# 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
+# 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'
#
# To allow/not allow editing (cut, copy, and paste): allow_editing
# Example: 'allow_editing: yes'
#
+# To allow/not allow thicker strokes for very small trees: allow_thick_strokes
+# Example: 'allow_thick_strokes: yes'
+#
# NH/NHX/Nexus file parsing
# -------------------------
# To replace underscores with spaces during NH/NHX/Nexus file parsing:
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
-show_branch_length_values: no
-cladogram_type: ext_node_sum_dep
+cladogram_type: lined_up
phylogeny_graphics_type: rectangular
node_label_direction: horizontal
show_default_node_shapes_internal: no
show_default_node_shapes_external: no
+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
color_labels_same_as_branch_length_values: no
display_sequence_relations: no
show_domain_labels: yes
+line_up_renderable_data: yes
+right_align_domain_architectures: no
show_seq_annotation_ref_sources: yes
branch_length_value_digits: 3
-confidence_value_digits: 3
+confidence_value_digits: 2
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: Return_Node_Data
+allow_thick_strokes: no
+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
write_confidence_values: display ?
+write_branch_length_values: display no
write_events: display ?
use_visual_styles: display no
width_branches: display no
show_domain_architectures: display no
+show_msa: display no
show_binary_characters: display no
show_binary_character_counts: display no
display_internal_data: display yes
# 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
species_color: BOVIN 0x5C3317
species_color: CANFA 0x8B2323
species_color: HUMAN 0xFF2400
-species_color: Homo_sapiens 0xFF2400
species_color: PANTR 0xCC2400
species_color: MOUSE 0xFF7F00
species_color: RAT 0xFFEF00
species_color: TETNG 0x0000AA
species_color: ORYLA 0x000088
species_color: GASAC 0x000066
-species_color: CAEEL 0xA0A0A0
+species_color: CAEEL 0x666699
species_color: CAEBR 0xB0B0B0
-species_color: DROME 0x706F00
-species_color: DROPS 0x504F00
+species_color: DROME 0x663366
+species_color: DROPS 0x996699
species_color: APIME 0x7A7700
species_color: AEDAE 0x8C5900
species_color: TRICA 0x918E00
-species_color: NEMVE 0xAABADD
-species_color: HYDAT 0x7C9BCF
+species_color: NEMVE 0x0066CC
+species_color: HYDAT 0x3399FF
+species_color: HYDVU 0x3399FF
species_color: LUBBA 0xF7B5CB
species_color: GEOCY 0xF5A0BD
+species_color: AMPQE 0x009966
species_color: SUBDO 0xC790B9
species_color: MONBE 0xFC0FC0
-species_color: DICPU 0x23238E
-species_color: DICDI 0x4D4DFF
+species_color: DICPU 0xFFCC33
+species_color: DICDI 0xFFCC00
species_color: ENTHI 0x5959AB
species_color: ARATH 0x00FF00
species_color: POPTR 0x006400
species_color: Chordata 0x8470FF
species_color: Echinodermata 0x6495ED
species_color: Hemichordata 0x7EC0EE
-species_color: Arthropoda 0x7AC5CD
+species_color: Arthropoda 0x7AC5CD
species_color: Nematoda 0x7171C6
species_color: Tardigrada 0x388E8E
species_color: Annelida 0xC67171
git://source.jalview.org / jalview.git / blobdiff