From bfce447df472221a32215b465c5bb236250230cb Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 4 Oct 2012 02:04:11 +0000 Subject: [PATCH] in progress --- .../_aptx_configuration_file_1 | 69 ++++++++++---------- 1 file changed, 35 insertions(+), 34 deletions(-) diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 index 5f7c0a7..beaacc4 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 @@ -69,8 +69,8 @@ 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 @@ -78,6 +78,12 @@ native_ui: ? # 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' @@ -128,7 +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 @@ -158,29 +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: nodisplay no -show_domain_architectures: nodisplay no -show_binary_characters: nodisplay no -show_binary_character_counts: nodisplay no +width_branches: display 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 @@ -196,11 +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 @@ -247,11 +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 @@ -290,8 +293,6 @@ use_tabbed_display: yes - - # Application Specific Settings # ----------------------------- @@ -396,4 +397,4 @@ species_color: Archaea 0x0000FF species_color: Eukaryota 0xFF0000 species_color: eukaryotes 0xFF0000 -# END +# END \ No newline at end of file -- 1.7.10.2