X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file;h=2ca3dc79e7cd2f758eca2486c1495c186fd0b0a2;hb=bf7b5c06715bf64a338402aea20825ad9dbad43c;hp=b858bf027b6ab292b16464fc5b8c8d4719e0bc3e;hpb=1a9e4edf701d2cbef55dcc25f49ef57c71dc08f1;p=jalview.git diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index b858bf0..2ca3dc7 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' +# 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' +# # 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 @@ -53,61 +64,119 @@ 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: 'show_default_node_shapes': values: 'yes'/'no' +# +# 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 # gradient # none -# To determine what data field to return by clicking on "return external descendents data": -# '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 +# domains +# domains_collapsed +# seq_annotations +# go_term_ids +# user_selected +# +# 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 "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' +# # 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' -# To replace underscores with spaces during NH/NHX/Nexus file parsing (application only): -# 'replace_underscores_in_nh_parsing' -# To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694') -# during NH/NHX/Nexus file parsing (application only): 'extract_pfam_tax_codes_in_nh_parsing' -# Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only): -# 'internal_labels_are_confidence_values' - +# +# 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: +# 'replace_underscores_in_nh_parsing', possible values are 'yes', '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 +# phyloXML applications and to detect malformatted and +# possibly erroneous data, it is strongly recommended +# to enable validation of all phyloXML files +# against the XSD Schema (see: http://www.phyloxml.org/), +# with: +# 'validate_against_phyloxml_xsd_schema: true' min_confidence_value: 0.0 -font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans +font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica font_size: 10 +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 -show_default_node_shapes: no -default_node_size: 6 -default_node_shape: circle -default_node_fill: gradient -taxonomy_colorize_node_shapes: no +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 @@ -118,29 +187,22 @@ 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 -# NH/NHX/Nexus file parsing (application only): +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 -extract_taxonomy_codes_in_nh_parsing: yes -ext_descendents_data_to_return: sequence_mol_seq - - -# phyloXML parsing -# ---------------- -# To ensure compatibility with all current and future -# phyloXML applications and to detect malformatted and -# possibly erroneous data, it is strongly recommended -# to enable validation of all phyloXML files -# against the XSD Schema (see: http://www.phyloxml.org/), -# with: -# 'validate_against_phyloxml_xsd_schema: true' - -validate_against_phyloxml_xsd_schema: true - +taxonomy_extraction_in_nh_parsing: no +validate_against_phyloxml_xsd_schema: true # Checkbox Display Selection @@ -157,31 +219,36 @@ 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 dynamically_hide_data: display yes -show_relation_confidence: display no +show_relation_confidence: display no show_properties: display no show_vector_data: display no + # Combo-box Display Selection # --------------------------- # Format: 'name: display/nodisplay' @@ -192,7 +259,10 @@ 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 @@ -201,6 +271,7 @@ click_to: paste_subtree display click_to: delete display click_to: add_new_node display click_to: edit_node_data display +click_to: select_nodes display click_to: get_ext_descendents_data display # Default click-to option (any of the above if set to "display") @@ -213,18 +284,21 @@ 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 @@ -247,40 +321,25 @@ 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) +# ----------------------------------------------------- +# To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes' -# Web Links -# --------- -# Format: web_link: -# E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB" -# is not used at the moment. -# corresponds to the element for , -# and to the of (see www.phyloxml.org). - -web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB -web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl -web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI -web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq -web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro -web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB -web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam -web_link: http://tolweb.org/ ToL tol -web_link: http://www.eol.org/pages/ EOL eol -web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot -web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi -web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID -# not working at the moment: -web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl +midpoint_reroot: yes -# Settings Specific for ArchaeopteryxE -# ------------------------------------ +# Settings Specific for ArchaeopteryxE Applets +# -------------------------------------------- # To hide controls and menus: 'hide_controls_and_menus: yes' # To use tabbed display : 'use_tabbed_display: yes' @@ -295,81 +354,87 @@ use_tabbed_display: yes default_number_of_bootstrap_resamples: 100 mafft_local: /bin/mafft -clustalo_local: C:\Users\zma\SOFTWARE\clustal-omega-1.1.0-win32\clustalo.exe fastme_local: /bin/fastme raxml_local: /bin/raxml -# Application Specific Settings -# ----------------------------- + +# Sequence colors +# --------------- +# Format: species_color: sequencename hexcolor +sequence_color: Tubulin-alpha 0xEE0000 +sequence_color: Tubulin-beta 0x00EE00 + # Species colors # -------------- # Format: species_color: speciesname hexcolor -species_color: BRAFL 0x00FFFF -species_color: SPHGR 0x9620F0 -species_color: STRPU 0x9620F0 -species_color: CIOIN 0xFF1CAE -species_color: CIOSA 0xFF2CAE -species_color: BOVIN 0x5C3317 -species_color: CANFA 0x8B2323 -species_color: HUMAN 0xFF2400 -species_color: PANTR 0xCC2400 -species_color: MOUSE 0xFF7F00 -species_color: RAT 0xFFEF00 -species_color: MONDO 0xEE9A49 -species_color: ORNAN 0xCD853F -species_color: XENLA 0x6BAA23 -species_color: XENTR 0x6BAA23 -species_color: CHICK 0xFFC125 -species_color: FUGRU 0x0000FF -species_color: BRARE 0x0000DD -species_color: DANRE 0x0000BB -species_color: TETNG 0x0000AA -species_color: ORYLA 0x000088 -species_color: GASAC 0x000066 -species_color: CAEEL 0xA0A0A0 -species_color: CAEBR 0xB0B0B0 -species_color: DROME 0x706F00 -species_color: DROPS 0x504F00 -species_color: APIME 0x7A7700 -species_color: AEDAE 0x8C5900 -species_color: TRICA 0x918E00 -species_color: NEMVE 0xAABADD -species_color: HYDAT 0x7C9BCF -species_color: LUBBA 0xF7B5CB -species_color: GEOCY 0xF5A0BD -species_color: SUBDO 0xC790B9 -species_color: MONBE 0xFC0FC0 -species_color: DICPU 0x23238E -species_color: DICDI 0x4D4DFF -species_color: ENTHI 0x5959AB -species_color: ARATH 0x00FF00 -species_color: POPTR 0x006400 -species_color: VITVI 0x00CD00 -species_color: GLYMA 0x00FF7F -species_color: ORYSA 0x008B00 -species_color: ORYSJ 0x008C00 -species_color: SORBI 0x00EE76 -species_color: SELMO 0x238E23 -species_color: PHYPA 0x09F911 -species_color: OSTLU 0x7FFF00 -species_color: OSTTA 0x7FFF00 -species_color: OSTRC 0x7FFF00 -species_color: MICPU 0x66CD00 -species_color: MIC99 0x66CD00 -species_color: CHLRE 0xB3EE3A -species_color: VOLCA 0xC0FF3E -species_color: CHLSP 0x6B8E23 -species_color: CYAME 0xD02090 -species_color: YEAST 0xAAAAAA -species_color: BACFR 0xFF0000 -species_color: BACTN 0xFFFF00 -species_color: MYXXD 0x0000FF -species_color: STIAU 0x00FFFF -species_color: BACOV 0x8C5900 -species_color: BACUN 0x66CD00 -species_color: PORGI 0x918E00 +species_color: BRAFL 0x00FFFF +species_color: SPHGR 0x9620F0 +species_color: STRPU 0x9620F0 +species_color: CIOIN 0xFF1CAE +species_color: CIOSA 0xFF2CAE +species_color: BOVIN 0x5C3317 +species_color: CANFA 0x8B2323 +species_color: HUMAN 0xFF2400 +species_color: PANTR 0xCC2400 +species_color: MOUSE 0xFF7F00 +species_color: RAT 0xFFEF00 +species_color: MONDO 0xEE9A49 +species_color: ORNAN 0xCD853F +species_color: XENLA 0x6BAA23 +species_color: XENTR 0x6BAA23 +species_color: CHICK 0xFFC125 +species_color: FUGRU 0x0000FF +species_color: BRARE 0x0000DD +species_color: DANRE 0x0000BB +species_color: TETNG 0x0000AA +species_color: ORYLA 0x000088 +species_color: GASAC 0x000066 +species_color: CAEEL 0x666699 +species_color: CAEBR 0xB0B0B0 +species_color: DROME 0x663366 +species_color: DROPS 0x996699 +species_color: APIME 0x7A7700 +species_color: AEDAE 0x8C5900 +species_color: TRICA 0x918E00 +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 0xFFCC33 +species_color: DICDI 0xFFCC00 +species_color: ENTHI 0x5959AB +species_color: ARATH 0x00FF00 +species_color: POPTR 0x006400 +species_color: VITVI 0x00CD00 +species_color: GLYMA 0x00FF7F +species_color: ORYSA 0x008B00 +species_color: ORYSJ 0x008C00 +species_color: SORBI 0x00EE76 +species_color: SELMO 0x238E23 +species_color: PHYPA 0x09F911 +species_color: OSTLU 0x7FFF00 +species_color: OSTTA 0x7FFF00 +species_color: OSTRC 0x7FFF00 +species_color: MICPU 0x66CD00 +species_color: MIC99 0x66CD00 +species_color: CHLRE 0xB3EE3A +species_color: VOLCA 0xC0FF3E +species_color: CHLSP 0x6B8E23 +species_color: CYAME 0xD02090 +species_color: YEAST 0xAAAAAA +species_color: BACFR 0xFF0000 +species_color: BACTN 0xFFFF00 +species_color: MYXXD 0x0000FF +species_color: STIAU 0x00FFFF +species_color: BACOV 0x8C5900 +species_color: BACUN 0x66CD00 +species_color: PORGI 0x918E00 # rank: Class species_color: Mammalia 0xFF0000 species_color: mammals 0xFF0000 @@ -377,7 +442,7 @@ 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 @@ -404,63 +469,40 @@ 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: 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 -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: NOPS 0x505000 -domain_color: RRM_1 0x004400 -domain_color: fn3 0xFFCC00 -domain_color: Ank 0xCC33FF -domain_color: Pkinase 0x339900 -domain_color: Pkinase_Tyr 0x336600 -domain_color: ig 0x660066 -domain_color: zf-C3HC4 0x6699FF -domain_color: zf-CCHC 0x6699EE -domain_color: zf-C2H2 0x6699CC -domain_color: zf-B_box 0x6699DD -domain_color: PDZ 0x66FFCC -domain_color: SH3_2 0x996600 -domain_color: MIRO 0xCCFF00 -domain_color: Myb_DNA-binding 0xDDDDDD -domain_color: NHL 0x336666 -domain_color: PKD_channel 0x336666 -domain_color: Ion_trans 0x996666 -domain_color: CAP_GLY 0xCC9900 -domain_color: LRR_1 0xFFFF99 -domain_color: LRR_2 0xFFFF66 -domain_color: LRR_3 0xFFFF33 -domain_color: LRR_adjacent 0xFFFF00 -domain_color: LRRCT 0xFFCC99 -domain_color: LRRNT 0xFFCC66 -domain_color: LRRNT_2 0xFFCC33 -domain_color: Ank 0x990099 -domain_color: Sushi 0x004400 -domain_color: ZU5 0xFF9999 -domain_color: V-set 0x3399FF -domain_color: TPR_1 0xFF1493 -domain_color: TPR_2 0xFF69B4 -domain_color: TPR_3 0xCD6090 -domain_color: TPR_4 0xFF6A6A -domain_color: TPR_MLP1_2 0x33FF00 -domain_color: Collagen 0xFF7F00 -domain_color: MIF 0xADD8E6 # Annotation colors # ----------------- - annotation_color: dehydrogenase 0x0000FF annotation_color: kinase 0xFF00FF annotation_color: protease 0x009900