--- /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: 'show_default_node_shapes': 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'
+# Possible values: node_name
+# sequence_name
+# sequence_acc
+# sequence_mol_seq
+# sequence_symbol
+# 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'
+# 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'
+
+
+
+min_confidence_value: 0.0
+font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
+font_size: 10
+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
+#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
+branch_length_value_digits: 3
+confidence_value_digits: 3
+background_gradient: no
+allow_editing: yes
+# NH/NHX/Nexus file parsing (application only):
+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_name
+
+
+# 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_species: nodisplay no
+color_according_to_annotation: nodisplay no
+show_node_names: display yes
+show_gene_names: nodisplay no
+show_gene_symbols: nodisplay no
+show_sequence_acc: nodisplay no
+show_taxonomy_code: nodisplay no
+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_events: nodisplay no
+color_branches: display no
+width_branches: display no
+show_domain_architectures: 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_tax_web nodisplay
+click_to: blast nodisplay
+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: 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 0xDCDCDC
+display_color: taxonomy 0xB4B4B4
+display_color: confidence 0x38B0DE
+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: duplication 0xFF0000
+display_color: speciation 0x00FF00
+display_color: duplication_or_specation 0xFFFF00
+display_color: domains 0x7B68EE
+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
+
+
+# Domain Structure Display Colors
+# -------------------------------
+domain_structure_base_color: 0x202020
+domain_structure_font_color: 0x909090
+
+
+
+# Web Links
+# ---------
+# Format: web_link: <URL> <description> <source identifier>
+# E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
+# <description> is not used at the moment.
+# <source identifier> corresponds to the <source> element for <sequence> <accession>,
+# and to the <type> of <taxonomy> <id> (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
+
+
+
+# Settings Specific for ArchaeopteryxE
+# ------------------------------------
+# 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
+
+
+
+
+
+
+# Application Specific Settings
+# -----------------------------
+
+# 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
+# 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
+
+# END
git://source.jalview.org / jalview.git / commitdiff