X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file_1;h=cc250e3b9f1b76881e547fd62a2383a09aa3160d;hb=ce4170cc9535d21e751feef6d1a0850197d57ee7;hp=f1a9fa30daa1c3845cdea47d5b8cff658de789dd;hpb=2b3a47bd734b09f712841a8fd9a8e0106ec44a4b;p=jalview.git diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 index f1a9fa3..cc250e3 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 @@ -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' @@ -75,12 +76,19 @@ native_ui: ? # sequence_name # sequence_acc # sequence_mol_seq +# sequence_mol_seq_fasta # sequence_symbol # taxonomy_scientific_name # taxonomy_code -# To determine where to return data by clicking on "Return ...": 'ext_descendents_data_to_return_on' -# Possible values: window -# console +# 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' # @@ -93,17 +101,27 @@ 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) 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' min_confidence_value: 0.0 -font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans +font_family: Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans font_size: 10 antialias_screen: yes show_scale: yes @@ -111,11 +129,11 @@ 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 -taxonomy_colorize_node_shapes: no +show_default_node_shapes_internal: no +show_default_node_shapes_external: no +default_node_size: 4 +default_node_shape: rectangle +default_node_fill: solid #graphics_export_x: 595 #graphics_export_y: 792 pdf_export_line_width: 0.5 @@ -130,13 +148,13 @@ 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: user_selected +#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 -ext_descendents_data_to_return_on: console -ext_descendents_data_to_return: node_name -#label_for_get_ext_descendents_data: Get_Node_Data +taxonomy_extraction_in_nh_parsing: pfam_relaxed @@ -204,6 +222,7 @@ click_to: swap display click_to: sort_descendants display click_to: color_subtree display click_to: open_seq_web nodisplay +click_to: open_pdb_web nodisplay click_to: open_tax_web nodisplay click_to: blast nodisplay click_to: cut_subtree nodisplay @@ -212,6 +231,7 @@ click_to: paste_subtree nodisplay click_to: delete nodisplay click_to: add_new_node nodisplay click_to: edit_node_data display +click_to: select_nodes nodisplay click_to: get_ext_descendents_data display # Default click-to option (any of the above if set to "display") @@ -230,7 +250,9 @@ 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 @@ -258,34 +280,16 @@ gui_button_border_color: 0x000000 +# Settings Specific for Archaeopteryx Applets (E and A) +# ----------------------------------------------------- +# To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes' -# 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 +midpoint_reroot: yes -# Settings Specific for ArchaeopteryxE -# ------------------------------------ +# Settings Specific for ArchaeopteryxE Applets +# -------------------------------------------- # To hide controls and menus: 'hide_controls_and_menus: yes' # To use tabbed display : 'use_tabbed_display: yes' @@ -294,77 +298,74 @@ use_tabbed_display: yes - -# Application Specific Settings -# ----------------------------- - # Species colors # -------------- # Format: species_color: speciesname hexcolor -species_color: BRAFL 0x00FFFF -species_color: SPHGR 0x9620F0 -species_color: STRPU 0x9620F0 -species_color: CIOIN 0xFF1CAE -species_color: CIOSA 0xFF2CAE -species_color: BOVIN 0x5C3317 -species_color: CANFA 0x8B2323 -species_color: HUMAN 0xFF2400 -species_color: PANTR 0xCC2400 -species_color: MOUSE 0xFF7F00 -species_color: RAT 0xFFEF00 -species_color: MONDO 0xEE9A49 -species_color: ORNAN 0xCD853F -species_color: XENLA 0x6BAA23 -species_color: XENTR 0x6BAA23 -species_color: CHICK 0xFFC125 -species_color: FUGRU 0x0000FF -species_color: BRARE 0x0000DD -species_color: DANRE 0x0000BB -species_color: TETNG 0x0000AA -species_color: ORYLA 0x000088 -species_color: GASAC 0x000066 -species_color: CAEEL 0xA0A0A0 -species_color: CAEBR 0xB0B0B0 -species_color: DROME 0x706F00 -species_color: DROPS 0x504F00 -species_color: APIME 0x7A7700 -species_color: AEDAE 0x8C5900 -species_color: TRICA 0x918E00 -species_color: NEMVE 0xAABADD -species_color: HYDAT 0x7C9BCF -species_color: LUBBA 0xF7B5CB -species_color: GEOCY 0xF5A0BD -species_color: SUBDO 0xC790B9 -species_color: MONBE 0xFC0FC0 -species_color: DICPU 0x23238E -species_color: DICDI 0x4D4DFF -species_color: ENTHI 0x5959AB -species_color: ARATH 0x00FF00 -species_color: POPTR 0x006400 -species_color: VITVI 0x00CD00 -species_color: GLYMA 0x00FF7F -species_color: ORYSA 0x008B00 -species_color: ORYSJ 0x008C00 -species_color: SORBI 0x00EE76 -species_color: SELMO 0x238E23 -species_color: PHYPA 0x09F911 -species_color: OSTLU 0x7FFF00 -species_color: OSTTA 0x7FFF00 -species_color: OSTRC 0x7FFF00 -species_color: MICPU 0x66CD00 -species_color: MIC99 0x66CD00 -species_color: CHLRE 0xB3EE3A -species_color: VOLCA 0xC0FF3E -species_color: CHLSP 0x6B8E23 -species_color: CYAME 0xD02090 -species_color: YEAST 0xAAAAAA -species_color: BACFR 0xFF0000 -species_color: BACTN 0xFFFF00 -species_color: MYXXD 0x0000FF -species_color: STIAU 0x00FFFF -species_color: BACOV 0x8C5900 -species_color: BACUN 0x66CD00 -species_color: PORGI 0x918E00 +species_color: BRAFL 0x00FFFF +species_color: SPHGR 0x9620F0 +species_color: STRPU 0x9620F0 +species_color: CIOIN 0xFF1CAE +species_color: CIOSA 0xFF2CAE +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: MONDO 0xEE9A49 +species_color: ORNAN 0xCD853F +species_color: XENLA 0x6BAA23 +species_color: XENTR 0x6BAA23 +species_color: CHICK 0xFFC125 +species_color: FUGRU 0x0000FF +species_color: BRARE 0x0000DD +species_color: DANRE 0x0000BB +species_color: TETNG 0x0000AA +species_color: ORYLA 0x000088 +species_color: GASAC 0x000066 +species_color: CAEEL 0xA0A0A0 +species_color: CAEBR 0xB0B0B0 +species_color: DROME 0x706F00 +species_color: DROPS 0x504F00 +species_color: APIME 0x7A7700 +species_color: AEDAE 0x8C5900 +species_color: TRICA 0x918E00 +species_color: NEMVE 0xAABADD +species_color: HYDAT 0x7C9BCF +species_color: LUBBA 0xF7B5CB +species_color: GEOCY 0xF5A0BD +species_color: SUBDO 0xC790B9 +species_color: MONBE 0xFC0FC0 +species_color: DICPU 0x23238E +species_color: DICDI 0x4D4DFF +species_color: ENTHI 0x5959AB +species_color: ARATH 0x00FF00 +species_color: POPTR 0x006400 +species_color: VITVI 0x00CD00 +species_color: GLYMA 0x00FF7F +species_color: ORYSA 0x008B00 +species_color: ORYSJ 0x008C00 +species_color: SORBI 0x00EE76 +species_color: SELMO 0x238E23 +species_color: PHYPA 0x09F911 +species_color: OSTLU 0x7FFF00 +species_color: OSTTA 0x7FFF00 +species_color: OSTRC 0x7FFF00 +species_color: MICPU 0x66CD00 +species_color: MIC99 0x66CD00 +species_color: CHLRE 0xB3EE3A +species_color: VOLCA 0xC0FF3E +species_color: CHLSP 0x6B8E23 +species_color: CYAME 0xD02090 +species_color: YEAST 0xAAAAAA +species_color: BACFR 0xFF0000 +species_color: BACTN 0xFFFF00 +species_color: MYXXD 0x0000FF +species_color: STIAU 0x00FFFF +species_color: BACOV 0x8C5900 +species_color: BACUN 0x66CD00 +species_color: PORGI 0x918E00 # rank: Class species_color: Mammalia 0xFF0000 species_color: mammals 0xFF0000