# Example: 'node_label_direction: horizontal'
# The two possible values are: horizontal
# radial
-# Show default node shape: 'show_default_node_shapes': values: 'yes'/'no'
+# 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'
# Possible values: solid
# gradient
# none
-# To determine what data field to return by clicking on "return external descendents data":
-# 'ext_descendents_data_to_return'
+#
+# 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
+# taxonomy_common_name
+# 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'
# 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'
+#
+# 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'
+
+validate_against_phyloxml_xsd_schema: true
min_confidence_value: 0.0
-font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
+font_family: Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
font_size: 10
+font_size_min: 2
+font_size_max: 20
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
+show_default_node_shapes_internal: no
+show_default_node_shapes_external: no
+default_node_size: 4
+default_node_shape: rectangle
+default_node_fill: solid
taxonomy_colorize_node_shapes: no
#graphics_export_x: 595
#graphics_export_y: 792
confidence_value_digits: 3
background_gradient: no
allow_editing: yes
-# NH/NHX/Nexus file parsing (application only):
+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
-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
+taxonomy_extraction_in_nh_parsing: no
# Checkbox Display Selection
show_binary_character_counts: display no
display_internal_data: display yes
dynamically_hide_data: display yes
-show_relation_confidence: display no
+show_relation_confidence: display no
show_properties: display no
show_vector_data: display no
+
# Combo-box Display Selection
# ---------------------------
# Format: 'name: display/nodisplay'
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
-#
-label_for_get_ext_descendents_data get_sequences
+
# Default Tree Display Colors
# ---------------------------
gui_button_border_color: 0x000000
+
# Domain Structure Display Colors
# -------------------------------
domain_structure_base_color: 0x202020
-# 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
-# ------------------------------------
+# 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'
default_number_of_bootstrap_resamples: 100
mafft_local: /bin/mafft
-clustalo_local: C:\Users\zma\SOFTWARE\clustal-omega-1.1.0-win32\clustalo.exe
fastme_local: /bin/fastme
raxml_local: /bin/raxml
-# 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
+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: Homo_sapiens 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
git://source.jalview.org / jalview.git / blobdiff