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
53 settings and specify your default web browser.
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="../webServices/webServicesPrefs.html"><strong>"Web
68 Service"</strong> Preferences</a> tab allows you to configure the <a
69 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
70 servers that Jalview uses, and change the layout of the
71 alignment's Web Services menu.
76 <strong><a name="visual">Visual</a> Preferences tab</strong>
79 <em>Maximise Window</em> - If this is selected, a new alignment
80 window will stretch to fit the available space.
83 <em>Open Overview Window</em> - When this is selected, the <a
84 href="overview.html">alignment overview</a> panel is opened
85 by default for a new alignment window.
88 <em>Show Annotations</em> - If this is selected the new window will
89 display an annotation panel below the sequences. This annotation
90 panel may have several rows describing the whole alignment. The 4
91 standard annotations <em>Conservation</em>, <em>Quality</em>,
92 <em>Occupancy</em> and <em>Consensus</em> for the alignment may
93 be shown or hidden by default using the checkboxes adjacent and
97 <em>Show group: Conservation and Consensus</em> controls the display
98 of per-group automatic annotation.
101 <em>Consensus: Histogram and Logo</em> checkboxes control the
102 display of the consensus histogram and sequence logo for consensus
106 <em>Full Sequence ID</em> - If selected the ID panel will display
107 the name of a sequence plus the start and end residues in the format
108 name/start-end. If not selected, the displayed ID will be the name
112 <em>Right Align IDs</em> - select to align all sequence IDs to the
113 left-hand edge of the sequence alignment, rather than the left-hand
114 edge of the alignment display window.
117 <em>Font</em> - The default font name, size and style can be set for
118 a new alignment window.
121 <em>Sequence ID Tooltip</em>: Control the display of Database
122 References and Non-positional annotation in the tooltip displayed
123 when the mouse is over a sequence's ID.
126 <em>Show Unconserved</em> - When this is selected, all consensus
127 sequence symbols will be rendered as a '.', highlighting mutations
128 in highly conserved alignments.
131 <em>Sequence Name Italics</em> - select to apply the italicised
132 version of the font to sequence labels.
135 <em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
136 rendering of the alignment.
139 <em>Gap Symbol</em> - The default gap symbol may be set to either
140 "-" or "."
143 <em>Wrap Alignment</em> - Select whether to open new alignment
144 windows in wrapped mode or not.
147 <em>Sort alignment by</em> - When the alignment is loaded in, it can
148 be ordered as read (No sort), or sorted by Id or pairwise identity.
151 <em>Sort annotations by</em> - Annotations can be unsorted, sorted
152 by the order of the related sequences in the alignment, or by label.
153 Autocalculated annotations (e.g. Consensus) can be shown either last
154 (below sequence annotations) or first (above sequence annotations).
155 <em>Since Jalview 2.8.2.</em>
158 <em>Open file</em> - If this is selected then the default alignment
159 file will be opened when Jalview is started. You can change the
160 default file by clicking on file name and either typing in the file
161 path or selecting it from the file chooser window.<br /> <em>Note:
162 The default example alignment is updated periodically to
163 demonstrate new features in Jalview.</em>
166 <a name="colours"><strong>"Colours"
167 Preferences tab</strong>
170 <em>Alignment Colour</em> - The default colour scheme for a new
171 alignment window. If the chosen option is "User Defined"
172 then the last User Defined Colour loaded or saved via the User
173 Defined Colours panel will be loaded.
176 <em>Annotation Shading Default</em> - set the default minimum and
177 maximum colours used when <a
178 href="../colourSchemes/annotationColouring.html">Colour
179 by Annotation...</a> is selected from the alignment window's colours
183 <a name="overview"><strong>"Overview"
184 Preferences tab</strong>
187 <em>Use legacy gap colouring (gaps are white)</em> - when enabled,
188 Jalview's overview shows gaps as white, and sequences with no
189 colourscheme applied as grey.
192 <em>Show Hidden regions when opening overview</em> - default setting
193 for inclusion of hidden regions.
196 <em>Gap Colour</em> - When legacy gap colouring is not enabled, this
197 configures the default colour for gaps in the overview.
200 <em>Hidden Colour</em> - colour used to highlight regions in the
201 overview that are hidden in the alignment.
204 <a name="structure"><strong>"Structure"
205 Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
208 <em>Process secondary structure from PDB</em> - if selected, then
209 structure information read from PDB will be processed and annotation
210 added to associated sequences.
212 <em>Use RNAView for secondary structure</em> - if selected, the
213 pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
214 will be called to derive secondary structure information for RNA
217 <em>Add secondary structure annotation to alignment</em> - if
218 selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
219 implementation DSSP</a> will be used to add annotation to polypeptide
220 chains in the structure.
222 <em>Add Temperature Factor annotation to alignment</em> - if
223 selected, values extracted from the Temperature Factor column for
224 the backbone atoms in the PDB file will be extracted as annotation
225 lines shown on the alignment.
227 <em>Default structure viewer</em> - choose Jmol or CHIMERA for
228 viewing 3D structures.
230 <em>Path to Chimera program</em> - Optional, as Jalview will search
231 standard installation paths for Windows, Linux or MacOS. If you have
232 installed Chimera in a non-standard location, you can specify it
233 here, by entering the full path to the Chimera executable program.
234 Double-click this field to open a file chooser dialog.
237 <em>PDB Fields shown in Search and Structure Summaries</em> - ticks
238 in this table indicate fields shown by default when browsing results
239 of a free text search via the PDB sequence fetcher, or 3D structures
240 offered by the 3D Structure Chooser.<p>
242 <a name="connections"><strong>"Connections"
243 Preferences tab</strong></a>
246 <em>Default Browser (Unix)</em><br> It's difficult in Java to
247 detect the default web browser for Unix users. If Jalview can't find
248 your default web browser, enter the name or full path to your web
252 <em>Proxy Server</em><br>
253 There are three settings to choose from:<br>
255 <li><em>No proxy servers</em> will configure Jalview to use a
256 direct internet connection.</li>
257 <li><em>System proxy servers</em> will configure Jalview to use
258 the proxy server passed to it by your system at startup.</li>
259 <li><em>Use these proxy servers:</em> allows you to set a custom
262 If you normally use a proxy server for using the internet, you must
263 choose one of <em>System proxy servers</em>, or if these have not been
264 passed correctly you should set your own proxy servers to use by selecting
265 <em>Use these proxy servers</em>.
266 You will then need to enter the host and port details as necessary.
267 Web Services will not work if you are using a proxy server and do
268 not choose the system proxy or enter your own settings here.<br>
269 There are separate host and port settings for HTTP and HTTPS proxies.
270 Often these are the same but you should enter the host and port into both
272 You can also check the <em>Authentication required</em> box if your proxy
273 requires username and password authentication. You can enter both the
274 <em>Username</em> and <em>Password</em> but only the <em>Username</em> will
275 be stored in Jalview's preferences file, the password will only be stored
276 until the end of the current Jalview session.<br>
277 This means that if the proxy settings are still valid, Jalview will ask for
278 the password when it starts the next session.
281 <em>Usage statistics, Questionnaire and Version checks</em><br>
282 Uncheck these options to prevent Jalview from submitting usage
283 statistics to google analytics, checking for Jalview questionnaires
284 or retrieving details of the latest release version (at
285 www.jalview.org). See the <a href="../privacy.html">user privacy
286 statement</a> for more information.
289 <a name="backups"><strong>The "Backups" Preferences Tab</strong></a>
291 <p>Since Jalview 2.11.0, overwriting an existing file when saving
292 or exporting data will by default trigger a backup file to be
293 created. Several options are provided to control how backup files
294 are named, and how many old versions will be kept.</p>
296 <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.
298 <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>.
300 <p><em>Scheme Examples</em> - shows how backup files will appear according to the currently selected scheme and parameters.
302 <p><em>Deleting Old Backup Files</em> - these settings control how many backups are kept.</p>
303 <p><em>Backup filename strategy</em> - specify the naming convention for numbered backups and how they are ordered.</p>
305 <a name="links"><strong>The "Links" Preferences
309 This panel shows a table, and two sections - <em>Edit</em> and <em>Filter</em>.
310 The table shows the available URL link definitions (consisting of a
311 database, Name, and URL template string), a checkbox <em>In
312 Menu</em> which indicates if the link is enabled, and <em>Double
313 Click</em> which marks the link that will be opened if a sequence's ID
314 is double clicked. The table can be sorted by clicking on the column headers.
316 <p><em>Edit Links</em><br /> This section contains three buttons,
317 <em>New</em>, <em>Edit</em> and <em>Delete</em>, which allow you to
318 create, modify and remove user-defined URL links from the Sequence
322 <em>Filter</em><br /> The <em>Filter text</em> box allows you to
323 quickly show rows in the table containing a particular text string.
324 The <em>Custom only</em> button limits the entries in the table to
325 just those you have configured yourself <em>via</em> the <em>Edit
326 Links</em> buttons. Press <em>Show all</em> to clear any filters.
328 <p>The links table is prepopulated with persistent URLs for many common
329 bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
330 the <em>identifiers.org</em> website, and the names and URLs are not
332 <a href="../webServices/urllinks.html#urllinks">Read more about configuring
336 <a name="output"><strong>Output Preferences tab</strong></a>
339 <em>EPS Rendering Style</em><br> This is a selection box which
340 allows the user to set a default rendering style for EPS export:
342 <li>"Prompt each time"<br> Choose this to be
343 asked to select between Lineart and Text each time you make an EPS
346 <li>"Lineart"<br> EPS files will accurately
347 reproduce the alignment view in Jalview and all characters will be
348 converted into line art. Files generated in this way are large and
349 are not easily editable, but have no font table dependencies.
351 <li>"Text"<br> EPS files will be a mixture of
352 text and lineart. This produces compact files that can be edited
353 easily in programs like Microsoft Word and Adobe Illustrator, but
354 can be problematic if the fonts available to Jalview are not
355 accessible by the program reading the EPS file.
358 <em>Automatically set ID width</em><br> When enabled, the
359 column containing sequence and annotation labels at the left hand
360 side of an exported figure will be made large enough to display each
361 sequence ID and annotation label in its own line. Enable this if you
362 have particularly long sequence IDs and need to generate EPS or PNG
363 figures or web pages.
366 <em>Figure ID column width</em><br> Manually specify the width
367 of the left hand column where sequence IDs and annotation labels
368 will be rendered in exported alignment figures. This setting will be
369 ignored if <em>"Automatically set ID width"</em> is set.
372 <em>Sequence/Start-End Numbering</em><br> The output tab also
373 has a group of checkboxes for each file format. If these are ticked,
374 then Jalview will write files with the start and end sequence
375 positions appended to each sequence id:
380 <p>If the boxes are left unchecked for a particular format, the
381 sequence limits will not be appended to the sequence id.</p>
383 <em>Embed BioJSON to HTML export</em>
386 When this option is enabled, Jalview embeds <a
387 href="bioJsonFormat.html">BioJSON</a> data within HTML files
388 exported from Jalview at generation time. This enables the exported
389 HTML files to be extracted and imported back into the Jalview
390 desktop application at a later time.
392 <em>Use Modeller Output</em>
395 This option only applies to PIR format output. Jalview automatically
396 reads PIR files with sequence descriptions compatible with the
397 program <a href="http://salilab.org/modeller/">Modeller</a>. If this
398 option is selected <a href="../io/modellerpir.html">Jalview will
399 write Modeller style PIR files</a> with correct start/end numbering
400 and PDB file association (if available). The Jalview id/start-end
401 option is ignored if Modeller output is selected.
403 <a name="editing"><strong>"Editing" Preferences tab</strong></a>
405 <p>There are currently three options available which can be
406 selected / deselected.</p>
408 <em>AutoCalculate Consensus</em> - For large alignments it can be
409 useful to deselect "Autocalculate Consensus" when editing.
410 This prevents lengthy calculations which are performed after each
411 sequence edit. New alignment windows will have their
412 "Autocalculate Consensus" option set according to this
416 <em>Pad Gaps when Editing</em> - New alignment windows will
417 "Pad Gaps" according to this setting.
420 <em>Sort with New Tree</em> - When selected, any trees calculated or
421 loaded onto the alignment will automatically sort the alignment.
424 <em>Web Services Preferences</em> - documentation for this tab is
426 <a href="../webServices/webServicesPrefs.html">Web Services
427 Preferences section</a>.