# 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_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'
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
+taxonomy_extraction_in_nh_parsing: pfam
+
# phyloXML parsing
validate_against_phyloxml_xsd_schema: true
+
# Checkbox Display Selection
# --------------------------
# This is used to select which checkboxes to display
phylogram: display ?
rollover: display yes
-color_according_to_species: nodisplay no
-color_according_to_annotation: nodisplay no
+color_according_to_species: display 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
+show_gene_names: display yes
+show_gene_symbols: nodisplay no
+show_sequence_acc: nodisplay no
+show_taxonomy_code: display yes
+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
+write_events: nodisplay no
color_branches: display no
-width_branches: nodisplay no
-show_domain_architectures: nodisplay no
-show_binary_characters: nodisplay no
-show_binary_character_counts: nodisplay 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
+show_relation_confidence: nodisplay no
+show_properties: nodisplay no
+show_vector_data: nodisplay no
# Combo-box Display Selection
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: cut_subtree nodisplay
+click_to: copy_subtree nodisplay
+click_to: paste_subtree nodisplay
+click_to: delete nodisplay
+click_to: add_new_node nodisplay
click_to: edit_node_data display
+click_to: select_nodes nodisplay
click_to: get_ext_descendents_data display
# Default click-to option (any of the above if set to "display")
gui_button_border_color: 0x000000
-# Domain Structure Display Colors
-# -------------------------------
-domain_structure_base_color: 0x202020
-domain_structure_font_color: 0x909090
-
# Web Links
-
-
# Application Specific Settings
# -----------------------------
species_color: Eukaryota 0xFF0000
species_color: eukaryotes 0xFF0000
-# END
+# END
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff