hb=09e03be003bce073d48b4a7e0b1d9b088aafa8a3;hp=2b179eef0ed12416d5f2a4f0c910c342e8737671;hpb=f767e459c55061d7769189c3460ada0f23f4493a;p=jalview.git diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index 2b179ee..47e84d0 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file @@ -91,6 +91,7 @@ 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 @@ -162,7 +163,6 @@ 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 phylogeny_graphics_type: rectangular node_label_direction: horizontal @@ -171,7 +171,6 @@ 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 @@ -182,6 +181,8 @@ 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: no +right_align_domain_architectures: no show_seq_annotation_ref_sources: yes branch_length_value_digits: 3 confidence_value_digits: 3 @@ -211,22 +212,26 @@ validate_against_phyloxml_xsd_schema: true 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_branch_length_values: display no write_events: display ? -color_branches: display no +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 @@ -247,7 +252,10 @@ 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 @@ -269,18 +277,21 @@ 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 0xB4B4B4 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 -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 @@ -303,12 +314,13 @@ 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) @@ -340,6 +352,13 @@ 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 @@ -442,27 +461,40 @@ 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