inprogress

[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 2b179ee..b347a26 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -91,6 +91,7 @@ native_ui: ?
 #  To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return'
 #     Possible values: node_name
 #                      sequence_name
+#                      gene_name
 #                      sequence_acc
 #                      sequence_mol_seq
 #                      sequence_mol_seq_fasta
@@ -171,7 +172,6 @@ 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
 pdf_export_line_width:                     0.5
@@ -211,20 +211,21 @@ validate_against_phyloxml_xsd_schema:      true
 
 phylogram:                      display   ?
 rollover:                       display   yes
-color_according_to_species:     display   yes
+color_according_to_species:     display   no
 color_according_to_annotation:  display   no
 show_node_names:                display   yes
+show_seq_names:                 display   yes
+show_seq_symbols:               display   yes
+show_seq_acc:                   display   no
 show_gene_names:                display   yes
-show_gene_symbols:              display   yes
-show_sequence_acc:              display   no
 show_taxonomy_code:             display   yes
 show_taxonomy_scientific_names: display   yes
 show_taxonomy_common_names:     display   no
-show_taxonomy_images:           display   yes
+show_taxonomy_images:           display   no
 show_annotations:               display   no
 write_confidence_values:        display   ?
 write_events:                   display   ?
-color_branches:                 display   no
+use_visual_styles:              display   no
 width_branches:                 display   no
 show_domain_architectures:      display   no
 show_binary_characters:         display   no
@@ -247,7 +248,10 @@ click_to: subtree                  display
 click_to: swap                     display
 click_to: sort_descendants         display
 click_to: color_subtree            display
+click_to: change_node_font         display
+click_to: color_node_font          display
 click_to: open_seq_web             display
+click_to: open_pdb_web             display
 click_to: open_tax_web             display
 click_to: blast                    display
 click_to: cut_subtree              display
@@ -269,14 +273,16 @@ default_click_to: display_node_data
 
 display_color: background                 0x000000
 display_color: background_gradient_bottom 0x0000FF
-display_color: sequence                   0xDCDCDC
-display_color: taxonomy                   0xB4B4B4
-display_color: confidence                 0x38B0DE
+display_color: sequence                   0xE6E6E6
+display_color: taxonomy                   0xFFDCDC
+display_color: confidence                 0x38B0FF
 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
@@ -445,19 +451,34 @@ species_color: eukaryotes     0xFF0000
 #  Domain colors
 #  -------------
 
-domain_color: Cofilin_ADF   0xFC0FC0
-domain_color: TIR           0x900000
-domain_color: NACHT         0x202020
-domain_color: CARD          0xFF0000
-domain_color: Peptidase_C14 0x00FF00
-domain_color: Death         0x0000FF
-domain_color: DED           0x00FFFF
-domain_color: BIR           0xCCFF33
-domain_color: PAAD_DAPIN    0x9999CC
-domain_color: NB-ARC        0x500050
-domain_color: WD40          0x888888
-domain_color: RVT_1         0x999900
-
+domain_color: Cofilin_ADF     0xFC0FC0
+domain_color: TIR             0x900000
+domain_color: NACHT           0x202020
+domain_color: CARD            0xFF0000
+domain_color: Peptidase_C14   0x00FF00
+domain_color: Death           0x0000FF
+domain_color: DED             0x00FFFF
+domain_color: BIR             0xCCFF33
+domain_color: PAAD_DAPIN      0x9999CC
+domain_color: NB-ARC          0x500050
+domain_color: WD40            0x888888
+domain_color: RVT_1           0x999900
+
+domain_color: CBM_48          0xFF0000
+domain_color: Alpha-amylase   0x0000FF
+domain_color: Alpha-amylase_C 0x0080FF
+
+domain_color: CBM_48          0xFF0000
+domain_color: Alpha-amylase   0x0000FF
+domain_color: Alpha-amylase_C 0x0080FF
+
+domain_color: GDE_N           0x009000
+domain_color: GDE_C           0x00FF00
+domain_color: hGDE_N          0x990099
+domain_color: GDE_N_bis       0x007000
+domain_color: hGDE_central    0xFF8000
+domain_color: hGDE_amylase    0x0000EE
+domain_color: hDGE_amylase    0x0000EE
 
 
 #  Annotation colors