forked from ryanb/dotfiles
-
Notifications
You must be signed in to change notification settings - Fork 1
/
aptxrc
401 lines (356 loc) · 15.7 KB
/
aptxrc
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
# User Interface Look and Feel
# ----------------------------
# Possible values for 'native_ui'
# 'yes' to use native (system) "look and feel"
# 'no' to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below)
# '?' to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected,
# Archaeopteryx-style "look and feel" otherwise
native_ui: ?
# Default Values for Options
# --------------------------
# Minimal confidence value to be displayed: 'min_confidence_value':
# Example: 'min_confidence_value: 50.0' (a commonly used
# value for bootstrap support)
# Font family name: 'font_family':
# Example: 'font_family: Arial,Calibri,Helvetica'
# It is advisable to use more than one value for font_family (in
# decreasing order of preference). Font family names have to be
# comma separated (no spaces). Spaces in font names have to be
# replaced by underscores (e.g. 'Times_New_Roman').
# Font size: 'font_size':
# Example: 'font_size: 10'
# Screen antialias: 'antialias_screen':
# Example: 'antialias_screen: yes'
# Show Scale: 'show_scale':
# Example: 'show_scale: yes'
# Show branch length branch values: 'show_branch_length_values':
# Example: 'show_branch_length_values: no'
# Do/do not line up cladogram display: 'non_lined_up_cladogram':
# Example: 'non_lined_up_cladogram: yes'
# Cladogram display type: 'cladogram_type'
# Example: 'cladogram_type: ext_node_sum_dep'
# The three possible values are: non_lined_up
# ext_node_sum_dep
# total_node_sum_dep (for "uniform" branch lengths)
# Default size for graphics export and printing: 'graphics_export_x' and 'graphics_export_y':
# (Archaeopteryx tries to guess the locale, so setting these is not always necessary)
# Example: For A4 (portrait):
# 'graphics_export_x: 595'
# 'graphics_export_y: 845'
# For US Letter (portrait):
# 'graphics_export_x: 612'
# 'graphics_export_y: 792'
# Default line width for PDF export: 'pdf_export_line_wdith':
# Example: 'pdf_export_line_width: 0.5'
# Show overview: 'show_overview'
# Phylogeny graphics type: 'phylogeny_graphics_type':
# Example: 'phylogeny_graphics_type: euro_style'
# The eight possible values are: rectangular
# euro_style
# rounded
# curved
# triangular
# convex
# unrooted
# circular
# Node label direction for circular
# and unrooted type: 'node_label_direction':
# Example: 'node_label_direction: horizontal'
# The two possible values are: horizontal
# radial
# Number of fraction digits for branch length values: 'branch_length_value_digits'
# Number of fraction digits for confidence values: 'confidence_value_digits'
# To turn on/off background color gradient: background_gradient
# Example: 'background_gradient: yes'
# To allow/not allow editing (cut, copy, and paste): allow_editing
# Example: 'allow_editing: yes'
# To replace underscores with spaces during NH/NHX/Nexus file parsing (application only):
# 'replace_underscores_in_nh_parsing'
# To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694')
# during NH/NHX/Nexus file parsing (application only): 'extract_pfam_tax_codes_in_nh_parsing'
# Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only):
# 'internal_labels_are_confidence_values'
# Ignore quotation marks (" and ') during NH/NHX/Nexus file parsing (application only),
# if quotation mark are not ignored, spaces in labels are retained:
# 'internal_labels_are_confidence_values'
min_confidence_value: 0.0
font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
font_size: 10
antialias_screen: yes
show_scale: yes
show_branch_length_values: no
cladogram_type: ext_node_sum_dep
phylogeny_graphics_type: rectangular
#graphics_export_x: 595
#graphics_export_y: 792
pdf_export_line_width: 0.5
show_overview: yes
overview_width: 120
overview_height: 120
overview_placement_type: upper_left
node_label_direction: horizontal
branch_length_value_digits: 3
confidence_value_digits: 3
background_gradient: no
allow_editing: yes
# NH/NHX/Nexus file parsing (application only):
internal_labels_are_confidence_values: no
replace_underscores_in_nh_parsing: no
ignore_quotation_marks_in_nh_parsing: yes
extract_taxonomy_codes_in_nh_parsing: yes
display_sequence_relations: no
# phyloXML parsing
# ----------------
# To ensure compatibility with all current and future
# phyloXML applications and to detect malformatted and
# possibly erroneous data, it is strongly recommended
# to enable validation of all phyloXML files
# against the XSD Schema (see: http://www.phyloxml.org/),
# with:
# 'validate_against_phyloxml_xsd_schema: true'
validate_against_phyloxml_xsd_schema: true
# Checkbox Display Selection
# --------------------------
# This is used to select which checkboxes to display
# and what their initial values should be.
# Format: 'name: display|nodisplay yes|no'
# Note: if an option is not displayed, it will not be enabled
#
# For the following use '?' to let Archaeopteryx decide (depending on tree):
# - 'phylogram'
# - 'write_confidence_values'
# - 'write_events'
phylogram: display ?
rollover: display yes
color_according_to_species: display yes
color_according_to_annotation: display no
show_node_names: display yes
show_gene_names: display yes
show_gene_symbols: display yes
show_sequence_acc: display no
show_taxonomy_code: display yes
show_taxonomy_scientific_names: display yes
show_taxonomy_common_names: display no
show_annotations: display no
show_property: nodisplay no
write_confidence_values: display no
write_events: display ?
color_branches: display yes
width_branches: display yes
show_domain_architectures: display no
show_binary_characters: display no
show_binary_character_counts: display no
display_internal_data: display yes
dynamically_hide_data: display yes
show_relation_confidence: display no
# Combo-box Display Selection
# ---------------------------
# Format: 'name: display/nodisplay'
click_to: display_node_data display
click_to: collapse_uncollapse display
click_to: reroot display
click_to: subtree display
click_to: swap display
click_to: color_subtree display
click_to: open_seq_web display
click_to: open_tax_web display
click_to: cut_subtree display
click_to: copy_subtree display
click_to: paste_subtree display
click_to: delete display
click_to: add_new_node display
click_to: edit_node_data display
# Default click-to option (any of the above if set to "display")
default_click_to: display_node_data
# Default Tree Display Colors
# ---------------------------
## Flip these for black and white background (esp useful for publication)
display_color: background 0x000000
display_color: branch 0x544E5A
#display_color: background 0xFFFFFF
#display_color: branch 0xCCCCCC
display_color: matching_nodes 0x00FF00
display_color: background_gradient_bottom 0x0000FF
display_color: sequence 0xDCDCDC
display_color: taxonomy 0xB4B4B4
display_color: confidence 0x38B0DE
display_color: branch_length 0x8C8C8C
display_color: node_box 0xFFFFFF
display_color: collapsed 0xFFFF00
display_color: duplication 0xFF0000
display_color: speciation 0x00FF00
display_color: duplication_or_specation 0xFFFF00
display_color: domains 0x7B68EE
display_color: binary_domain_combinations 0x4169FF
display_color: annotation 0xADFF2F
display_color: overview 0x828282
# GUI (graphical user interface) Colors
# -------------------------------------
#
# These are ignored if native (system) "look and feel"
# is being used ('native_ui: yes').
gui_background_color: 0x202020
gui_checkbox_text_color: 0xDCDCDC
gui_checkbox_and_button_active_color: 0xFF0000
gui_button_text_color: 0xFFFFFF
gui_button_background_color: 0x404040
gui_menu_background_color: 0x000000
gui_menu_text_color: 0xFFFFFF
gui_button_border_color: 0x000000
# Domain Structure Display Colors
# -------------------------------
domain_structure_base_color: 0x202020
domain_structure_font_color: 0x909090
# Web Links
# ---------
# Format: web_link: <URL> <description> <source identifier>
# E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
# <description> is not used at the moment.
# <source identifier> corresponds to the <source> element for <sequence> <accession>,
# and to the <type> of <taxonomy> <id> (see www.phyloxml.org).
web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB
web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl
web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI
web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq
web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro
web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB
web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam
web_link: http://tolweb.org/ ToL tol
web_link: http://www.eol.org/pages/ EOL eol
web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot
web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi
# not working at the moment:
web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl
# Settings Specific for ArchaeopteryxE
# ------------------------------------
# To hide controls and menus: 'hide_controls_and_menus: yes'
# To use tabbed display : 'use_tabbed_display: yes'
hide_controls_and_menus: no
use_tabbed_display: yes
# Application Specific Settings
# -----------------------------
# Species colors
# --------------
# Format: species_color: speciesname hexcolor
species_color: BRAFL 0x00FFFF
species_color: SPHGR 0x9620F0
species_color: STRPU 0x9620F0
species_color: CIOIN 0xFF1CAE
species_color: CIOSA 0xFF2CAE
species_color: BOVIN 0x5C3317
species_color: CANFA 0x8B2323
species_color: HUMAN 0xFF2400
species_color: PANTR 0xCC2400
species_color: MOUSE 0xFF7F00
species_color: RAT 0xFFEF00
species_color: MONDO 0xEE9A49
species_color: ORNAN 0xCD853F
species_color: XENLA 0x6BAA23
species_color: XENTR 0x6BAA23
species_color: CHICK 0xFFC125
species_color: FUGRU 0x0000FF
species_color: BRARE 0x0000DD
species_color: DANRE 0x0000BB
species_color: TETNG 0x0000AA
species_color: ORYLA 0x000088
species_color: GASAC 0x000066
species_color: CAEEL 0xA0A0A0
species_color: CAEBR 0xB0B0B0
species_color: DROME 0x706F00
species_color: DROPS 0x504F00
species_color: APIME 0x7A7700
species_color: AEDAE 0x8C5900
species_color: TRICA 0x918E00
species_color: NEMVE 0xAABADD
species_color: HYDAT 0x7C9BCF
species_color: LUBBA 0xF7B5CB
species_color: GEOCY 0xF5A0BD
species_color: SUBDO 0xC790B9
species_color: MONBE 0xFC0FC0
species_color: DICPU 0x23238E
species_color: DICDI 0x4D4DFF
species_color: ENTHI 0x5959AB
species_color: ARATH 0x00FF00
species_color: POPTR 0x006400
species_color: VITVI 0x00CD00
species_color: GLYMA 0x00FF7F
species_color: ORYSA 0x008B00
species_color: ORYSJ 0x008C00
species_color: SORBI 0x00EE76
species_color: SELMO 0x238E23
species_color: PHYPA 0x09F911
species_color: OSTLU 0x7FFF00
species_color: OSTTA 0x7FFF00
species_color: OSTRC 0x7FFF00
species_color: MICPU 0x66CD00
species_color: MIC99 0x66CD00
species_color: CHLRE 0xB3EE3A
species_color: VOLCA 0xC0FF3E
species_color: CHLSP 0x6B8E23
species_color: CYAME 0xD02090
species_color: YEAST 0xAAAAAA
species_color: BACFR 0xFF0000
species_color: BACTN 0xFFFF00
species_color: MYXXD 0x0000FF
species_color: STIAU 0x00FFFF
species_color: BACOV 0x8C5900
species_color: BACUN 0x66CD00
species_color: PORGI 0x918E00
# Domain colors
# -------------
domain_color: Cofilin_ADF 0xFC0FC0
domain_color: TIR 0x900000
domain_color: NACHT 0x202020
domain_color: CARD 0xFF0000
domain_color: Peptidase_C14 0x00FF00
domain_color: Death 0x0000FF
domain_color: DED 0x00FFFF
domain_color: BIR 0xCCFF33
domain_color: PAAD_DAPIN 0x9999CC
domain_color: NB-ARC 0x500050
domain_color: WD40 0x888888
domain_color: RVT_1 0x999900
domain_color: NOPS 0x505000
domain_color: RRM_1 0x004400
domain_color: fn3 0xFFCC00
domain_color: Ank 0xCC33FF
domain_color: Pkinase 0x339900
domain_color: Pkinase_Tyr 0x336600
domain_color: ig 0x660066
domain_color: zf-C3HC4 0x6699FF
domain_color: zf-CCHC 0x6699EE
domain_color: zf-C2H2 0x6699CC
domain_color: zf-B_box 0x6699DD
domain_color: PDZ 0x66FFCC
domain_color: SH3_2 0x996600
domain_color: MIRO 0xCCFF00
domain_color: Myb_DNA-binding 0xDDDDDD
domain_color: NHL 0x336666
domain_color: PKD_channel 0x336666
domain_color: Ion_trans 0x996666
domain_color: CAP_GLY 0xCC9900
domain_color: LRR_1 0xFFFF99
domain_color: LRR_2 0xFFFF66
domain_color: LRR_3 0xFFFF33
domain_color: LRR_adjacent 0xFFFF00
domain_color: LRRCT 0xFFCC99
domain_color: LRRNT 0xFFCC66
domain_color: LRRNT_2 0xFFCC33
domain_color: Ank 0x990099
domain_color: Sushi 0x004400
domain_color: ZU5 0xFF9999
domain_color: V-set 0x3399FF
domain_color: TPR_1 0xFF1493
domain_color: TPR_2 0xFF69B4
domain_color: TPR_3 0xCD6090
domain_color: TPR_4 0xFF6A6A
domain_color: TPR_MLP1_2 0x33FF00
domain_color: Collagen 0xFF7F00
domain_color: MIF 0xADD8E6
# Annotation colors
# -----------------
annotation_color: dehydrogenase 0x0000FF
annotation_color: kinase 0xFF00FF
annotation_color: protease 0x009900
annotation_color: transcription 0xAAAA00
# END