From: cmzmasek@gmail.com Date: Wed, 25 Sep 2013 00:43:28 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f767e459c55061d7769189c3460ada0f23f4493a;p=jalview.git inprogress --- diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index acf39bb..2b179ee 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file @@ -15,23 +15,31 @@ native_ui: ? # Minimal confidence value to be displayed: 'min_confidence_value': # Example: 'min_confidence_value: 50.0' (a commonly used # value for bootstrap support) +# # Font family name: 'font_family': # Example: 'font_family: Arial,Calibri,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'). +# # Font size: 'font_size': # Example: 'font_size: 10' +# # Screen antialias: 'antialias_screen': values: 'yes'/'no' +# # Show Scale: 'show_scale': values: 'yes'/'no' +# # Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no' +# # Do/do not line up cladogram display: 'non_lined_up_cladogram': values: 'yes'/'no' +# # Cladogram display type: 'cladogram_type' # Example: 'cladogram_type: ext_node_sum_dep' # The three possible values are: non_lined_up # ext_node_sum_dep # total_node_sum_dep (for "uniform" branch lengths) +# # Default size for graphics export and printing: 'graphics_export_x' and 'graphics_export_y': # (Archaeopteryx tries to guess the locale, so setting these is not always necessary) # Example: For A4 (portrait): @@ -40,9 +48,12 @@ native_ui: ? # For US Letter (portrait): # 'graphics_export_x: 612' # 'graphics_export_y: 792' +# # Default line width for PDF export: 'pdf_export_line_wdith': # Example: 'pdf_export_line_width: 0.5' +# # Show overview: 'show_overview': values: 'yes'/'no' +# # Phylogeny graphics type: 'phylogeny_graphics_type': # Example: 'phylogeny_graphics_type: euro_style' # The eight possible values are: rectangular @@ -53,18 +64,24 @@ native_ui: ? # convex # unrooted # circular +# # Node label direction for circular and unrooted type: 'node_label_direction': # Example: 'node_label_direction: horizontal' # The two possible values are: horizontal # radial +# # Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no' +# # Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no' +# # Default node shape size: 'default_node_size' # Example: 'default_node_size: 6' +# # Default node shape type: 'default_node_shape' # Example: 'default_node_shape: ' # Possible values: circle # rectangle +# # Default node shape fill: 'default_node_fill' # Example: 'default_node_fill: ' # Possible values: solid @@ -94,12 +111,20 @@ native_ui: ? # 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' +# +# Do/not show reference sources for sequence annotation: 'show_seq_annotation_ref_sources': values: 'yes'/'no' +# # Number of fraction digits for branch length values: 'branch_length_value_digits' +# # Number of fraction digits for confidence values: 'confidence_value_digits' +# # To turn on/off background color gradient: background_gradient # Example: 'background_gradient: yes' +# # To allow/not allow editing (cut, copy, and paste): allow_editing # Example: 'allow_editing: yes' # @@ -118,9 +143,7 @@ native_ui: ? # # 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 @@ -131,9 +154,6 @@ native_ui: ? # with: # 'validate_against_phyloxml_xsd_schema: true' -validate_against_phyloxml_xsd_schema: true - - min_confidence_value: 0.0 font_family: Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans @@ -162,17 +182,19 @@ overview_placement_type: upper_left color_labels_same_as_branch_length_values: no display_sequence_relations: no show_domain_labels: yes +show_seq_annotation_ref_sources: yes branch_length_value_digits: 3 confidence_value_digits: 3 background_gradient: no allow_editing: yes ext_descendents_data_to_return_on: window ext_descendents_data_to_return: user_selected -#label_for_get_ext_descendents_data: Get_Node_Data +#label_for_get_ext_descendents_data: Return_Node_Data # NH/NHX/Nexus file parsing: internal_labels_are_confidence_values: no replace_underscores_in_nh_parsing: no taxonomy_extraction_in_nh_parsing: no +validate_against_phyloxml_xsd_schema: true # Checkbox Display Selection