# 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
# sequence_symbol
# taxonomy_scientific_name
# taxonomy_code
+# taxonomy_common_name
# user_selected
#
# To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on'
# 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'
#
# To replace underscores with spaces during NH/NHX/Nexus file parsing:
# 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
#
-# To extract UniProt taxonomy codes (e.g. CAEEL) from node names during NH/NHX/Nexus file parsing:
-# 'taxonomy_extraction_in_nh_parsing',
-# possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), 'no'
+# To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names)
+# from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing'
+# possible values are:
+# 'no'
+# 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453)
+# 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090)
+# 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis)
#
# 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
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: sequence_mol_seq_fasta
-#label_for_get_ext_descendents_data: Get_Node_Data
+ext_descendents_data_to_return: user_selected
+#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: yes
+taxonomy_extraction_in_nh_parsing: no
+validate_against_phyloxml_xsd_schema: true
# Checkbox Display Selection
color_according_to_species: display yes
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
click_to: sort_descendants display
click_to: color_subtree 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
git://source.jalview.org / jalview.git / blobdiff