X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file;h=088df9ab90c020b55ba4998081639d768788dea7;hb=80160ba33817d2f7f35171ec5f430b23467fff2d;hp=bf0577a678e9da7fa43c4b9f75431f9b88be13c2;hpb=3f88e7f7fe5ceab9154fa84c0f16d7df947a9a3f;p=jalview.git diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index bf0577a..088df9a 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' @@ -69,6 +70,28 @@ native_ui: ? # Possible values: solid # gradient # none +# +# To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return' +# Possible values: node_name +# sequence_name +# sequence_acc +# sequence_mol_seq +# sequence_mol_seq_fasta +# sequence_symbol +# taxonomy_scientific_name +# taxonomy_code +# user_selected +# +# To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on' +# 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' +# # 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' @@ -78,27 +101,51 @@ native_ui: ? # 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 (application only): -# 'replace_underscores_in_nh_parsing' -# To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694') -# during NH/NHX/Nexus file parsing (application only): 'extract_pfam_tax_codes_in_nh_parsing' -# Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only): -# 'internal_labels_are_confidence_values' +# +# NH/NHX/Nexus file parsing +# ------------------------- +# 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' +# +# 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 +# phyloXML applications and to detect malformatted and +# possibly erroneous data, it is strongly recommended +# to enable validation of all phyloXML files +# against the XSD Schema (see: http://www.phyloxml.org/), +# with: +# 'validate_against_phyloxml_xsd_schema: true' + +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 @@ -114,25 +161,13 @@ branch_length_value_digits: 3 confidence_value_digits: 3 background_gradient: no allow_editing: yes -# NH/NHX/Nexus file parsing (application only): +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 +# NH/NHX/Nexus file parsing: internal_labels_are_confidence_values: no replace_underscores_in_nh_parsing: no -extract_taxonomy_codes_in_nh_parsing: yes - - - -# phyloXML parsing -# ---------------- -# To ensure compatibility with all current and future -# phyloXML applications and to detect malformatted and -# possibly erroneous data, it is strongly recommended -# to enable validation of all phyloXML files -# against the XSD Schema (see: http://www.phyloxml.org/), -# with: -# 'validate_against_phyloxml_xsd_schema: true' - -validate_against_phyloxml_xsd_schema: true - +taxonomy_extraction_in_nh_parsing: yes # Checkbox Display Selection @@ -169,11 +204,12 @@ 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 + # Combo-box Display Selection # --------------------------- # Format: 'name: display/nodisplay' @@ -193,6 +229,7 @@ click_to: paste_subtree display click_to: delete display click_to: add_new_node display click_to: edit_node_data display +click_to: select_nodes display click_to: get_ext_descendents_data display # Default click-to option (any of the above if set to "display") @@ -239,6 +276,7 @@ gui_menu_text_color: 0xFFFFFF gui_button_border_color: 0x000000 + # Domain Structure Display Colors # ------------------------------- domain_structure_base_color: 0x202020 @@ -246,33 +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 (E and A) +# ----------------------------------------------------- +# 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' @@ -287,7 +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 @@ -411,43 +431,7 @@ domain_color: PAAD_DAPIN 0x9999CC domain_color: NB-ARC 0x500050 domain_color: WD40 0x888888 domain_color: RVT_1 0x999900 -domain_color: NOPS 0x505000 -domain_color: RRM_1 0x004400 -domain_color: fn3 0xFFCC00 -domain_color: Ank 0xCC33FF -domain_color: Pkinase 0x339900 -domain_color: Pkinase_Tyr 0x336600 -domain_color: ig 0x660066 -domain_color: zf-C3HC4 0x6699FF -domain_color: zf-CCHC 0x6699EE -domain_color: zf-C2H2 0x6699CC -domain_color: zf-B_box 0x6699DD -domain_color: PDZ 0x66FFCC -domain_color: SH3_2 0x996600 -domain_color: MIRO 0xCCFF00 -domain_color: Myb_DNA-binding 0xDDDDDD -domain_color: NHL 0x336666 -domain_color: PKD_channel 0x336666 -domain_color: Ion_trans 0x996666 -domain_color: CAP_GLY 0xCC9900 -domain_color: LRR_1 0xFFFF99 -domain_color: LRR_2 0xFFFF66 -domain_color: LRR_3 0xFFFF33 -domain_color: LRR_adjacent 0xFFFF00 -domain_color: LRRCT 0xFFCC99 -domain_color: LRRNT 0xFFCC66 -domain_color: LRRNT_2 0xFFCC33 -domain_color: Ank 0x990099 -domain_color: Sushi 0x004400 -domain_color: ZU5 0xFF9999 -domain_color: V-set 0x3399FF -domain_color: TPR_1 0xFF1493 -domain_color: TPR_2 0xFF69B4 -domain_color: TPR_3 0xCD6090 -domain_color: TPR_4 0xFF6A6A -domain_color: TPR_MLP1_2 0x33FF00 -domain_color: Collagen 0xFF7F00 -domain_color: MIF 0xADD8E6 + # Annotation colors