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 eca2b05..a384a57 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -211,6 +211,7 @@ validate_against_phyloxml_xsd_schema:      true
 
 phylogram:                      display   ?
 rollover:                       display   yes
+color_according_to_sequence:    display   no
 color_according_to_species:     display   no
 color_according_to_annotation:  display   no
 show_node_names:                display   yes
@@ -225,7 +226,7 @@ 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
@@ -274,19 +275,20 @@ default_click_to: display_node_data
 display_color: background                 0x000000
 display_color: background_gradient_bottom 0x0000FF
 display_color: sequence                   0xE6E6E6
-display_color: taxonomy                   0xFFDCDC
-display_color: confidence                 0x38B0FF
+display_color: taxonomy                   0xB4B4B4
+display_color: confidence                 0xB4B4B4
 display_color: branch_length              0x8C8C8C
 display_color: branch                     0xFFFFFF
 display_color: node_box                   0xFFFFFF
-display_color: collapsed                  0xFFFF00
+display_color: collapsed                  0xFFFFFF
 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
-display_color: domains                    0x7B68EE
+display_color: domain_label               0xE6E6E6
+display_color: domain_base                0x646464
 display_color: binary_domain_combinations 0x4169FF
 display_color: annotation                 0xADFF2F
 display_color: overview                   0x828282
@@ -309,12 +311,13 @@ gui_menu_text_color:                  0xFFFFFF
 gui_button_border_color:              0x000000
 
 
-
-#  Domain Structure Display Colors
-#  -------------------------------
-domain_structure_base_color:          0x202020
-domain_structure_font_color:          0x909090
-
+#  Vector Data Display Colors and Sizes
+#  ------------------------------------
+vector_data_min_color:                0x0000FF
+vector_data_max_color:                0xFFFF00
+vector_data_mean_color:               0x000000
+vector_data_width:                    120
+vector_data_height:                   12
 
 
 #  Settings Specific for Archaeopteryx Applets (E and A)
@@ -346,6 +349,13 @@ raxml_local:                            /bin/raxml
 
 
 
+#  Sequence colors
+#  ---------------
+#  Format: species_color: sequencename hexcolor
+sequence_color: Tubulin-alpha        0xEE0000
+sequence_color: Tubulin-beta         0x00EE00
+
+
 #  Species colors
 #  --------------
 #  Format: species_color: speciesname hexcolor
@@ -448,9 +458,10 @@ species_color: Archaea        0x0000FF
 species_color: Eukaryota      0xFF0000
 species_color: eukaryotes     0xFF0000
 
+
+
 #  Domain colors
 #  -------------
-
 domain_color: Cofilin_ADF     0xFC0FC0
 domain_color: TIR             0x900000
 domain_color: NACHT           0x202020
@@ -463,15 +474,12 @@ 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
@@ -481,9 +489,9 @@ domain_color: hGDE_amylase    0x0000EE
 domain_color: hDGE_amylase    0x0000EE
 
 
+
 #  Annotation colors
 #  -----------------
-
 annotation_color: dehydrogenase 0x0000FF
 annotation_color: kinase        0xFF00FF
 annotation_color: protease      0x009900