X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file;h=557f6225c35fa82a11414273e5e846a1a0c94d92;hb=01a0ff8da9b487ca626059dab5f6bf9eea98ae77;hp=76e4617d23340044d7a251ca6e8d9435ff795048;hpb=ea9680e31258a26c47104bd8c38812d583669977;p=jalview.git diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index 76e4617..557f622 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file @@ -57,7 +57,8 @@ native_ui: ? # Example: 'node_label_direction: horizontal' # The two possible values are: horizontal # radial -# Show default node shape: 'show_default_node_shapes': values: 'yes'/'no' +# 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' @@ -75,6 +76,7 @@ native_ui: ? # sequence_name # sequence_acc # sequence_mol_seq +# sequence_mol_seq_fasta # sequence_symbol # taxonomy_scientific_name # taxonomy_code @@ -131,16 +133,19 @@ validate_against_phyloxml_xsd_schema: true min_confidence_value: 0.0 font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans 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: no -default_node_size: 6 -default_node_shape: circle -default_node_fill: gradient +show_default_node_shapes_internal: no +show_default_node_shapes_external: no +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 @@ -157,12 +162,12 @@ confidence_value_digits: 3 background_gradient: no allow_editing: yes ext_descendents_data_to_return_on: window -ext_descendents_data_to_return: user_selected +ext_descendents_data_to_return: sequence_mol_seq_fasta #label_for_get_ext_descendents_data: Get_Node_Data # NH/NHX/Nexus file parsing: internal_labels_are_confidence_values: no replace_underscores_in_nh_parsing: no -taxonomy_extraction_in_nh_parsing: pfam +taxonomy_extraction_in_nh_parsing: yes # Checkbox Display Selection @@ -199,7 +204,7 @@ show_binary_characters: display no show_binary_character_counts: display no display_internal_data: display yes dynamically_hide_data: display yes -show_relation_confidence: display no +show_relation_confidence: display no show_properties: display no show_vector_data: display no @@ -279,33 +284,16 @@ domain_structure_font_color: 0x909090 -# Web Links -# --------- -# Format: web_link: -# E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB" -# is not used at the moment. -# corresponds to the element for , -# and to the of (see www.phyloxml.org). - -web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB -web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl -web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI -web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq -web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro -web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB -web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam -web_link: http://tolweb.org/ ToL tol -web_link: http://www.eol.org/pages/ EOL eol -web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot -web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi -web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID -# not working at the moment: -web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl - - - -# Settings Specific for ArchaeopteryxE -# ------------------------------------ +# Settings Specific for Archaeopteryx Applets +# ------------------------------------------- +# To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes' + +midpoint_reroot: yes + + + +# Settings Specific for ArchaeopteryxE Applets +# -------------------------------------------- # To hide controls and menus: 'hide_controls_and_menus: yes' # To use tabbed display : 'use_tabbed_display: yes' @@ -320,7 +308,6 @@ use_tabbed_display: yes default_number_of_bootstrap_resamples: 100 mafft_local: /bin/mafft -clustalo_local: C:\Users\zma\SOFTWARE\clustal-omega-1.1.0-win32\clustalo.exe fastme_local: /bin/fastme raxml_local: /bin/raxml