work on taxonomy extraction for applets for aLeaves MAFFT suite

diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
index 5d721dd..36217a6 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -97,12 +97,15 @@ native_ui: ?
 #
 #  NH/NHX/Nexus file parsing
 #  -------------------------
-#  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): 'taxonomy_extraction_in_nh_parsing'
-#  Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only):
-#     'internal_labels_are_confidence_values'
+#  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'
 
 
 
@@ -148,14 +151,13 @@ branch_length_value_digits:                3
 confidence_value_digits:                   3
 background_gradient:                       no
 allow_editing:                             yes
-#  NH/NHX/Nexus file parsing (application only):
-internal_labels_are_confidence_values:     no
-replace_underscores_in_nh_parsing:         no
-taxonomy_extraction_in_nh_parsing:         pfam
 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
+taxonomy_extraction_in_nh_parsing:         pfam
 
 
 #  Checkbox Display Selection

diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
index aafebdb..69cf370 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
@@ -94,12 +94,18 @@ native_ui: ?
 #     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'
 
 
 
@@ -131,13 +137,13 @@ branch_length_value_digits:                3
 confidence_value_digits:                   3
 background_gradient:                       no
 allow_editing:                             yes
-#  NH/NHX/Nexus file parsing (application only):
-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:         window
-ext_descendents_data_to_return:            node_name
+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:         pfam