inprogress

[jalview.git] / forester / aptx / aptx_configuration_files / _aptx_configuration_file

diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
index 645d671..acf39bb 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -80,6 +80,7 @@ native_ui: ?
 #                      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'
@@ -107,9 +108,13 @@ native_ui: ?
 #  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'
+#  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'
@@ -162,12 +167,12 @@ confidence_value_digits:                   3
 background_gradient:                       no
 allow_editing:                             yes
 ext_descendents_data_to_return_on:         window
-ext_descendents_data_to_return:            sequence_mol_seq_fasta
+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
-taxonomy_extraction_in_nh_parsing:         yes
+taxonomy_extraction_in_nh_parsing:         no
 
 
 #  Checkbox Display Selection