work on data buffer for aLeaves MAFFT suite + clean up

[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 72b1b5f..76e4617 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -79,9 +79,14 @@ native_ui: ?
 #                      taxonomy_scientific_name
 #                      taxonomy_code
 #                      user_selected
-#  To determine where to return data by clicking on "Return ...": 'ext_descendents_data_to_return_on'
-#     Possible values: window
-#                      console
+#
+#  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'
 # 
@@ -94,12 +99,32 @@ 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'
+
+
+
+#  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
 
 
 
@@ -131,28 +156,13 @@ 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:            user_selected
 #label_for_get_ext_descendents_data:        Get_Node_Data         
-
-
-
-#  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
-
+#  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