1 # User Interface Look and Feel
2 # ----------------------------
3 # Possible values for 'native_ui'
4 # 'yes' to use native (system) "look and feel"
5 # 'no' to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below)
6 # '?' to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected,
7 # Archaeopteryx-style "look and feel" otherwise
13 # Default Values for Options
14 # --------------------------
15 # Minimal confidence value to be displayed: 'min_confidence_value':
16 # Example: 'min_confidence_value: 50.0' (a commonly used
17 # value for bootstrap support)
18 # Font family name: 'font_family':
19 # Example: 'font_family: Arial,Calibri,Helvetica'
20 # It is advisable to use more than one value for font_family (in
21 # decreasing order of preference). Font family names have to be
22 # comma separated (no spaces). Spaces in font names have to be
23 # replaced by underscores (e.g. 'Times_New_Roman').
24 # Font size: 'font_size':
25 # Example: 'font_size: 10'
26 # Screen antialias: 'antialias_screen': values: 'yes'/'no'
27 # Show Scale: 'show_scale': values: 'yes'/'no'
28 # Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no'
29 # Do/do not line up cladogram display: 'non_lined_up_cladogram': values: 'yes'/'no'
30 # Cladogram display type: 'cladogram_type'
31 # Example: 'cladogram_type: ext_node_sum_dep'
32 # The three possible values are: non_lined_up
34 # total_node_sum_dep (for "uniform" branch lengths)
35 # Default size for graphics export and printing: 'graphics_export_x' and 'graphics_export_y':
36 # (Archaeopteryx tries to guess the locale, so setting these is not always necessary)
37 # Example: For A4 (portrait):
38 # 'graphics_export_x: 595'
39 # 'graphics_export_y: 845'
40 # For US Letter (portrait):
41 # 'graphics_export_x: 612'
42 # 'graphics_export_y: 792'
43 # Default line width for PDF export: 'pdf_export_line_wdith':
44 # Example: 'pdf_export_line_width: 0.5'
45 # Show overview: 'show_overview': values: 'yes'/'no'
46 # Phylogeny graphics type: 'phylogeny_graphics_type':
47 # Example: 'phylogeny_graphics_type: euro_style'
48 # The eight possible values are: rectangular
56 # Node label direction for circular and unrooted type: 'node_label_direction':
57 # Example: 'node_label_direction: horizontal'
58 # The two possible values are: horizontal
60 # Show default node shape: 'show_default_node_shapes': values: 'yes'/'no'
61 # Default node shape size: 'default_node_size'
62 # Example: 'default_node_size: 6'
63 # Default node shape type: 'default_node_shape'
64 # Example: 'default_node_shape: '
65 # Possible values: circle
67 # Default node shape fill: 'default_node_fill'
68 # Example: 'default_node_fill: '
69 # Possible values: solid
73 # To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return'
74 # Possible values: node_name
79 # taxonomy_scientific_name
83 # To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on'
84 # Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
85 # classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
86 # Possible values: window (for output to window and buffer)
87 # console (for output to console and buffer)
88 # buffer_only (for output to buffer only)
90 # To override label for menu item to return data of external nodes (default ""Return ..."): 'label_for_get_ext_descendents_data'
91 # Example: 'label_for_get_ext_descendents_data: Get_Node_Data'
93 # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
94 # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
95 # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
96 # Number of fraction digits for branch length values: 'branch_length_value_digits'
97 # Number of fraction digits for confidence values: 'confidence_value_digits'
98 # To turn on/off background color gradient: background_gradient
99 # Example: 'background_gradient: yes'
100 # To allow/not allow editing (cut, copy, and paste): allow_editing
101 # Example: 'allow_editing: yes'
103 # NH/NHX/Nexus file parsing
104 # -------------------------
105 # To replace underscores with spaces during NH/NHX/Nexus file parsing:
106 # 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
108 # To extract UniProt taxonomy codes (e.g. CAEEL) from node names during NH/NHX/Nexus file parsing:
109 # 'taxonomy_extraction_in_nh_parsing',
110 # possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), 'no'
112 # Internal node labels are confidence values during NH/NHX/Nexus file parsing:
113 # 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
117 min_confidence_value: 0.0
118 font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
120 antialias_screen: yes
122 show_branch_length_values: no
123 cladogram_type: ext_node_sum_dep
124 phylogeny_graphics_type: rectangular
125 node_label_direction: horizontal
126 show_default_node_shapes: no
128 default_node_shape: circle
129 default_node_fill: gradient
130 taxonomy_colorize_node_shapes: no
131 #graphics_export_x: 595
132 #graphics_export_y: 792
133 pdf_export_line_width: 0.5
137 overview_placement_type: upper_left
138 color_labels_same_as_branch_length_values: no
139 display_sequence_relations: no
140 show_domain_labels: yes
141 branch_length_value_digits: 3
142 confidence_value_digits: 3
143 background_gradient: no
145 ext_descendents_data_to_return_on: window
146 ext_descendents_data_to_return: user_selected
147 #label_for_get_ext_descendents_data: Get_Node_Data
148 # NH/NHX/Nexus file parsing:
149 internal_labels_are_confidence_values: no
150 replace_underscores_in_nh_parsing: no
151 taxonomy_extraction_in_nh_parsing: pfam
157 # To ensure compatibility with all current and future
158 # phyloXML applications and to detect malformatted and
159 # possibly erroneous data, it is strongly recommended
160 # to enable validation of all phyloXML files
161 # against the XSD Schema (see: http://www.phyloxml.org/),
163 # 'validate_against_phyloxml_xsd_schema: true'
165 validate_against_phyloxml_xsd_schema: true
169 # Checkbox Display Selection
170 # --------------------------
171 # This is used to select which checkboxes to display
172 # and what their initial values should be.
173 # Format: 'name: display|nodisplay yes|no'
174 # Note: if an option is not displayed, it will not be enabled
176 # For the following use '?' to let Archaeopteryx decide (depending on tree):
178 # - 'write_confidence_values'
182 rollover: display yes
183 color_according_to_species: display no
184 color_according_to_annotation: nodisplay no
185 show_node_names: display yes
186 show_gene_names: display yes
187 show_gene_symbols: nodisplay no
188 show_sequence_acc: nodisplay no
189 show_taxonomy_code: display yes
190 show_taxonomy_scientific_names: nodisplay no
191 show_taxonomy_common_names: nodisplay no
192 show_taxonomy_images: nodisplay no
193 show_annotations: nodisplay no
194 write_confidence_values: display ?
195 write_events: nodisplay no
196 color_branches: display no
197 width_branches: display no
198 show_domain_architectures: nodisplay no
199 show_binary_characters: nodisplay no
200 show_binary_character_counts: nodisplay no
201 display_internal_data: display yes
202 dynamically_hide_data: display yes
203 show_relation_confidence: nodisplay no
204 show_properties: nodisplay no
205 show_vector_data: nodisplay no
208 # Combo-box Display Selection
209 # ---------------------------
210 # Format: 'name: display/nodisplay'
211 click_to: display_node_data display
212 click_to: collapse_uncollapse display
213 click_to: reroot display
214 click_to: subtree display
215 click_to: swap display
216 click_to: sort_descendants display
217 click_to: color_subtree display
218 click_to: open_seq_web nodisplay
219 click_to: open_tax_web nodisplay
220 click_to: blast nodisplay
221 click_to: cut_subtree nodisplay
222 click_to: copy_subtree nodisplay
223 click_to: paste_subtree nodisplay
224 click_to: delete nodisplay
225 click_to: add_new_node nodisplay
226 click_to: edit_node_data display
227 click_to: select_nodes nodisplay
228 click_to: get_ext_descendents_data display
230 # Default click-to option (any of the above if set to "display")
231 default_click_to: display_node_data
234 # Default Tree Display Colors
235 # ---------------------------
237 display_color: background 0x000000
238 display_color: background_gradient_bottom 0x0000FF
239 display_color: sequence 0xDCDCDC
240 display_color: taxonomy 0xB4B4B4
241 display_color: confidence 0x38B0DE
242 display_color: branch_length 0x8C8C8C
243 display_color: branch 0xFFFFFF
244 display_color: node_box 0xFFFFFF
245 display_color: collapsed 0xFFFF00
246 display_color: matching_nodes 0x00FF00
247 display_color: duplication 0xFF0000
248 display_color: speciation 0x00FF00
249 display_color: duplication_or_specation 0xFFFF00
250 display_color: domains 0x7B68EE
251 display_color: binary_domain_combinations 0x4169FF
252 display_color: annotation 0xADFF2F
253 display_color: overview 0x828282
257 # GUI (graphical user interface) Colors
258 # -------------------------------------
260 # These are ignored if native (system) "look and feel"
261 # is being used ('native_ui: yes').
263 gui_background_color: 0x202020
264 gui_checkbox_text_color: 0xDCDCDC
265 gui_checkbox_and_button_active_color: 0xFF0000
266 gui_button_text_color: 0xFFFFFF
267 gui_button_background_color: 0x404040
268 gui_menu_background_color: 0x000000
269 gui_menu_text_color: 0xFFFFFF
270 gui_button_border_color: 0x000000
277 # Format: web_link: <URL> <description> <source identifier>
278 # E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
279 # <description> is not used at the moment.
280 # <source identifier> corresponds to the <source> element for <sequence> <accession>,
281 # and to the <type> of <taxonomy> <id> (see www.phyloxml.org).
283 web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB
284 web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl
285 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI
286 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq
287 web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro
288 web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB
289 web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam
290 web_link: http://tolweb.org/ ToL tol
291 web_link: http://www.eol.org/pages/ EOL eol
292 web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot
293 web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi
294 web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID
295 # not working at the moment:
296 web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl
300 # Settings Specific for ArchaeopteryxE
301 # ------------------------------------
302 # To hide controls and menus: 'hide_controls_and_menus: yes'
303 # To use tabbed display : 'use_tabbed_display: yes'
305 hide_controls_and_menus: no
306 use_tabbed_display: yes
311 # Application Specific Settings
312 # -----------------------------
316 # Format: species_color: speciesname hexcolor
317 species_color: BRAFL 0x00FFFF
318 species_color: SPHGR 0x9620F0
319 species_color: STRPU 0x9620F0
320 species_color: CIOIN 0xFF1CAE
321 species_color: CIOSA 0xFF2CAE
322 species_color: BOVIN 0x5C3317
323 species_color: CANFA 0x8B2323
324 species_color: HUMAN 0xFF2400
325 species_color: PANTR 0xCC2400
326 species_color: MOUSE 0xFF7F00
327 species_color: RAT 0xFFEF00
328 species_color: MONDO 0xEE9A49
329 species_color: ORNAN 0xCD853F
330 species_color: XENLA 0x6BAA23
331 species_color: XENTR 0x6BAA23
332 species_color: CHICK 0xFFC125
333 species_color: FUGRU 0x0000FF
334 species_color: BRARE 0x0000DD
335 species_color: DANRE 0x0000BB
336 species_color: TETNG 0x0000AA
337 species_color: ORYLA 0x000088
338 species_color: GASAC 0x000066
339 species_color: CAEEL 0xA0A0A0
340 species_color: CAEBR 0xB0B0B0
341 species_color: DROME 0x706F00
342 species_color: DROPS 0x504F00
343 species_color: APIME 0x7A7700
344 species_color: AEDAE 0x8C5900
345 species_color: TRICA 0x918E00
346 species_color: NEMVE 0xAABADD
347 species_color: HYDAT 0x7C9BCF
348 species_color: LUBBA 0xF7B5CB
349 species_color: GEOCY 0xF5A0BD
350 species_color: SUBDO 0xC790B9
351 species_color: MONBE 0xFC0FC0
352 species_color: DICPU 0x23238E
353 species_color: DICDI 0x4D4DFF
354 species_color: ENTHI 0x5959AB
355 species_color: ARATH 0x00FF00
356 species_color: POPTR 0x006400
357 species_color: VITVI 0x00CD00
358 species_color: GLYMA 0x00FF7F
359 species_color: ORYSA 0x008B00
360 species_color: ORYSJ 0x008C00
361 species_color: SORBI 0x00EE76
362 species_color: SELMO 0x238E23
363 species_color: PHYPA 0x09F911
364 species_color: OSTLU 0x7FFF00
365 species_color: OSTTA 0x7FFF00
366 species_color: OSTRC 0x7FFF00
367 species_color: MICPU 0x66CD00
368 species_color: MIC99 0x66CD00
369 species_color: CHLRE 0xB3EE3A
370 species_color: VOLCA 0xC0FF3E
371 species_color: CHLSP 0x6B8E23
372 species_color: CYAME 0xD02090
373 species_color: YEAST 0xAAAAAA
374 species_color: BACFR 0xFF0000
375 species_color: BACTN 0xFFFF00
376 species_color: MYXXD 0x0000FF
377 species_color: STIAU 0x00FFFF
378 species_color: BACOV 0x8C5900
379 species_color: BACUN 0x66CD00
380 species_color: PORGI 0x918E00
382 species_color: Mammalia 0xFF0000
383 species_color: mammals 0xFF0000
385 species_color: Chordata 0x8470FF
386 species_color: Echinodermata 0x6495ED
387 species_color: Hemichordata 0x7EC0EE
388 species_color: Arthropoda 0x7AC5CD
389 species_color: Nematoda 0x7171C6
390 species_color: Tardigrada 0x388E8E
391 species_color: Annelida 0xC67171
392 species_color: Mollusca 0x00F5FF
393 species_color: Ctenophora 0xBBFFFF
394 species_color: Cnidaria 0xFF83FA
395 species_color: Placozoa 0xEED2EE
396 species_color: Porifera 0xFF3E96
397 species_color: Microsporidia 0x8B8378
398 species_color: Ascomycota 0xFF6347
399 species_color: Basidiomycota 0xFFD700
400 species_color: Chlorophyta 0x00C78C
401 species_color: Streptophyta 0x00C957
403 species_color: Viridiplantae 0x00FF00
404 species_color: plants 0x00FF00
405 species_color: Metazoa 0x0000FF
406 species_color: animals 0x0000FF
407 species_color: Fungi 0xFF9912
409 species_color: Viruses 0xFFD700
410 species_color: Bacteria 0x00FF00
411 species_color: Archaea 0x0000FF
412 species_color: Eukaryota 0xFF0000
413 species_color: eukaryotes 0xFF0000