# sequence_symbol
# taxonomy_scientific_name
# taxonomy_code
-# To determine where to return data by clicking on "Return ...": 'ext_descendents_data_to_return_on'
-# Possible values: window
-# console
+# 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'
#
# 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_on: console
-ext_descendents_data_to_return: node_name
-#label_for_get_ext_descendents_data: Get_Node_Data
+taxonomy_extraction_in_nh_parsing: pfam
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")