From 10cf37eee3568e62a565136d9a8894dc7c820924 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Thu, 27 Sep 2012 05:23:34 +0000 Subject: [PATCH] more simple --- .../_aptx_configuration_file_1 | 397 ++++++++++++++++++++ 1 file changed, 397 insertions(+) create mode 100644 forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 new file mode 100644 index 0000000..d1a70da --- /dev/null +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 @@ -0,0 +1,397 @@ +# 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: +# E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB" +# is not used at the moment. +# corresponds to the element for , +# and to the of (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 -- 1.7.10.2