in progress...

[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 1ffa5d8..cb99cab 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: Sans,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'
@@ -32,22 +32,10 @@ native_ui: ?
 #
 #  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):
-#               'graphics_export_x: 595'
-#               'graphics_export_y: 845'
-#             For US Letter (portrait):
-#               'graphics_export_x: 612'
-#               'graphics_export_y: 792'
+#     Example: 'cladogram_type: non_lined_up'
+#     The three possible values are: lined_up
+#                                    non_lined_up
 #
 #  Default line width for PDF export: 'pdf_export_line_wdith':
 #     Example: 'pdf_export_line_width: 0.5'
@@ -162,13 +150,13 @@ native_ui: ?
 
 
 min_confidence_value:                      0.0
-font_family:                               SansSerif,Sans-serif,Sans,Dialog,Tahoma,Helvetica,Arial,Verdana
-font_size:                                 10
+font_family:                               Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica
+font_size:                                 11
 font_size_min:                             2
 font_size_max:                             20
 antialias_screen:                          yes
 show_scale:                                yes
-cladogram_type:                            ext_node_sum_dep
+cladogram_type:                            lined_up
 phylogeny_graphics_type:                   rectangular
 node_label_direction:                      horizontal
 show_default_node_shapes_internal:         no
@@ -177,8 +165,6 @@ show_node_shapes_for_nodes_with_vis_data:  yes
 default_node_size:                         4
 default_node_shape:                        rectangle
 default_node_fill:                         solid
-#graphics_export_x:                         595
-#graphics_export_y:                         792
 pdf_export_line_width:                     0.5
 show_overview:                             yes
 overview_width:                            120
@@ -202,6 +188,7 @@ list_node_data_custom_label:
 internal_labels_are_confidence_values:     no
 replace_underscores_in_nh_parsing:         no
 taxonomy_extraction_in_nh_parsing:         no
+#  phyloXML parsing:
 validate_against_phyloxml_xsd_schema:      true
 
 
@@ -229,6 +216,7 @@ show_seq_acc:                   display   no
 show_gene_names:                display   yes
 show_taxonomy_code:             display   yes
 show_taxonomy_scientific_names: display   yes
+show_taxonomy_rank:             display   no
 show_taxonomy_common_names:     display   no
 show_taxonomy_images:           display   no
 show_annotations:               display   no
@@ -254,9 +242,11 @@ show_vector_data:               display   no
 #  Format: 'name: display/nodisplay'
 click_to: display_node_data        display
 click_to: collapse_uncollapse      display
+click_to: uncollapse_all           display
 click_to: reroot                   display
 click_to: subtree                  display
 click_to: swap                     display
+click_to: order_subtree            display
 click_to: sort_descendants         display
 click_to: color_subtree            display
 click_to: change_node_font         display