X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file;h=50e877651fc56a3c774e9b881934f6df2c284701;hb=1dbc2c4a09d50805fe80b5ab3826d865153a3124;hp=9fc8c84cd54839a71e08f854d5ef8dfd00c81815;hpb=eefa926fb5765feb6880a77088e64aefed794176;p=jalview.git

diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
index 9fc8c84..50e8776 100644
--- 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:                   no
+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
@@ -319,13 +323,6 @@ vector_data_width:                    120
 vector_data_height:                   12
 
 
-#  Domain Structure Display Colors
-#  -------------------------------
-domain_structure_base_color:          0x202020
-domain_structure_font_color:          0x909090
-
-
-
 #  Settings Specific for Archaeopteryx Applets (E and A)
 #  -----------------------------------------------------
 #  To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'