+++ /dev/null
-# 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,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):
-# 'graphics_export_x: 595'
-# 'graphics_export_y: 845'
-# 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
-# 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 "Return ...": 'ext_descendents_data_to_return'
-# Possible values: node_name
-# sequence_name
-# sequence_acc
-# sequence_mol_seq
-# sequence_mol_seq_fasta
-# sequence_symbol
-# taxonomy_scientific_name
-# taxonomy_code
-# user_selected
-#
-# To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on'
-# 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'
-#
-# 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'
-# 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'
-#
-# 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'
-
-
-
-min_confidence_value: 0.0
-font_family: Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
-font_size: 10
-antialias_screen: yes
-show_scale: yes
-cladogram_type: ext_node_sum_dep
-phylogeny_graphics_type: rectangular
-node_label_direction: horizontal
-show_default_node_shapes_internal: no
-show_default_node_shapes_external: no
-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
-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: no
-right_align_domain_architectures: no
-branch_length_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: Get_Node_Data
-# NH/NHX/Nexus file parsing:
-internal_labels_are_confidence_values: no
-replace_underscores_in_nh_parsing: no
-taxonomy_extraction_in_nh_parsing: pfam_relaxed
-
-
-
-# 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
-
-
-
-# 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: nodisplay no
-show_node_names: display yes
-show_gene_names: display yes
-show_gene_symbols: nodisplay no
-show_sequence_acc: nodisplay no
-show_taxonomy_code: display yes
-show_taxonomy_scientific_names: nodisplay no
-show_taxonomy_common_names: nodisplay no
-show_taxonomy_images: nodisplay no
-show_annotations: nodisplay no
-write_confidence_values: display ?
-write_branch_length_values: display no
-write_events: nodisplay no
-use_visual_styles: display no
-width_branches: display no
-show_domain_architectures: nodisplay no
-show_msa: nodisplay no
-show_binary_characters: nodisplay no
-show_binary_character_counts: nodisplay no
-display_internal_data: display yes
-dynamically_hide_data: display yes
-show_relation_confidence: nodisplay no
-show_properties: nodisplay no
-show_vector_data: nodisplay no
-
-
-# Combo-box Display Selection
-# ---------------------------
-# Format: 'name: display/nodisplay'
-click_to: display_node_data display
-click_to: collapse_uncollapse display
-click_to: reroot display
-click_to: subtree display
-click_to: swap display
-click_to: sort_descendants display
-click_to: color_subtree display
-click_to: open_seq_web nodisplay
-click_to: open_pdb_web nodisplay
-click_to: open_tax_web nodisplay
-click_to: blast nodisplay
-click_to: cut_subtree nodisplay
-click_to: copy_subtree nodisplay
-click_to: paste_subtree nodisplay
-click_to: delete nodisplay
-click_to: add_new_node nodisplay
-click_to: edit_node_data display
-click_to: select_nodes nodisplay
-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
-
-
-
-# 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
-
-
-
-# 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
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff