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 937f8fd..76e4617 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -69,13 +69,27 @@ native_ui: ?
 #     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'
@@ -85,12 +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
 
 
 
@@ -122,25 +156,13 @@ branch_length_value_digits:                3
 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
-
-
-#  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
-
+taxonomy_extraction_in_nh_parsing:         pfam
 
 
 #  Checkbox Display Selection
@@ -182,6 +204,7 @@ show_properties:                display   no
 show_vector_data:               display   no
 
 
+
 #  Combo-box Display Selection
 #  ---------------------------
 #  Format: 'name: display/nodisplay'
@@ -201,6 +224,7 @@ click_to: paste_subtree            display
 click_to: delete                   display
 click_to: add_new_node             display
 click_to: edit_node_data           display
+click_to: select_nodes             display
 click_to: get_ext_descendents_data display
 
 #   Default click-to option (any of the above if set to "display")
@@ -247,6 +271,7 @@ gui_menu_text_color:                  0xFFFFFF
 gui_button_border_color:              0x000000
 
 
+
 #  Domain Structure Display Colors
 #  -------------------------------
 domain_structure_base_color:          0x202020