3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
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11 * of the License, or (at your option) any later version.
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14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Preferences</title>
28 <strong>Preferences</strong>
31 The preferences panel is opened from the Jalview Desktop’s <strong><em>Tools</em></strong>
34 <p>There are eight tabs in the Preferences dialog box:
36 <li>The <a href="#visual"><strong>"Visual"</strong>
37 Preferences</a> tab allows you to configure the default display for
38 a new alignment window.
40 <li>The <a href="#colours"><strong>"Colours"</strong>
41 Preferences</a> tab allows you to configure default colourschemes
42 for a new alignment window.
44 <li>The <a href="#overview"><strong>"Overview"</strong>
45 Preferences</a> tab configures defaults for the overview window.
47 <li>The <a href="#structure"><strong>"Structure"</strong>
48 Preferences</a> tab allows you to configure options for obtaining
49 and displaying structure information.
51 <li>The <a href="#connections"><strong>"Connections"</strong>
52 Preferences</a> tab allows you to configure Jalview's internet
55 <li>The <a href="#links"><strong>"Links"</strong>
56 Preferences</a> tab shows the currently configured <em>URL
57 Links</em> shown in the <strong>Link</strong> submenu in the Sequence
60 <li>The <a href="#output"><strong>"Output"</strong>
61 Preferences</a> tab contains settings affecting the export of
62 sequence alignments and EPS files.
64 <li>The <a href="#editing"><strong>"Editing"</strong>
65 Preferences</a> tab contains settings affecting behaviour when editing alignments.
67 <li>The <a href="#startup"><strong>"Startup"</strong>
68 Preferences</a> tab allows you to adjust how much memory is
69 allocated to Jalview when it is launched.
71 <li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web
72 Service"</strong> Preferences</a> tab allows you to configure the <a
73 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
74 servers that Jalview uses, and change the layout of the
75 alignment's Web Services menu.
80 <strong><a name="visual">Visual</a> Preferences tab</strong>
83 <em>Maximise Window</em> - If this is selected, a new alignment
84 window will stretch to fit the available space.
87 <em>Open Overview Window</em> - When this is selected, the <a
88 href="overview.html">alignment overview</a> panel is opened
89 by default for a new alignment window.
92 <em>Show Annotations</em> - If this is selected the new window will
93 display an annotation panel below the sequences. This annotation
94 panel may have several rows describing the whole alignment. The 4
95 standard annotations <em>Conservation</em>, <em>Quality</em>,
96 <em>Occupancy</em> and <em>Consensus</em> for the alignment may
97 be shown or hidden by default using the checkboxes adjacent and
101 <em>Show group: Conservation and Consensus</em> controls the display
102 of per-group automatic annotation.
105 <em>Consensus: Histogram and Logo</em> checkboxes control the
106 display of the consensus histogram and sequence logo for consensus
110 <em>Full Sequence ID</em> - If selected the ID panel will display
111 the name of a sequence plus the start and end residues in the format
112 name/start-end. If not selected, the displayed ID will be the name
116 <em>Right Align IDs</em> - select to align all sequence IDs to the
117 left-hand edge of the sequence alignment, rather than the left-hand
118 edge of the alignment display window.
121 <em>Font</em> - The default font name, size and style can be set for
122 a new alignment window.
125 <em>Sequence ID Tooltip</em>: Control the display of Database
126 References and Non-positional annotation in the tooltip displayed
127 when the mouse is over a sequence's ID.
130 <em>Show Unconserved</em> - When this is selected, all consensus
131 sequence symbols will be rendered as a '.', highlighting mutations
132 in highly conserved alignments.
135 <em>Sequence Name Italics</em> - select to apply the italicised
136 version of the font to sequence labels.
139 <em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
140 rendering of the alignment.
143 <em>Gap Symbol</em> - The default gap symbol may be set to either
144 "-" or "."
147 <em>Wrap Alignment</em> - Select whether to open new alignment
148 windows in wrapped mode or not.
151 <em>Sort alignment by</em> - When the alignment is loaded in, it can
152 be ordered as read (No sort), or sorted by Id or pairwise identity.
155 <em>Sort annotations by</em> - Annotations can be unsorted, sorted
156 by the order of the related sequences in the alignment, or by label.
157 Autocalculated annotations (e.g. Consensus) can be shown either last
158 (below sequence annotations) or first (above sequence annotations).
159 <em>Since Jalview 2.8.2.</em>
162 <em>Open file</em> - If this is selected then the default alignment
163 file will be opened when Jalview is started. You can change the
164 default file by clicking on file name and either typing in the file
165 path or selecting it from the file chooser window.<br /> <em>Note:
166 The default example alignment is updated periodically to
167 demonstrate new features in Jalview.</em>
170 <a name="colours"><strong>"Colours"
171 Preferences tab</strong>
174 <em>Alignment Colour</em> - The default colour scheme for a new
175 alignment window. If the chosen option is "User Defined"
176 then the last User Defined Colour loaded or saved via the User
177 Defined Colours panel will be loaded.
180 <em>Annotation Shading Default</em> - set the default minimum and
181 maximum colours used when <a
182 href="../colourSchemes/annotationColouring.html">Colour
183 by Annotation...</a> is selected from the alignment window's colours
187 <a name="overview"><strong>"Overview"
188 Preferences tab</strong>
191 <em>Use legacy gap colouring (gaps are white)</em> - when enabled,
192 Jalview's overview shows gaps as white, and sequences with no
193 colourscheme applied as grey.
196 <em>Show Hidden regions when opening overview</em> - default setting
197 for inclusion of hidden regions.
200 <em>Gap Colour</em> - When legacy gap colouring is not enabled, this
201 configures the default colour for gaps in the overview.
204 <em>Hidden Colour</em> - colour used to highlight regions in the
205 overview that are hidden in the alignment.
208 <a name="structure"><strong>"Structure"
209 Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
212 <em>Process secondary structure from PDB</em> - if selected, then
213 structure information read from PDB will be processed and annotation
214 added to associated sequences.
216 <em>Use RNAView for secondary structure</em> - if selected, the
217 pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
218 will be called to derive secondary structure information for RNA
221 <em>Add secondary structure annotation to alignment</em> - if
222 selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
223 implementation DSSP</a> will be used to add annotation to polypeptide
224 chains in the structure.
226 <em>Add Temperature Factor annotation to alignment</em> - if
227 selected, values extracted from the Temperature Factor column for
228 the backbone atoms in the PDB file will be extracted as annotation
229 lines shown on the alignment.<br/><em>Since 2.11.2, scores from the Temperature Column for structures imported via the 3D-Beacons network may be shown instead as model quality or reliability scores.</em>
231 <em>Default structure viewer</em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
232 viewing 3D structures.
234 <em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
235 standard installation paths for Windows, Linux or MacOS. If Jalview cannot locate the installation for your selected structure viewer, a dialog will be shown. If you have
236 installed the chosen viewer in a non-standard location, you can specify it
237 here, by entering the full path to its executable.<br/>For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also <em>double-click this field</em> to open a file chooser dialog.</p>
239 <em>Sequence <-> Structure Mapping Method</em> - This setting controls whether
240 Jalview attempts to retrieve mappings between Uniprot protein
241 sequences and 3D structures in the PDBe with SIFTS, or constructs a
242 mapping by conservative alignment between the sequences and chains
243 in the 3D structure data using the Needleman and Wunsch algorithm.
244 SIFTS is enabled by default.
246 <em>PDB Fields shown in Search and Structure Summaries</em> - ticks
247 in this table indicate fields shown by default when browsing results
248 of a free text search via the PDB sequence fetcher, or 3D structures
249 offered by the 3D Structure Chooser.<p>
251 <a name="connections"><strong>"Connections"
252 Preferences tab</strong></a>
255 <em>Default Browser (Unix)</em><br> It's difficult in Java to
256 detect the default web browser for Unix users. If Jalview can't find
257 your default web browser, enter the name or full path to your web
261 <em>Proxy Server</em><br>
262 There are three settings to choose from:<br>
264 <li><em>No proxy servers</em> will configure Jalview to use a
265 direct internet connection.</li>
266 <li><em>System proxy servers</em> will configure Jalview to use
267 the proxy server passed to it by your system at startup.</li>
268 <li><em>Use these proxy servers:</em> allows you to set a custom
271 If you normally use a proxy server for using the internet, you must
272 choose one of <em>System proxy servers</em>, or if these have not been
273 passed correctly you should set your own proxy servers to use by selecting
274 <em>Use these proxy servers</em>.
275 You will then need to enter the host and port details as necessary.
276 Web Services will not work if you are using a proxy server and do
277 not choose the system proxy or enter your own settings here.<br>
278 There are separate host and port settings for HTTP and HTTPS proxies.
279 Often these are the same but you should enter the host and port into both
281 You can also check the <em>Authentication required</em> box if your proxy
282 requires username and password authentication. You can enter both the
283 <em>Username</em> and <em>Password</em> but only the <em>Username</em> will
284 be stored in Jalview's preferences file, the password will only be stored
285 until the end of the current Jalview session.<br>
286 This means that if the proxy settings are still valid, Jalview will ask for
287 the password when it starts the next session.
290 <em>Usage statistics, Questionnaire and Version checks</em><br>
291 Uncheck these options to prevent Jalview from submitting usage
292 statistics to google analytics, checking for Jalview questionnaires
293 or retrieving details of the latest release version (at
294 www.jalview.org). See the <a href="../privacy.html">user privacy
295 statement</a> for more information.
298 <a name="backups"><strong>The "Backups" Preferences Tab</strong></a>
300 <p>Since Jalview 2.11.0, overwriting an existing file when saving
301 or exporting data will by default trigger a backup file to be
302 created. Several options are provided to control how backup files
303 are named, and how many old versions will be kept.</p>
305 <em>Schemes</em> - select from three default schemes <em>Single Backup</em>, <em>Keep All Versions</em>, and <em>Rolled Backup Files</em>, or choose <em>Custom</em> to enable a previously defined custom scheme.
307 <em>Custom</em> - Check this box to adjust the parameters of the currently selected scheme. Once <em>OK</em> is selected these parameters will be saved as the <em>Custom</em> scheme in your user preferences. To revert changes hit <em>Cancel</em>.
309 <p><em>Scheme Examples</em> - shows how backup files will appear according to the currently selected scheme and parameters.
311 <p><em>Deleting Old Backup Files</em> - these settings control how many backups are kept.</p>
312 <p><em>Backup filename strategy</em> - specify the naming convention for numbered backups and how they are ordered.</p>
314 <a name="links"><strong>The "Links" Preferences
318 This panel shows a table, and two sections - <em>Edit</em> and <em>Filter</em>.
319 The table shows the available URL link definitions (consisting of a
320 database, Name, and URL template string), a checkbox <em>In
321 Menu</em> which indicates if the link is enabled, and <em>Double
322 Click</em> which marks the link that will be opened if a sequence's ID
323 is double clicked. The table can be sorted by clicking on the column headers.
325 <p><em>Edit Links</em><br /> This section contains three buttons,
326 <em>New</em>, <em>Edit</em> and <em>Delete</em>, which allow you to
327 create, modify and remove user-defined URL links from the Sequence
331 <em>Filter</em><br /> The <em>Filter text</em> box allows you to
332 quickly show rows in the table containing a particular text string.
333 The <em>Custom only</em> button limits the entries in the table to
334 just those you have configured yourself <em>via</em> the <em>Edit
335 Links</em> buttons. Press <em>Show all</em> to clear any filters.
337 <p>The links table is prepopulated with persistent URLs for many common
338 bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
339 the <em>identifiers.org</em> website, and the names and URLs are not
341 <a href="../webServices/urllinks.html#urllinks">Read more about configuring
345 <a name="output"><strong>Output Preferences tab</strong></a>
348 <em>EPS Rendering Style</em><br> This is a selection box which
349 allows the user to set a default rendering style for EPS export:
351 <li>"Prompt each time"<br> Choose this to be
352 asked to select between Lineart and Text each time you make an EPS
355 <li>"Lineart"<br> EPS files will accurately
356 reproduce the alignment view in Jalview and all characters will be
357 converted into line art. Files generated in this way are large and
358 are not easily editable, but have no font table dependencies.
360 <li>"Text"<br> EPS files will be a mixture of
361 text and lineart. This produces compact files that can be edited
362 easily in programs like Microsoft Word and Adobe Illustrator, but
363 can be problematic if the fonts available to Jalview are not
364 accessible by the program reading the EPS file.
367 <em>Automatically set ID width</em><br> When enabled, the
368 column containing sequence and annotation labels at the left hand
369 side of an exported figure will be made large enough to display each
370 sequence ID and annotation label in its own line. Enable this if you
371 have particularly long sequence IDs and need to generate EPS or PNG
372 figures or web pages.
375 <em>Figure ID column width</em><br> Manually specify the width
376 of the left hand column where sequence IDs and annotation labels
377 will be rendered in exported alignment figures. This setting will be
378 ignored if <em>"Automatically set ID width"</em> is set.
381 <em>Sequence/Start-End Numbering</em><br> The output tab also
382 has a group of checkboxes for each file format. If these are ticked,
383 then Jalview will write files with the start and end sequence
384 positions appended to each sequence id:
389 <p>If the boxes are left unchecked for a particular format, the
390 sequence limits will not be appended to the sequence id.</p>
392 <em>Embed BioJSON to HTML export</em>
395 When this option is enabled, Jalview embeds <a
396 href="bioJsonFormat.html">BioJSON</a> data within HTML files
397 exported from Jalview at generation time. This enables the exported
398 HTML files to be extracted and imported back into the Jalview
399 desktop application at a later time.
401 <em>Use Modeller Output</em>
404 This option only applies to PIR format output. Jalview automatically
405 reads PIR files with sequence descriptions compatible with the
406 program <a href="http://salilab.org/modeller/">Modeller</a>. If this
407 option is selected <a href="../io/modellerpir.html">Jalview will
408 write Modeller style PIR files</a> with correct start/end numbering
409 and PDB file association (if available). The Jalview id/start-end
410 option is ignored if Modeller output is selected.
412 <a name="editing"><strong>"Editing" Preferences tab</strong></a>
414 <p>There are currently three options available which can be
415 selected / deselected.</p>
417 <em>AutoCalculate Consensus</em> - For large alignments it can be
418 useful to deselect "Autocalculate Consensus" when editing.
419 This prevents lengthy calculations which are performed after each
420 sequence edit. New alignment windows will have their
421 "Autocalculate Consensus" option set according to this
425 <em>Pad Gaps when Editing</em> - New alignment windows will
426 "Pad Gaps" according to this setting.
429 <em>Sort with New Tree</em> - When selected, any trees calculated or
430 loaded onto the alignment will automatically sort the alignment.
434 <a name="startup"><strong>Startup</strong></a>
437 When Jalview is launched it by default examines the available memory
438 and requests up to 90% to be allocated to the application, or 32G,
439 which ever is smaller. The <em>Startup</em> tab allows you to adjust
440 the maximum percentage and hard limits for Jalview memory allocation
441 stored in your .jalview_properties file.
444 <em>Web Services Preferences</em> - documentation for this tab is
446 <a href="../webServices/webServicesPrefs.html">Web Services
447 Preferences section</a>.