work on: add ability to perform GSDI in applets

[jalview.git] / forester / aptx / aptx_configuration_files / _aptx_configuration_file

diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
index ce8cb3b..088df9a 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -76,6 +76,7 @@ native_ui: ?
 #                      sequence_name
 #                      sequence_acc
 #                      sequence_mol_seq
+#                      sequence_mol_seq_fasta
 #                      sequence_symbol
 #                      taxonomy_scientific_name
 #                      taxonomy_code
@@ -132,6 +133,8 @@ 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
@@ -140,9 +143,9 @@ phylogeny_graphics_type:                   rectangular
 node_label_direction:                      horizontal
 show_default_node_shapes_internal:         no
 show_default_node_shapes_external:         no
-default_node_size:                         6
-default_node_shape:                        circle
-default_node_fill:                         gradient
+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
@@ -159,12 +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
@@ -281,33 +284,16 @@ domain_structure_font_color:          0x909090
 
 
 
-#  Web Links
-#  --------- 
-#  Format: web_link: <URL> <description> <source identifier>
-#  E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB   UniProtKB"
-#  <description> is not used at the moment.
-#  <source identifier> corresponds to the <source> element for <sequence> <accession>,
-#  and to the <type> of <taxonomy> <id> (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'
 
@@ -322,7 +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