in progress

[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 727c91a..630414d 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -53,11 +53,23 @@ native_ui: ?
 #                                    convex
 #                                    unrooted
 #                                    circular
-#  Node label direction for circular
-#     and unrooted type: 'node_label_direction':
+#  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: 'show_default_node_shapes': 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
+#                      gradient
+#                      none
+#  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'
 #  Number of fraction digits for branch length values: 'branch_length_value_digits'
@@ -82,6 +94,12 @@ 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
+taxonomy_colorize_node_shapes:             no
 #graphics_export_x:                         595
 #graphics_export_y:                         792
 pdf_export_line_width:                     0.5
@@ -89,8 +107,8 @@ show_overview:                             yes
 overview_width:                            120
 overview_height:                           120
 overview_placement_type:                   upper_left
-node_label_direction:                      horizontal
 color_labels_same_as_branch_length_values: no
+display_sequence_relations:                no
 show_domain_labels:                        yes
 branch_length_value_digits:                3
 confidence_value_digits:                   3
@@ -100,7 +118,7 @@ allow_editing:                             yes
 internal_labels_are_confidence_values:     no
 replace_underscores_in_nh_parsing:         no
 extract_taxonomy_codes_in_nh_parsing:      yes
-display_sequence_relations:                no
+
 
 
 #  phyloXML parsing
@@ -142,7 +160,6 @@ show_taxonomy_scientific_names: display   yes
 show_taxonomy_common_names:     display   no
 show_taxonomy_images:           display   yes
 show_annotations:               display   no
-show_property:                  nodisplay no
 write_confidence_values:        display   ?
 write_events:                   display   ?
 color_branches:                 display   no
@@ -153,6 +170,7 @@ show_binary_character_counts:   display   no
 display_internal_data:          display   yes
 dynamically_hide_data:          display   yes
 show_relation_confidence:       display          no
+show_properties:                display   no
 show_vector_data:               display   no
 
 
@@ -164,9 +182,11 @@ click_to: collapse_uncollapse  display
 click_to: reroot               display
 click_to: subtree              display
 click_to: swap                 display
+click_to: sort_descendants     display
 click_to: color_subtree        display
 click_to: open_seq_web         display
 click_to: open_tax_web         display
+click_to: blast                display
 click_to: cut_subtree          display
 click_to: copy_subtree         display
 click_to: paste_subtree        display
@@ -265,7 +285,10 @@ use_tabbed_display:      yes
 #  EXPERIMENTAL: DO NOT USE!!
 
 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
 
 
 #  Application Specific Settings
@@ -338,7 +361,39 @@ 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
+# rank: Phylum
+species_color: Chordata       0x8470FF
+species_color: Echinodermata  0x6495ED
+species_color: Hemichordata   0x7EC0EE
+species_color: Arthropoda     0x7AC5CD 
+species_color: Nematoda       0x7171C6
+species_color: Tardigrada     0x388E8E
+species_color: Annelida       0xC67171
+species_color: Mollusca       0x00F5FF
+species_color: Ctenophora     0xBBFFFF
+species_color: Cnidaria       0xFF83FA
+species_color: Placozoa       0xEED2EE
+species_color: Porifera       0xFF3E96
+species_color: Microsporidia  0x8B8378
+species_color: Ascomycota     0xFF6347
+species_color: Basidiomycota  0xFFD700
+species_color: Chlorophyta    0x00C78C
+species_color: Streptophyta   0x00C957
+# rank: Kingdom
+species_color: Viridiplantae  0x00FF00
+species_color: plants         0x00FF00
+species_color: Metazoa        0x0000FF
+species_color: animals        0x0000FF
+species_color: Fungi          0xFF9912
+# rank: Superkingdom
+species_color: Viruses        0xFFD700
+species_color: Bacteria       0x00FF00
+species_color: Archaea        0x0000FF
+species_color: Eukaryota      0xFF0000
+species_color: eukaryotes     0xFF0000
 
 #  Domain colors
 #  -------------