# 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):
# 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
# 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
# To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return'
# Possible values: node_name
# sequence_name
+# gene_name
# sequence_acc
# sequence_mol_seq
# sequence_mol_seq_fasta
# 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'
#
#
# 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
# 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
default_node_size: 4
default_node_shape: rectangle
default_node_fill: solid
-taxonomy_colorize_node_shapes: no
#graphics_export_x: 595
#graphics_export_y: 792
pdf_export_line_width: 0.5
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
phylogram: display ?
rollover: display yes
-color_according_to_species: display yes
+color_according_to_species: display no
color_according_to_annotation: display no
show_node_names: display yes
+show_seq_names: display yes
+show_seq_symbols: display yes
+show_seq_acc: display no
show_gene_names: display yes
-show_gene_symbols: display yes
-show_sequence_acc: display no
show_taxonomy_code: display yes
show_taxonomy_scientific_names: display yes
show_taxonomy_common_names: display no
-show_taxonomy_images: display yes
+show_taxonomy_images: display no
show_annotations: display no
write_confidence_values: display ?
write_events: display ?
-color_branches: display no
+use_visual_styles: display no
width_branches: display no
show_domain_architectures: display no
show_binary_characters: display no
click_to: swap display
click_to: sort_descendants display
click_to: color_subtree display
+click_to: change_node_font display
+click_to: color_node_font display
click_to: open_seq_web display
+click_to: open_pdb_web display
click_to: open_tax_web display
click_to: blast display
click_to: cut_subtree display
display_color: background 0x000000
display_color: background_gradient_bottom 0x0000FF
-display_color: sequence 0xDCDCDC
-display_color: taxonomy 0xB4B4B4
-display_color: confidence 0x38B0DE
+display_color: sequence 0xE6E6E6
+display_color: taxonomy 0xFFDCDC
+display_color: confidence 0x38B0FF
display_color: branch_length 0x8C8C8C
display_color: branch 0xFFFFFF
display_color: node_box 0xFFFFFF
display_color: collapsed 0xFFFF00
-display_color: matching_nodes 0x00FF00
+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
# Domain colors
# -------------
-domain_color: Cofilin_ADF 0xFC0FC0
-domain_color: TIR 0x900000
-domain_color: NACHT 0x202020
-domain_color: CARD 0xFF0000
-domain_color: Peptidase_C14 0x00FF00
-domain_color: Death 0x0000FF
-domain_color: DED 0x00FFFF
-domain_color: BIR 0xCCFF33
-domain_color: PAAD_DAPIN 0x9999CC
-domain_color: NB-ARC 0x500050
-domain_color: WD40 0x888888
-domain_color: RVT_1 0x999900
-
+domain_color: Cofilin_ADF 0xFC0FC0
+domain_color: TIR 0x900000
+domain_color: NACHT 0x202020
+domain_color: CARD 0xFF0000
+domain_color: Peptidase_C14 0x00FF00
+domain_color: Death 0x0000FF
+domain_color: DED 0x00FFFF
+domain_color: BIR 0xCCFF33
+domain_color: PAAD_DAPIN 0x9999CC
+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: GDE_N_bis 0x007000
+domain_color: hGDE_central 0xFF8000
+domain_color: hGDE_amylase 0x0000EE
+domain_color: hDGE_amylase 0x0000EE
# Annotation colors
git://source.jalview.org / jalview.git / blobdiff