X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file;h=76e4617d23340044d7a251ca6e8d9435ff795048;hb=ea9680e31258a26c47104bd8c38812d583669977;hp=fa77d1e952609160fbcb2f421786af1892533f12;hpb=4a093bc9b8f77665116721065802efeca131b301;p=jalview.git

diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
index fa77d1e..76e4617 100644
--- 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'
 # 
@@ -97,12 +102,15 @@ 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'
 
 
 
@@ -148,18 +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
-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