new itext version, plus minor changes

[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 b2c18ad..2ca3dc7 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -17,11 +17,11 @@ native_ui: ?
 #     value for bootstrap support)
 #
 #  Font family name: 'font_family':
-#     Example: 'font_family: Arial,Calibri,Helvetica'
+#     Example: 'font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica'
 #     It is advisable to use more than one value for font_family (in
 #     decreasing order of preference). Font family names have to be
 #     comma separated (no spaces). Spaces in font names have to be
-#     replaced by underscores (e.g. 'Times_New_Roman').
+#     replaced by underscores (e.g. 'Arial_Unicode_MS').
 #
 #  Font size: 'font_size':
 #     Example: 'font_size: 10'
@@ -88,32 +88,30 @@ native_ui: ?
 #                      gradient
 #                      none
 #
-#  To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return'
+#  To determine what data field to return by clicking on "List Node Data": 'list_node_data_field'
 #     Possible values: node_name
 #                      sequence_name
 #                      gene_name
 #                      sequence_acc
-#                      sequence_mol_seq
 #                      sequence_mol_seq_fasta
 #                      sequence_symbol
 #                      taxonomy_scientific_name
 #                      taxonomy_code
-#                      taxonomy_common_name
-#                      user_selected
 #                      domains
 #                      domains_collapsed
 #                      seq_annotations
 #                      go_term_ids
+#                      user_selected
 #
-#  To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on'
+#  To determine where to return data selected by user clicking on "List Node Data": 'list_node_data_in'
 #     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'
+#  To override label for menu item to return data of external nodes (default "List Node Data"): 'list_node_data_custom_label'
+#     Example: 'list_node_data_custom_label: Get_Node_Data'
 # 
 #  Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
 #
@@ -164,7 +162,7 @@ native_ui: ?
 
 
 min_confidence_value:                      0.0
-font_family:                               Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
+font_family:                               Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica
 font_size:                                 10
 font_size_min:                             2
 font_size_max:                             20
@@ -197,9 +195,9 @@ confidence_value_digits:                   2
 background_gradient:                       no
 allow_editing:                             yes
 allow_thick_strokes:                       no
-ext_descendents_data_to_return_on:         window
-ext_descendents_data_to_return:            user_selected
-#label_for_get_ext_descendents_data:        Return_Node_Data         
+list_node_data_in:                         window
+list_node_data_field:                      user_selected
+list_node_data_custom_label:         
 #  NH/NHX/Nexus file parsing:
 internal_labels_are_confidence_values:     no
 replace_underscores_in_nh_parsing:         no