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[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 1c417bb..1a674d2 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -163,7 +163,6 @@ font_size_min:                             2
 font_size_max:                             20
 antialias_screen:                          yes
 show_scale:                                yes
-show_branch_length_values:                 no
 cladogram_type:                            ext_node_sum_dep
 phylogeny_graphics_type:                   rectangular
 node_label_direction:                      horizontal
@@ -182,9 +181,11 @@ overview_placement_type:                   upper_left
 color_labels_same_as_branch_length_values: no
 display_sequence_relations:                no
 show_domain_labels:                        yes
+line_up_renderable_data:                   yes
+right_align_domain_architectures:          no
 show_seq_annotation_ref_sources:           yes
 branch_length_value_digits:                3
-confidence_value_digits:                   3
+confidence_value_digits:                   2
 background_gradient:                       no
 allow_editing:                             yes
 ext_descendents_data_to_return_on:         window
@@ -225,10 +226,12 @@ show_taxonomy_common_names:     display   no
 show_taxonomy_images:           display   no
 show_annotations:               display   no
 write_confidence_values:        display   ?
+write_branch_length_values:     display   no
 write_events:                   display   ?
 use_visual_styles:              display   no
 width_branches:                 display   no
 show_domain_architectures:      display   no
+show_msa:                       display   no
 show_binary_characters:         display   no
 show_binary_character_counts:   display   no
 display_internal_data:          display   yes
@@ -276,7 +279,7 @@ display_color: background                 0x000000
 display_color: background_gradient_bottom 0x0000FF
 display_color: sequence                   0xE6E6E6
 display_color: taxonomy                   0xB4B4B4
-display_color: confidence                 0x38B0FF
+display_color: confidence                 0xB4B4B4
 display_color: branch_length              0x8C8C8C
 display_color: branch                     0xFFFFFF
 display_color: node_box                   0xFFFFFF
@@ -287,7 +290,8 @@ 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
@@ -310,12 +314,13 @@ 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)
@@ -365,7 +370,6 @@ species_color: CIOSA        0xFF2CAE
 species_color: BOVIN        0x5C3317
 species_color: CANFA        0x8B2323
 species_color: HUMAN        0xFF2400
-species_color: Homo_sapiens 0xFF2400
 species_color: PANTR        0xCC2400
 species_color: MOUSE        0xFF7F00
 species_color: RAT          0xFFEF00
@@ -380,21 +384,23 @@ species_color: DANRE        0x0000BB
 species_color: TETNG        0x0000AA
 species_color: ORYLA        0x000088
 species_color: GASAC        0x000066
-species_color: CAEEL        0xA0A0A0
+species_color: CAEEL        0x666699
 species_color: CAEBR        0xB0B0B0
-species_color: DROME        0x706F00
-species_color: DROPS        0x504F00
+species_color: DROME        0x663366
+species_color: DROPS        0x996699
 species_color: APIME        0x7A7700
 species_color: AEDAE        0x8C5900
 species_color: TRICA        0x918E00
-species_color: NEMVE        0xAABADD
-species_color: HYDAT        0x7C9BCF
+species_color: NEMVE        0x0066CC
+species_color: HYDAT        0x3399FF
+species_color: HYDVU        0x3399FF
 species_color: LUBBA        0xF7B5CB
 species_color: GEOCY        0xF5A0BD
+species_color: AMPQE        0x009966
 species_color: SUBDO        0xC790B9
 species_color: MONBE        0xFC0FC0
-species_color: DICPU        0x23238E
-species_color: DICDI        0x4D4DFF
+species_color: DICPU        0xFFCC33
+species_color: DICDI        0xFFCC00
 species_color: ENTHI        0x5959AB
 species_color: ARATH        0x00FF00
 species_color: POPTR        0x006400
@@ -429,7 +435,7 @@ species_color: mammals        0xFF0000
 species_color: Chordata       0x8470FF
 species_color: Echinodermata  0x6495ED
 species_color: Hemichordata   0x7EC0EE
-species_color: Arthropoda     0x7AC5CD 
+species_color: Arthropoda     0x7AC5CD
 species_color: Nematoda       0x7171C6
 species_color: Tardigrada     0x388E8E
 species_color: Annelida       0xC67171