--- /dev/null
++# PLEASE DON'T MOVE ME
+# 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: yes
+
+
+
+# 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: 12
+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: yes
+show_default_node_shapes_external: yes
+show_node_shapes_for_nodes_with_vis_data: yes
+default_node_size: 5
+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_right
+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 yes
+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 0xFFFFFF
+display_color: background_gradient_bottom 0xFFFFFF
+display_color: sequence 0x111111
+display_color: taxonomy 0x8D8D8D
+display_color: confidence 0xAEAEAE
+display_color: branch_length 0x3A3A3A
+display_color: branch 0x000000
+display_color: node_box 0x000000
+display_color: collapsed 0x000000
+display_color: matching_a 0xCC6600
+display_color: matching_b 0x0000CC
+display_color: matching_a_and_b 0xCC70CC
+display_color: duplication 0xFF00FF
+display_color: speciation 0xFFFF00
+display_color: duplication_or_specation 0xFFAA20
+display_color: domain_label 0x939393
+display_color: domain_base 0x505050
+display_color: binary_domain_combinations 0x4169FF
+display_color: annotation 0xFFCC00
+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
git://source.jalview.org / jalview.git / commitdiff