diff options
Diffstat (limited to 'academic/archeopteryx/_aptx_configuration_file.txt')
| -rw-r--r-- | academic/archeopteryx/_aptx_configuration_file.txt | 502 |
1 files changed, 0 insertions, 502 deletions
diff --git a/academic/archeopteryx/_aptx_configuration_file.txt b/academic/archeopteryx/_aptx_configuration_file.txt deleted file mode 100644 index a7230a4272..0000000000 --- a/academic/archeopteryx/_aptx_configuration_file.txt +++ /dev/null @@ -1,502 +0,0 @@ -# User Interface Look and Feel -# ---------------------------- -# Possible values for 'native_ui' -# 'yes' to use native (system) "look and feel" -# 'no' to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below) -# '?' to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected, -# Archaeopteryx-style "look and feel" otherwise - -native_ui: ? - - - -# Default Values for Options -# -------------------------- -# 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_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. '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' -# -# Cladogram display type: 'cladogram_type' -# 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' -# -# 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 -# euro_style -# rounded -# curved -# triangular -# 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 -# gradient -# none -# -# 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_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 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: 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 -cladogram_type: non_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 -pdf_export_line_width: 0.5 -show_overview: yes -overview_width: 120 -overview_height: 120 -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: 2 -background_gradient: no -allow_editing: yes -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 - - -# Checkbox Display Selection -# -------------------------- -# This is used to select which checkboxes to display -# and what their initial values should be. -# Format: 'name: display|nodisplay yes|no' -# Note: if an option is not displayed, it will not be enabled -# -# For the following use '?' to let Archaeopteryx decide (depending on tree): -# - 'phylogram' -# - 'write_confidence_values' -# - 'write_events' - -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 -show_seq_names: display yes -show_seq_symbols: display yes -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 -dynamically_hide_data: display yes -show_relation_confidence: display no -show_properties: display no -show_vector_data: display no - - - -# Combo-box Display Selection -# --------------------------- -# 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 -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 -click_to: copy_subtree display -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") -default_click_to: display_node_data - - - -# Default Tree Display Colors -# --------------------------- - -display_color: background 0x000000 -display_color: background_gradient_bottom 0x0000FF -display_color: sequence 0xE6E6E6 -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 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: domain_label 0xE6E6E6 -display_color: domain_base 0x646464 -display_color: binary_domain_combinations 0x4169FF -display_color: annotation 0xADFF2F -display_color: overview 0x828282 - - - -# GUI (graphical user interface) Colors -# ------------------------------------- -# -# These are ignored if native (system) "look and feel" -# is being used ('native_ui: yes'). - -gui_background_color: 0x202020 -gui_checkbox_text_color: 0xDCDCDC -gui_checkbox_and_button_active_color: 0xFF0000 -gui_button_text_color: 0xFFFFFF -gui_button_background_color: 0x404040 -gui_menu_background_color: 0x000000 -gui_menu_text_color: 0xFFFFFF -gui_button_border_color: 0x000000 - - -# 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' - -midpoint_reroot: yes - - - -# Settings Specific for ArchaeopteryxE Applets -# -------------------------------------------- -# To hide controls and menus: 'hide_controls_and_menus: yes' -# To use tabbed display : 'use_tabbed_display: yes' - -hide_controls_and_menus: no -use_tabbed_display: yes - - - -# Settings For Phylogenetic Inference -# ----------------------------------- -# EXPERIMENTAL: DO NOT USE!! - -default_number_of_bootstrap_resamples: 100 -mafft_local: /bin/mafft -fastme_local: /bin/fastme -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 -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 -# rank: Phylum -species_color: Chordata 0x8470FF -species_color: Echinodermata 0x6495ED -species_color: Hemichordata 0x7EC0EE -species_color: Arthropoda 0x7AC5CD -species_color: Nematoda 0x7171C6 -species_color: Tardigrada 0x388E8E -species_color: Annelida 0xC67171 -species_color: Mollusca 0x00F5FF -species_color: Ctenophora 0xBBFFFF -species_color: Cnidaria 0xFF83FA -species_color: Placozoa 0xEED2EE -species_color: Porifera 0xFF3E96 -species_color: Microsporidia 0x8B8378 -species_color: Ascomycota 0xFF6347 -species_color: Basidiomycota 0xFFD700 -species_color: Chlorophyta 0x00C78C -species_color: Streptophyta 0x00C957 -# rank: Kingdom -species_color: Viridiplantae 0x00FF00 -species_color: plants 0x00FF00 -species_color: Metazoa 0x0000FF -species_color: animals 0x0000FF -species_color: Fungi 0xFF9912 -# rank: Superkingdom -species_color: Viruses 0xFFD700 -species_color: Bacteria 0x00FF00 -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 - - - -# Annotation colors -# ----------------- -annotation_color: dehydrogenase 0x0000FF -annotation_color: kinase 0xFF00FF -annotation_color: protease 0x009900 -annotation_color: transcription 0xAAAA00 - - -# END |