# 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'
# 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_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica
font_size: 10
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
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
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
phylogram: display ?
rollover: display yes
+color_according_to_sequence: display no
color_according_to_species: display no
color_according_to_annotation: display no
show_node_names: display yes
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
display_color: background 0x000000
display_color: background_gradient_bottom 0x0000FF
display_color: sequence 0xE6E6E6
-display_color: taxonomy 0xFFDCDC
-display_color: confidence 0x38B0FF
+display_color: taxonomy 0xB4B4B4
+display_color: confidence 0xB4B4B4
display_color: branch_length 0x8C8C8C
display_color: branch 0xFFFFFF
display_color: node_box 0xFFFFFF
-display_color: collapsed 0xFFFF00
+display_color: collapsed 0xFFFFFF
display_color: matching_a 0x00FF00
display_color: matching_b 0xFF0000
display_color: matching_a_and_b 0xFFFF00
display_color: duplication 0xFF0000
display_color: speciation 0x00FF00
display_color: duplication_or_specation 0xFFFF00
-display_color: domains 0x7B68EE
+display_color: domain_label 0xE6E6E6
+display_color: domain_base 0x646464
display_color: binary_domain_combinations 0x4169FF
display_color: annotation 0xADFF2F
display_color: overview 0x828282
gui_button_border_color: 0x000000
-
-# Domain Structure Display Colors
-# -------------------------------
-domain_structure_base_color: 0x202020
-domain_structure_font_color: 0x909090
-
+# Vector Data Display Colors and Sizes
+# ------------------------------------
+vector_data_min_color: 0x0000FF
+vector_data_max_color: 0xFFFF00
+vector_data_mean_color: 0x000000
+vector_data_width: 120
+vector_data_height: 12
# Settings Specific for Archaeopteryx Applets (E and A)
+# Sequence colors
+# ---------------
+# Format: species_color: sequencename hexcolor
+sequence_color: Tubulin-alpha 0xEE0000
+sequence_color: Tubulin-beta 0x00EE00
+
+
# Species colors
# --------------
# Format: species_color: speciesname hexcolor
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
species_color: Eukaryota 0xFF0000
species_color: eukaryotes 0xFF0000
+
+
# Domain colors
# -------------
-
domain_color: Cofilin_ADF 0xFC0FC0
domain_color: TIR 0x900000
domain_color: NACHT 0x202020
domain_color: NB-ARC 0x500050
domain_color: WD40 0x888888
domain_color: RVT_1 0x999900
-
domain_color: CBM_48 0xFF0000
domain_color: Alpha-amylase 0x0000FF
domain_color: Alpha-amylase_C 0x0080FF
-
domain_color: CBM_48 0xFF0000
domain_color: Alpha-amylase 0x0000FF
domain_color: Alpha-amylase_C 0x0080FF
-
domain_color: GDE_N 0x009000
domain_color: GDE_C 0x00FF00
domain_color: hGDE_N 0x990099
domain_color: hDGE_amylase 0x0000EE
+
# Annotation colors
# -----------------
-
annotation_color: dehydrogenase 0x0000FF
annotation_color: kinase 0xFF00FF
annotation_color: protease 0x009900
git://source.jalview.org / jalview.git / blobdiff