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.
18 * You should have received a copy of the GNU General Public License
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 the export of
66 sequence alignments and EPS files.
68 <li>The <a href="dassettings.html"><strong>"DAS
69 Settings"</strong> Preferences</a> tab allows you to select which DAS
70 sources to use when fetching DAS Features.
72 <li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web
73 Service"</strong> Preferences</a> tab allows you to configure the <a
74 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
75 servers that Jalview uses, and change the layout of the
76 alignment's Web Services menu.
81 <strong><a name="visual">Visual</a> Preferences tab</strong>
84 <em>Maximise Window</em> - If this is selected, a new alignment
85 window will stretch to fit the available space.
88 <em>Open Overview Window</em> - When this is selected, the <a
89 href="overview.html">alignment overview</a> panel is opened
90 by default for a new alignment window.
93 <em>Show Annotations</em> - If this is selected the new window will
94 display an annotation panel below the sequences. This annotation
95 panel may have several rows describing the whole alignment. The 4
96 standard annotations <em>Conservation</em>, <em>Quality</em>,
97 <em>Occupancy</em> and <em>Consensus</em> for the alignment may
98 be shown or hidden by default using the checkboxes adjacent and
102 <em>Show group: Conservation and Consensus</em> controls the display
103 of per-group automatic annotation.
106 <em>Consensus: Histogram and Logo</em> checkboxes control the
107 display of the consensus histogram and sequence logo for consensus
111 <em>Full Sequence ID</em> - If selected the ID panel will display
112 the name of a sequence plus the start and end residues in the format
113 name/start-end. If not selected, the displayed ID will be the name
117 <em>Right Align IDs</em> - select to align all sequence IDs to the
118 left-hand edge of the sequence alignment, rather than the left-hand
119 edge of the alignment display window.
122 <em>Font</em> - The default font name, size and style can be set for
123 a new alignment window.
126 <em>Sequence ID Tooltip</em>: Control the display of Database
127 References and Non-positional annotation in the tooltip displayed
128 when the mouse is over a sequence's ID.
131 <em>Show Unconserved</em> - When this is selected, all consensus
132 sequence symbols will be rendered as a '.', highlighting mutations
133 in highly conserved alignments.
136 <em>Sequence Name Italics</em> - select to apply the italicised
137 version of the font to sequence labels.
140 <em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
141 rendering of the alignment.
144 <em>Gap Symbol</em> - The default gap symbol may be set to either
145 "-" or "."
148 <em>Wrap Alignment</em> - Select whether to open new alignment
149 windows in wrapped mode or not.
152 <em>Sort alignment by</em> - When the alignment is loaded in, it can
153 be ordered as read (No sort), or sorted by Id or pairwise identity.
156 <em>Sort annotations by</em> - Annotations can be unsorted, sorted
157 by the order of the related sequences in the alignment, or by label.
158 Autocalculated annotations (e.g. Consensus) can be shown either last
159 (below sequence annotations) or first (above sequence annotations).
160 <em>Since Jalview 2.8.2.</em>
163 <em>Open file</em> - If this is selected then the default alignment
164 file will be opened when Jalview is started. You can change the
165 default file by clicking on file name and either typing in the file
166 path or selecting it from the file chooser window.<br /> <em>Note:
167 The default example alignment is updated periodically to
168 demonstrate new features in Jalview.</em>
171 <a name="colours"><strong>"Colours"
172 Preferences tab</strong>
175 <em>Alignment Colour</em> - The default colour scheme for a new
176 alignment window. If the chosen option is "User Defined"
177 then the last User Defined Colour loaded or saved via the User
178 Defined Colours panel will be loaded.
181 <em>Annotation Shading Default</em> - set the default minimum and
182 maximum colours used when <a
183 href="../colourSchemes/annotationColouring.html">Colour
184 by Annotation...</a> is selected from the alignment window's colours
188 <a name="overview"><strong>"Overview"
189 Preferences tab</strong>
192 <em>Use legacy gap colouring (gaps are white)</em> - when enabled,
193 Jalview's overview shows gaps as white, and sequences with no
194 colourscheme applied as grey.
197 <em>Show Hidden regions when opening overview</em> - default setting
198 for inclusion of hidden regions.
201 <em>Gap Colour</em> - When legacy gap colouring is not enabled, this
202 configures the default colour for gaps in the overview.
205 <em>Hidden Colour</em> - colour used to highlight regions in the
206 overview that are hidden in the alignment.
209 <em>Gap Colour</em> - The default colour scheme for a new alignment
210 window. If the chosen option is "User Defined" then the
211 last User Defined Colour loaded or saved via the User Defined
212 Colours panel will be loaded.
215 <a name="structure"><strong>"Structure"
216 Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
219 <em>Process secondary structure from PDB</em> - if selected, then
220 structure information read from PDB will be processed and annotation
221 added to associated sequences.
223 <em>Use RNAView for secondary structure</em> - if selected, the
224 pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
225 will be called to derive secondary structure information for RNA
228 <em>Add secondary structure annotation to alignment</em> - if
229 selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
230 implementation DSSP</a> will be used to add annotation to polypeptide
231 chains in the structure.
233 <em>Add Temperature Factor annotation to alignment</em> - if
234 selected, values extracted from the Temperature Factor column for
235 the backbone atoms in the PDB file will be extracted as annotation
236 lines shown on the alignment.
238 <em>Default structure viewer</em> - choose JMOL or CHIMERA for
239 viewing 3D structures.
241 <em>Path to Chimera program</em> - Optional, as Jalview will search
242 standard installation paths for Windows, Linux or MacOS. If you have
243 installed Chimera in a non-standard location, you can specify it
244 here, by entering the full path to the Chimera executable program.
245 Double-click this field to open a file chooser dialog.
247 <a name="connections"><strong>"Connections"
248 Preferences tab</strong></a>
251 <em>Default Browser (Unix)</em><br> Its difficult in Java to
252 detect the default web browser for Unix users. If Jalview can't find
253 your default web browser, enter the name or full path to your web
257 <em>Proxy Server</em><br> If you normally use a proxy server
258 for using the internet, you must tick the box "Use a Proxy
259 Server" and enter the address and port details as necessary.
260 Web Services will not work if you are using a proxy server and do
261 not enter the settings here.
264 <em>Usage statistics, Questionnaire and Version checks</em><br>
265 Uncheck these options to prevent Jalview from submitting usage
266 statistics to google analytics, checking for Jalview questionnaires
267 or retrieving details of the latest release version (at
268 www.jalview.org). See the <a href="../privacy.html">user privacy
269 statement</a> for more information.
272 <a name="links"><strong>The "Links" Preferences
276 This panel shows a table, and two sections - <em>Edit</em> and <em>Filter</em>.
277 The table shows the available URL link definitions (consisting of a
278 database, Name, and URL template string), a checkbox <em>In
279 Menu</em> which indicates if the link is enabled, and <em>Double
280 Click</em> which marks the link that will be opened if a sequence's ID
281 is double clicked. The table can be sorted by clicking on the column headers.
283 <p><em>Edit Links</em><br /> This section contains three buttons,
284 <em>New</em>, <em>Edit</em> and <em>Delete</em>, which allow you to
285 create, modify and remove user-defined URL links from the Sequence
289 <em>Filter</em><br /> The <em>Filter text</em> box allows you to
290 quickly show rows in the table containing a particular text string.
291 The <em>Custom only</em> button limits the entries in the table to
292 just those you have configured yourself <em>via</em> the <em>Edit
293 Links</em> buttons. Press <em>Show all</em> to clear any filters.
295 <p>The links table is prepoulated with persistent URLs for many common
296 bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
297 the <em>identifiers.org</em> website, and the names and URLs are not
299 <a href="../webServices/urllinks.html#urllinks">Read more about configuring
303 <a name="output"><strong>Output Preferences tab</strong></a>
306 <em>EPS Rendering Style</em><br> This is a selection box which
307 allows the user to set a default rendering style for EPS export:
309 <li>"Prompt each time"<br> Choose this to be
310 asked select between Lineart and Text each time you make an EPS
313 <li>"Lineart"<br> EPS files will accurately
314 reproduce the alignment view in Jalview and all characters will be
315 converted into line art. Files generated in this way are large and
316 are not easily editable, but have no font table dependencies.
318 <li>"Text"<br> EPS files will be a mixture of
319 text and lineart. This produces compact files that can be edited
320 easily in programs like Microsoft Word and Adobe Illustrator, but
321 can be problematic if the fonts available to Jalview are not
322 accessible by the program reading the EPS file.
325 <em>Automatically set ID width</em><br> When enabled, the
326 column containing sequence and annotation labels at the left hand
327 side of an exported figure will be made large enough to display each
328 sequence ID and annotation label in its own line. Enable this if you
329 have particularly long sequence IDs and need to generate EPS or PNG
330 figures or web pages.
333 <em>Figure ID column width</em><br> Manually specify the width
334 of the left hand column where sequence IDs and annotation labels
335 will be rendered in exported alignment figures. This setting will be
336 ignored if <em>"Automatically set ID width"</em> is set.
339 <em>Sequence//Start-End Numbering</em><br> The output tab also
340 has a group of checkboxes for each file format. If these are ticked,
341 then Jalview will write files with the start and end sequence
342 positions appended to each sequence id:
347 <p>If the boxes are left unchecked for a particular format, the
348 sequence limits will not be appended to the sequence id.</p>
350 <em>Embed BioJSON to HTML export</em>
353 When this option is enabled, Jalview embeds <a
354 href="bioJsonFormat.html">BioJSON</a> data within HTML files
355 exported from Jalview at generation time. This enables the exported
356 HTML files to be extracted and imported back into the Jalview
357 desktop application at a later time.
359 <em>Use Modeller Output</em>
362 This option only applies to PIR format output. Jalview automatically
363 reads PIR files with sequence descriptions compatible with the
364 program <a href="http://salilab.org/modeller/">Modeller</a>. If this
365 option is selected <a href="../io/modellerpir.html">Jalview will
366 write Modeller style PIR files</a> with correct start/end numbering
367 and PDB file association (if available). The Jalview id/start-end
368 option is ignored if Modeller output is selected.
370 <a name="editing"><strong>e"Editinge" Preferences tab</strong></a>
372 <p>There are currently three options available which can be
373 selected / deselected.</p>
375 <em>AutoCalculate Consensus</em> - For large alignments it can be
376 useful to deselect "Autocalculate Consensus" when editing.
377 This prevents lengthy calculations which are performed after each
378 sequence edit. New alignment windows will have their
379 "Autocalculate Consensus" option set according to this
383 <em>Pad Gaps when Editing</em> - New alignment windows will
384 "Pad Gaps" according to this setting.
387 <em>Sort with New Tree</em> - When selected, any trees calculated or
388 loaded onto the alignment will automatically sort the alignment.