git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
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
9fc8c84
..
50e8776
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
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
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
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
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
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 ?
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
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
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: 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
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: 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
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
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'
# Settings Specific for Archaeopteryx Applets (E and A)
# -----------------------------------------------------
# To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'