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.
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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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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="#hmmer"><strong>"HMMER"</strong>
72 Preferences</a> tab allows you to configure locally installed HMMER tools.
74 <li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web
75 Service"</strong> Preferences</a> tab allows you to configure the <a
76 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
77 servers that Jalview uses, and change the layout of the
78 alignment's Web Services menu.
83 <strong><a name="visual">Visual</a> Preferences tab</strong>
86 <em>Maximise Window</em> - If this is selected, a new alignment
87 window will stretch to fit the available space.
90 <em>Open Overview Window</em> - When this is selected, the <a
91 href="overview.html">alignment overview</a> panel is opened
92 by default for a new alignment window.
95 <em>Show Annotations</em> - If this is selected the new window will
96 display an annotation panel below the sequences. This annotation
97 panel may have several rows describing the whole alignment. The 4
98 standard annotations <em>Conservation</em>, <em>Quality</em>,
99 <em>Occupancy</em> and <em>Consensus</em> for the alignment may
100 be shown or hidden by default using the checkboxes adjacent and
104 <em>Show group: Conservation and Consensus</em> controls the display
105 of per-group automatic annotation.
108 <em>Consensus: Histogram and Logo</em> checkboxes control the
109 display of the consensus histogram and sequence logo for consensus
113 <em>Full Sequence ID</em> - If selected the ID panel will display
114 the name of a sequence plus the start and end residues in the format
115 name/start-end. If not selected, the displayed ID will be the name
119 <em>Right Align IDs</em> - select to align all sequence IDs to the
120 left-hand edge of the sequence alignment, rather than the left-hand
121 edge of the alignment display window.
124 <em>Font</em> - The default font name, size and style can be set for
125 a new alignment window.
128 <em>Sequence ID Tooltip</em>: Control the display of Database
129 References and Non-positional annotation in the tooltip displayed
130 when the mouse is over a sequence's ID.
133 <em>Show Unconserved</em> - When this is selected, all consensus
134 sequence symbols will be rendered as a '.', highlighting mutations
135 in highly conserved alignments.
138 <em>Sequence Name Italics</em> - select to apply the italicised
139 version of the font to sequence labels.
142 <em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
143 rendering of the alignment.
146 <em>Gap Symbol</em> - The default gap symbol may be set to either
147 "-" or "."
150 <em>Wrap Alignment</em> - Select whether to open new alignment
151 windows in wrapped mode or not.
154 <em>Sort alignment by</em> - When the alignment is loaded in, it can
155 be ordered as read (No sort), or sorted by Id or pairwise identity.
158 <em>Sort annotations by</em> - Annotations can be unsorted, sorted
159 by the order of the related sequences in the alignment, or by label.
160 Autocalculated annotations (e.g. Consensus) can be shown either last
161 (below sequence annotations) or first (above sequence annotations).
162 <em>Since Jalview 2.8.2.</em>
165 <em>Open file</em> - If this is selected then the default alignment
166 file will be opened when Jalview is started. You can change the
167 default file by clicking on file name and either typing in the file
168 path or selecting it from the file chooser window.<br /> <em>Note:
169 The default example alignment is updated periodically to
170 demonstrate new features in Jalview.</em>
173 <a name="colours"><strong>"Colours"
174 Preferences tab</strong>
177 <em>Alignment Colour</em> - The default colour scheme for a new
178 alignment window. If the chosen option is "User Defined"
179 then the last User Defined Colour loaded or saved via the User
180 Defined Colours panel will be loaded.
183 <em>Annotation Shading Default</em> - set the default minimum and
184 maximum colours used when <a
185 href="../colourSchemes/annotationColouring.html">Colour
186 by Annotation...</a> is selected from the alignment window's colours
190 <a name="overview"><strong>"Overview"
191 Preferences tab</strong>
194 <em>Use legacy gap colouring (gaps are white)</em> - when enabled,
195 Jalview's overview shows gaps as white, and sequences with no
196 colourscheme applied as grey.
199 <em>Show Hidden regions when opening overview</em> - default setting
200 for inclusion of hidden regions.
203 <em>Gap Colour</em> - When legacy gap colouring is not enabled, this
204 configures the default colour for gaps in the overview.
207 <em>Hidden Colour</em> - colour used to highlight regions in the
208 overview that are hidden in the alignment.
211 <a name="structure"><strong>"Structure"
212 Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
215 <em>Process secondary structure from PDB</em> - if selected, then
216 structure information read from PDB will be processed and annotation
217 added to associated sequences.
219 <em>Add secondary structure annotation to alignment</em> - if
220 selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
221 implementation DSSP</a> will be used to add annotation to polypeptide
222 chains in the structure.
224 <em>Add Temperature Factor annotation to alignment</em> - if
225 selected, values extracted from the Temperature Factor column for
226 the backbone atoms in the PDB file will be extracted as annotation
227 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>
229 <em><strong>Default structure viewer</strong></em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
230 viewing 3D structures.
232 <em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
233 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
234 installed the chosen viewer in a non-standard location, you can specify it
235 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>
237 <em>Sequence <-> Structure Mapping Method</em> - This setting controls whether
238 Jalview attempts to retrieve mappings between Uniprot protein
239 sequences and 3D structures in the PDBe with SIFTS, or constructs a
240 mapping by conservative alignment between the sequences and chains
241 in the 3D structure data using the Needleman and Wunsch algorithm.
242 SIFTS is enabled by default.
244 <em>PDB Fields shown in Search and Structure Summaries</em> - ticks
245 in this table indicate fields shown by default when browsing results
246 of a free text search via the PDB sequence fetcher, or 3D structures
247 offered by the 3D Structure Chooser.<p>
249 <a name="connections"><strong>"Connections"
250 Preferences tab</strong></a>
253 <em>Default Browser (Unix)</em><br> It's difficult in Java to
254 detect the default web browser for Unix users. If Jalview can't find
255 your default web browser, enter the name or full path to your web
259 <em>Proxy Server</em><br>
260 There are three settings to choose from:<br>
262 <li><em>No proxy servers</em> will configure Jalview to use a
263 direct internet connection.</li>
264 <li><em>System proxy servers</em> will configure Jalview to use
265 the proxy server passed to it by your system at startup.</li>
266 <li><em>Use these proxy servers:</em> allows you to set a custom
269 If you normally use a proxy server for using the internet, you must
270 choose one of <em>System proxy servers</em>, or if these have not been
271 passed correctly you should set your own proxy servers to use by selecting
272 <em>Use these proxy servers</em>.
273 You will then need to enter the host and port details as necessary.
274 Web Services will not work if you are using a proxy server and do
275 not choose the system proxy or enter your own settings here.<br>
276 There are separate host and port settings for HTTP and HTTPS proxies.
277 Often these are the same but you should enter the host and port into both
279 You can also check the <em>Authentication required</em> box if your proxy
280 requires username and password authentication. You can enter both the
281 <em>Username</em> and <em>Password</em> but only the <em>Username</em> will
282 be stored in Jalview's preferences file, the password will only be stored
283 until the end of the current Jalview session.<br>
284 This means that if the proxy settings are still valid, Jalview will ask for
285 the password when it starts the next session.
288 <em>Usage statistics, Questionnaire and Version checks</em><br>
289 Uncheck these options to prevent Jalview from submitting usage
290 statistics to google analytics, checking for Jalview questionnaires
291 or retrieving details of the latest release version (at
292 www.jalview.org). See the <a href="../privacy.html">user privacy
293 statement</a> for more information.
296 <a name="backups"><strong>The "Backups" Preferences Tab</strong></a>
298 <p>Since Jalview 2.11.0, overwriting an existing file when saving
299 or exporting data will by default trigger a backup file to be
300 created. Several options are provided to control how backup files
301 are named, and how many old versions will be kept.</p>
303 <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.
305 <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>.
307 <p><em>Scheme Examples</em> - shows how backup files will appear according to the currently selected scheme and parameters.
309 <p><em>Deleting Old Backup Files</em> - these settings control how many backups are kept.</p>
310 <p><em>Backup filename strategy</em> - specify the naming convention for numbered backups and how they are ordered.</p>
312 <a name="links"><strong>The "Links" Preferences
316 This panel shows a table, and two sections - <em>Edit</em> and <em>Filter</em>.
317 The table shows the available URL link definitions (consisting of a
318 database, Name, and URL template string), a checkbox <em>In
319 Menu</em> which indicates if the link is enabled, and <em>Double
320 Click</em> which marks the link that will be opened if a sequence's ID
321 is double clicked. The table can be sorted by clicking on the column headers.
323 <p><em>Edit Links</em><br /> This section contains three buttons,
324 <em>New</em>, <em>Edit</em> and <em>Delete</em>, which allow you to
325 create, modify and remove user-defined URL links from the Sequence
329 <em>Filter</em><br /> The <em>Filter text</em> box allows you to
330 quickly show rows in the table containing a particular text string.
331 The <em>Custom only</em> button limits the entries in the table to
332 just those you have configured yourself <em>via</em> the <em>Edit
333 Links</em> buttons. Press <em>Show all</em> to clear any filters.
335 <p>The links table is prepopulated with persistent URLs for many common
336 bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
337 the <em>identifiers.org</em> website, and the names and URLs are not
339 <a href="../webServices/urllinks.html#urllinks">Read more about configuring
343 <a name="output"><strong>Output Preferences tab</strong></a>
346 <em>EPS Rendering Style</em><br> This is a selection box which
347 allows the user to set a default rendering style for EPS export:
349 <li>"Prompt each time"<br> Choose this to be
350 asked to select between Lineart and Text each time you make an EPS
353 <li>"Lineart"<br> EPS files will accurately
354 reproduce the alignment view in Jalview and all characters will be
355 converted into line art. Files generated in this way are large and
356 are not easily editable, but have no font table dependencies.
358 <li>"Text"<br> EPS files will be a mixture of
359 text and lineart. This produces compact files that can be edited
360 easily in programs like Microsoft Word and Adobe Illustrator, but
361 can be problematic if the fonts available to Jalview are not
362 accessible by the program reading the EPS file.
365 <em>Automatically set ID width</em><br> When enabled, the
366 column containing sequence and annotation labels at the left hand
367 side of an exported figure will be made large enough to display each
368 sequence ID and annotation label in its own line. Enable this if you
369 have particularly long sequence IDs and need to generate EPS or PNG
370 figures or web pages.
373 <em>Figure ID column width</em><br> Manually specify the width
374 of the left hand column where sequence IDs and annotation labels
375 will be rendered in exported alignment figures. This setting will be
376 ignored if <em>"Automatically set ID width"</em> is set.
379 <em>Sequence/Start-End Numbering</em><br> The output tab also
380 has a group of checkboxes for each file format. If these are ticked,
381 then Jalview will write files with the start and end sequence
382 positions appended to each sequence id:
387 <p>If the boxes are left unchecked for a particular format, the
388 sequence limits will not be appended to the sequence id.</p>
390 <em>Embed BioJSON to HTML export</em>
393 When this option is enabled, Jalview embeds <a
394 href="bioJsonFormat.html">BioJSON</a> data within HTML files
395 exported from Jalview at generation time. This enables the exported
396 HTML files to be extracted and imported back into the Jalview
397 desktop application at a later time.
399 <em>Use Modeller Output</em>
402 This option only applies to PIR format output. Jalview automatically
403 reads PIR files with sequence descriptions compatible with the
404 program <a href="http://salilab.org/modeller/">Modeller</a>. If this
405 option is selected <a href="../io/modellerpir.html">Jalview will
406 write Modeller style PIR files</a> with correct start/end numbering
407 and PDB file association (if available). The Jalview id/start-end
408 option is ignored if Modeller output is selected.
410 <a name="editing"><strong>"Editing" Preferences tab</strong></a>
412 <p>There are currently three options available which can be
413 selected / deselected.</p>
415 <em>AutoCalculate Consensus</em> - For large alignments it can be
416 useful to deselect "Autocalculate Consensus" when editing.
417 This prevents lengthy calculations which are performed after each
418 sequence edit. New alignment windows will have their
419 "Autocalculate Consensus" option set according to this
423 <em>Pad Gaps when Editing</em> - New alignment windows will
424 "Pad Gaps" according to this setting.
427 <em>Sort with New Tree</em> - When selected, any trees calculated or
428 loaded onto the alignment will automatically sort the alignment.
432 <a name="startup"><strong>Startup</strong></a>
435 When Jalview is launched it by default examines the available memory
436 and requests up to 90% to be allocated to the application, or 32G,
437 which ever is smaller. The <em>Startup</em> tab allows you to adjust
438 the maximum percentage and hard limits for Jalview memory allocation
439 stored in your .jalview_properties file.
443 <a name="hmmer"><strong>"HMMER" Preferences tab</strong></a>
445 <p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),
446 then you should specify on this screen the location of the installation (the path to the folder
447 containing binary executable programs). Double-click in the input field to open a file browser.</p>
448 <p>When this path is configured, the <a href="../menus/alwhmmer.html">HMMER menu</a> will be
449 enabled in the Alignment window.</p>
451 <em>Web Services Preferences</em> - documentation for this tab is
453 <a href="../webServices/webServicesPrefs.html">Web Services
454 Preferences section</a>.