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
155 # Initial Window Size for Application and ArchaeopteryA applet
156 # ------------------------------------------------------------
157 window_initial_size_x: 640
158 window_initial_size_y: 580
164 # To ensure compatibility with all current and future
165 # phyloXML applications and to detect malformatted and
166 # possibly erroneous data, it is strongly recommended
167 # to enable validation of all phyloXML files
168 # against the XSD Schema (see: http://www.phyloxml.org/),
170 # 'validate_against_phyloxml_xsd_schema: true'
172 validate_against_phyloxml_xsd_schema: true
176 # Checkbox Display Selection
177 # --------------------------
178 # This is used to select which checkboxes to display
179 # and what their initial values should be.
180 # Format: 'name: display|nodisplay yes|no'
181 # Note: if an option is not displayed, it will not be enabled
183 # For the following use '?' to let Archaeopteryx decide (depending on tree):
185 # - 'write_confidence_values'
189 rollover: display yes
190 color_according_to_species: display no
191 color_according_to_annotation: nodisplay no
192 show_node_names: display yes
193 show_gene_names: display yes
194 show_gene_symbols: nodisplay no
195 show_sequence_acc: nodisplay no
196 show_taxonomy_code: display yes
197 show_taxonomy_scientific_names: nodisplay no
198 show_taxonomy_common_names: nodisplay no
199 show_taxonomy_images: nodisplay no
200 show_annotations: nodisplay no
201 write_confidence_values: display ?
202 write_events: nodisplay no
203 color_branches: display no
204 width_branches: display no
205 show_domain_architectures: nodisplay no
206 show_binary_characters: nodisplay no
207 show_binary_character_counts: nodisplay no
208 display_internal_data: display yes
209 dynamically_hide_data: display yes
210 show_relation_confidence: nodisplay no
211 show_properties: nodisplay no
212 show_vector_data: nodisplay no
215 # Combo-box Display Selection
216 # ---------------------------
217 # Format: 'name: display/nodisplay'
218 click_to: display_node_data display
219 click_to: collapse_uncollapse display
220 click_to: reroot display
221 click_to: subtree display
222 click_to: swap display
223 click_to: sort_descendants display
224 click_to: color_subtree display
225 click_to: open_seq_web nodisplay
226 click_to: open_tax_web nodisplay
227 click_to: blast nodisplay
228 click_to: cut_subtree nodisplay
229 click_to: copy_subtree nodisplay
230 click_to: paste_subtree nodisplay
231 click_to: delete nodisplay
232 click_to: add_new_node nodisplay
233 click_to: edit_node_data display
234 click_to: select_nodes nodisplay
235 click_to: get_ext_descendents_data display
237 # Default click-to option (any of the above if set to "display")
238 default_click_to: display_node_data
241 # Default Tree Display Colors
242 # ---------------------------
244 display_color: background 0x000000
245 display_color: background_gradient_bottom 0x0000FF
246 display_color: sequence 0xDCDCDC
247 display_color: taxonomy 0xB4B4B4
248 display_color: confidence 0x38B0DE
249 display_color: branch_length 0x8C8C8C
250 display_color: branch 0xFFFFFF
251 display_color: node_box 0xFFFFFF
252 display_color: collapsed 0xFFFF00
253 display_color: matching_nodes 0x00FF00
254 display_color: duplication 0xFF0000
255 display_color: speciation 0x00FF00
256 display_color: duplication_or_specation 0xFFFF00
257 display_color: domains 0x7B68EE
258 display_color: binary_domain_combinations 0x4169FF
259 display_color: annotation 0xADFF2F
260 display_color: overview 0x828282
264 # GUI (graphical user interface) Colors
265 # -------------------------------------
267 # These are ignored if native (system) "look and feel"
268 # is being used ('native_ui: yes').
270 gui_background_color: 0x202020
271 gui_checkbox_text_color: 0xDCDCDC
272 gui_checkbox_and_button_active_color: 0xFF0000
273 gui_button_text_color: 0xFFFFFF
274 gui_button_background_color: 0x404040
275 gui_menu_background_color: 0x000000
276 gui_menu_text_color: 0xFFFFFF
277 gui_button_border_color: 0x000000
284 # Format: web_link: <URL> <description> <source identifier>
285 # E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
286 # <description> is not used at the moment.
287 # <source identifier> corresponds to the <source> element for <sequence> <accession>,
288 # and to the <type> of <taxonomy> <id> (see www.phyloxml.org).
290 web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB
291 web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl
292 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI
293 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq
294 web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro
295 web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB
296 web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam
297 web_link: http://tolweb.org/ ToL tol
298 web_link: http://www.eol.org/pages/ EOL eol
299 web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot
300 web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi
301 web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID
302 # not working at the moment:
303 web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl
307 # Settings Specific for ArchaeopteryxE
308 # ------------------------------------
309 # To hide controls and menus: 'hide_controls_and_menus: yes'
310 # To use tabbed display : 'use_tabbed_display: yes'
312 hide_controls_and_menus: no
313 use_tabbed_display: yes
318 # Application Specific Settings
319 # -----------------------------
323 # Format: species_color: speciesname hexcolor
324 species_color: BRAFL 0x00FFFF
325 species_color: SPHGR 0x9620F0
326 species_color: STRPU 0x9620F0
327 species_color: CIOIN 0xFF1CAE
328 species_color: CIOSA 0xFF2CAE
329 species_color: BOVIN 0x5C3317
330 species_color: CANFA 0x8B2323
331 species_color: HUMAN 0xFF2400
332 species_color: PANTR 0xCC2400
333 species_color: MOUSE 0xFF7F00
334 species_color: RAT 0xFFEF00
335 species_color: MONDO 0xEE9A49
336 species_color: ORNAN 0xCD853F
337 species_color: XENLA 0x6BAA23
338 species_color: XENTR 0x6BAA23
339 species_color: CHICK 0xFFC125
340 species_color: FUGRU 0x0000FF
341 species_color: BRARE 0x0000DD
342 species_color: DANRE 0x0000BB
343 species_color: TETNG 0x0000AA
344 species_color: ORYLA 0x000088
345 species_color: GASAC 0x000066
346 species_color: CAEEL 0xA0A0A0
347 species_color: CAEBR 0xB0B0B0
348 species_color: DROME 0x706F00
349 species_color: DROPS 0x504F00
350 species_color: APIME 0x7A7700
351 species_color: AEDAE 0x8C5900
352 species_color: TRICA 0x918E00
353 species_color: NEMVE 0xAABADD
354 species_color: HYDAT 0x7C9BCF
355 species_color: LUBBA 0xF7B5CB
356 species_color: GEOCY 0xF5A0BD
357 species_color: SUBDO 0xC790B9
358 species_color: MONBE 0xFC0FC0
359 species_color: DICPU 0x23238E
360 species_color: DICDI 0x4D4DFF
361 species_color: ENTHI 0x5959AB
362 species_color: ARATH 0x00FF00
363 species_color: POPTR 0x006400
364 species_color: VITVI 0x00CD00
365 species_color: GLYMA 0x00FF7F
366 species_color: ORYSA 0x008B00
367 species_color: ORYSJ 0x008C00
368 species_color: SORBI 0x00EE76
369 species_color: SELMO 0x238E23
370 species_color: PHYPA 0x09F911
371 species_color: OSTLU 0x7FFF00
372 species_color: OSTTA 0x7FFF00
373 species_color: OSTRC 0x7FFF00
374 species_color: MICPU 0x66CD00
375 species_color: MIC99 0x66CD00
376 species_color: CHLRE 0xB3EE3A
377 species_color: VOLCA 0xC0FF3E
378 species_color: CHLSP 0x6B8E23
379 species_color: CYAME 0xD02090
380 species_color: YEAST 0xAAAAAA
381 species_color: BACFR 0xFF0000
382 species_color: BACTN 0xFFFF00
383 species_color: MYXXD 0x0000FF
384 species_color: STIAU 0x00FFFF
385 species_color: BACOV 0x8C5900
386 species_color: BACUN 0x66CD00
387 species_color: PORGI 0x918E00
389 species_color: Mammalia 0xFF0000
390 species_color: mammals 0xFF0000
392 species_color: Chordata 0x8470FF
393 species_color: Echinodermata 0x6495ED
394 species_color: Hemichordata 0x7EC0EE
395 species_color: Arthropoda 0x7AC5CD
396 species_color: Nematoda 0x7171C6
397 species_color: Tardigrada 0x388E8E
398 species_color: Annelida 0xC67171
399 species_color: Mollusca 0x00F5FF
400 species_color: Ctenophora 0xBBFFFF
401 species_color: Cnidaria 0xFF83FA
402 species_color: Placozoa 0xEED2EE
403 species_color: Porifera 0xFF3E96
404 species_color: Microsporidia 0x8B8378
405 species_color: Ascomycota 0xFF6347
406 species_color: Basidiomycota 0xFFD700
407 species_color: Chlorophyta 0x00C78C
408 species_color: Streptophyta 0x00C957
410 species_color: Viridiplantae 0x00FF00
411 species_color: plants 0x00FF00
412 species_color: Metazoa 0x0000FF
413 species_color: animals 0x0000FF
414 species_color: Fungi 0xFF9912
416 species_color: Viruses 0xFFD700
417 species_color: Bacteria 0x00FF00
418 species_color: Archaea 0x0000FF
419 species_color: Eukaryota 0xFF0000
420 species_color: eukaryotes 0xFF0000