# 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'
#
# 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'
# 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'
#
min_confidence_value: 0.0
-font_family: Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
-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
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
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
taxonomy_extraction_in_nh_parsing: no
+# phyloXML parsing:
validate_against_phyloxml_xsd_schema: true
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
# 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