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 d5a771b..262d76e 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -57,14 +57,14 @@ native_ui: ?
 #     Example: 'node_label_direction: horizontal'
 #     The two possible values are: horizontal
 #                                  radial
-#  Default node (shape) size: 'default_node_size'
+#  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: 'default_node_shape'
+#  Default node shape type: 'default_node_shape'
 #     Example: 'default_node_shape: '
 #     Possible values: circle
 #                      rectangle
-#                      none
-#  Default node (shape) fill: 'default_node_fill'
+#  Default node shape fill: 'default_node_fill'
 #     Example: 'default_node_fill: '
 #     Possible values: solid
 #                      gradient
@@ -95,10 +95,11 @@ show_branch_length_values:                 no
 cladogram_type:                            ext_node_sum_dep
 phylogeny_graphics_type:                   rectangular
 node_label_direction:                      horizontal
-default_node_size:                         4
-default_node_shape:                        rectangle
+show_default_node_shapes:                  no
+default_node_size:                         6
+default_node_shape:                        circle
 default_node_fill:                         gradient
-taxonomy_colorize_node_shapes:             yes
+taxonomy_colorize_node_shapes:             no
 #graphics_export_x:                         595
 #graphics_export_y:                         792
 pdf_export_line_width:                     0.5
@@ -107,6 +108,7 @@ overview_width:                            120
 overview_height:                           120
 overview_placement_type:                   upper_left
 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
@@ -116,7 +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
@@ -158,7 +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
@@ -169,6 +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
 
 
@@ -180,6 +182,7 @@ 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
@@ -354,7 +357,39 @@ 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
 #  -------------