# Possible values: solid
# gradient
# none
+#
+# 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_symbol
+# taxonomy_scientific_name
+# taxonomy_code
+# 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) from node names during NH/NHX/Nexus file parsing:
+# 'taxonomy_extraction_in_nh_parsing',
+# possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), 'no'
+#
+# 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
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
-
-
-
-# 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: pfam
# Checkbox Display Selection
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: 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 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: 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 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
gui_button_border_color: 0x000000
+
# Domain Structure Display Colors
# -------------------------------
domain_structure_base_color: 0x202020
# EXPERIMENTAL: DO NOT USE!!
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
domain_color: NB-ARC 0x500050
domain_color: WD40 0x888888
domain_color: RVT_1 0x999900
-domain_color: NOPS 0x505000
-domain_color: RRM_1 0x004400
-domain_color: fn3 0xFFCC00
-domain_color: Ank 0xCC33FF
-domain_color: Pkinase 0x339900
-domain_color: Pkinase_Tyr 0x336600
-domain_color: ig 0x660066
-domain_color: zf-C3HC4 0x6699FF
-domain_color: zf-CCHC 0x6699EE
-domain_color: zf-C2H2 0x6699CC
-domain_color: zf-B_box 0x6699DD
-domain_color: PDZ 0x66FFCC
-domain_color: SH3_2 0x996600
-domain_color: MIRO 0xCCFF00
-domain_color: Myb_DNA-binding 0xDDDDDD
-domain_color: NHL 0x336666
-domain_color: PKD_channel 0x336666
-domain_color: Ion_trans 0x996666
-domain_color: CAP_GLY 0xCC9900
-domain_color: LRR_1 0xFFFF99
-domain_color: LRR_2 0xFFFF66
-domain_color: LRR_3 0xFFFF33
-domain_color: LRR_adjacent 0xFFFF00
-domain_color: LRRCT 0xFFCC99
-domain_color: LRRNT 0xFFCC66
-domain_color: LRRNT_2 0xFFCC33
-domain_color: Ank 0x990099
-domain_color: Sushi 0x004400
-domain_color: ZU5 0xFF9999
-domain_color: V-set 0x3399FF
-domain_color: TPR_1 0xFF1493
-domain_color: TPR_2 0xFF69B4
-domain_color: TPR_3 0xCD6090
-domain_color: TPR_4 0xFF6A6A
-domain_color: TPR_MLP1_2 0x33FF00
-domain_color: Collagen 0xFF7F00
-domain_color: MIF 0xADD8E6
+
# Annotation colors
git://source.jalview.org / jalview.git / blobdiff