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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
9fc8c84
..
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
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: yes
+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'
@@
-373,7
+370,6
@@
species_color: CIOSA 0xFF2CAE
species_color: BOVIN 0x5C3317
species_color: CANFA 0x8B2323
species_color: HUMAN 0xFF2400
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
species_color: PANTR 0xCC2400
species_color: MOUSE 0xFF7F00
species_color: RAT 0xFFEF00
@@
-388,21
+384,23
@@
species_color: DANRE 0x0000BB
species_color: TETNG 0x0000AA
species_color: ORYLA 0x000088
species_color: GASAC 0x000066
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: 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: 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: LUBBA 0xF7B5CB
species_color: GEOCY 0xF5A0BD
+species_color: AMPQE 0x009966
species_color: SUBDO 0xC790B9
species_color: MONBE 0xFC0FC0
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
species_color: ENTHI 0x5959AB
species_color: ARATH 0x00FF00
species_color: POPTR 0x006400
@@
-437,7
+435,7
@@
species_color: mammals 0xFF0000
species_color: Chordata 0x8470FF
species_color: Echinodermata 0x6495ED
species_color: Hemichordata 0x7EC0EE
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
species_color: Nematoda 0x7171C6
species_color: Tardigrada 0x388E8E
species_color: Annelida 0xC67171