in progress

[jalview.git] / forester / aptx / aptx_configuration_files / _aptx_configuration_file_1

diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
index d1a70da..beaacc4 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
@@ -69,13 +69,21 @@ 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
+#  To determine where to return data by clicking on "Return ...": 'ext_descendents_data_to_return_on'
+#     Possible values: window
+#                      console
+#  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'
@@ -126,7 +134,9 @@ allow_editing:                             yes
 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
+ext_descendents_data_to_return_on:         console
+ext_descendents_data_to_return:            node_name
+#label_for_get_ext_descendents_data:        Get_Node_Data         
 
 
 #  phyloXML parsing
@@ -156,29 +166,29 @@ validate_against_phyloxml_xsd_schema: true
 
 phylogram:                      display   ?
 rollover:                       display   yes
-color_according_to_species:     nodisplay   no
-color_according_to_annotation:  nodisplay   no
+color_according_to_species:     display   no
+color_according_to_annotation:  nodisplay no
 show_node_names:                display   yes
-show_gene_names:                nodisplay   no
-show_gene_symbols:              nodisplay   no
-show_sequence_acc:              nodisplay   no
-show_taxonomy_code:             nodisplay   no
-show_taxonomy_scientific_names: nodisplay   no
-show_taxonomy_common_names:     nodisplay   no
-show_taxonomy_images:           nodisplay   no
-show_annotations:               nodisplay   no
+show_gene_names:                display   yes
+show_gene_symbols:              nodisplay no
+show_sequence_acc:              nodisplay no
+show_taxonomy_code:             display   yes
+show_taxonomy_scientific_names: nodisplay no
+show_taxonomy_common_names:     nodisplay no
+show_taxonomy_images:           nodisplay no
+show_annotations:               nodisplay no
 write_confidence_values:        display   ?
-write_events:                   nodisplay   no
+write_events:                   nodisplay no
 color_branches:                 display   no
 width_branches:                 display   no
-show_domain_architectures:      nodisplay   no
-show_binary_characters:         nodisplay   no
-show_binary_character_counts:   nodisplay   no
+show_domain_architectures:      nodisplay no
+show_binary_characters:         nodisplay no
+show_binary_character_counts:   nodisplay no
 display_internal_data:          display   yes
 dynamically_hide_data:          display   yes
-show_relation_confidence:       nodisplay   no
-show_properties:                nodisplay   no
-show_vector_data:               nodisplay   no
+show_relation_confidence:       nodisplay no
+show_properties:                nodisplay no
+show_vector_data:               nodisplay no
 
 
 #  Combo-box Display Selection
@@ -194,11 +204,11 @@ click_to: color_subtree            display
 click_to: open_seq_web             nodisplay
 click_to: open_tax_web             nodisplay
 click_to: blast                    nodisplay
-click_to: cut_subtree              display
-click_to: copy_subtree             display
-click_to: paste_subtree            display
-click_to: delete                   display
-click_to: add_new_node             display
+click_to: cut_subtree              nodisplay
+click_to: copy_subtree             nodisplay
+click_to: paste_subtree            nodisplay
+click_to: delete                   nodisplay
+click_to: add_new_node             nodisplay
 click_to: edit_node_data           display
 click_to: get_ext_descendents_data display
 
@@ -245,11 +255,6 @@ gui_menu_text_color:                  0xFFFFFF
 gui_button_border_color:              0x000000
 
 
-#  Domain Structure Display Colors
-#  -------------------------------
-domain_structure_base_color:          0x202020
-domain_structure_font_color:          0x909090
-
 
 
 #  Web Links
@@ -288,8 +293,6 @@ use_tabbed_display:      yes
 
 
 
-
-
 #  Application Specific Settings
 #  -----------------------------
 
@@ -394,4 +397,4 @@ species_color: Archaea        0x0000FF
 species_color: Eukaryota      0xFF0000
 species_color: eukaryotes     0xFF0000
 
-# END
+# END
\ No newline at end of file