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slackbuilds_ponce/academic/archeopteryx/_aptx_configuration_file.txt
Petar Petrov 3a448854ee
academic/archeopteryx: Updated for version 0.9917_beta. 
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
2016-12-03 07:17:45 +07:00

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# 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
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