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 the behaviour of alignments as you edit them.
67 <li>The <a href="#hmmer"><strong>"HMMER"</strong>
68 Preferences</a> tab allows you to configure locally installed HMMER tools.
70 <li>The <a href="dassettings.html"><strong>"DAS
71 Settings"</strong> Preferences</a> tab allows you to select which DAS
72 sources to use when fetching DAS Features.
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 <em>Gap Colour</em> - The default colour scheme for a new alignment
212 window. If the chosen option is "User Defined" then the
213 last User Defined Colour loaded or saved via the User Defined
214 Colours panel will be loaded.
217 <a name="structure"><strong>"Structure"
218 Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
221 <em>Process secondary structure from PDB</em> - if selected, then
222 structure information read from PDB will be processed and annotation
223 added to associated sequences.
225 <em>Use RNAView for secondary structure</em> - if selected, the
226 pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
227 will be called to derive secondary structure information for RNA
230 <em>Add secondary structure annotation to alignment</em> - if
231 selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
232 implementation DSSP</a> will be used to add annotation to polypeptide
233 chains in the structure.
235 <em>Add Temperature Factor annotation to alignment</em> - if
236 selected, values extracted from the Temperature Factor column for
237 the backbone atoms in the PDB file will be extracted as annotation
238 lines shown on the alignment.
240 <em>Default structure viewer</em> - choose JMOL or CHIMERA for
241 viewing 3D structures.
243 <em>Path to Chimera program</em> - Optional, as Jalview will search
244 standard installation paths for Windows, Linux or MacOS. If you have
245 installed Chimera in a non-standard location, you can specify it
246 here, by entering the full path to the Chimera executable program.
247 Double-click this field to open a file chooser dialog.
249 <a name="connections"><strong>"Connections"
250 Preferences tab</strong></a>
253 <em>Default Browser (Unix)</em><br> Its 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> If you normally use a proxy server
260 for using the internet, you must tick the box "Use a Proxy
261 Server" and enter the address and port details as necessary.
262 Web Services will not work if you are using a proxy server and do
263 not enter the settings here.
266 <em>Usage statistics, Questionnaire and Version checks</em><br>
267 Uncheck these options to prevent Jalview from submitting usage
268 statistics to google analytics, checking for Jalview questionnaires
269 or retrieving details of the latest release version (at
270 www.jalview.org). See the <a href="../privacy.html">user privacy
271 statement</a> for more information.
274 <a name="links"><strong>The "Links" Preferences
278 This panel shows a table, and two sections - <em>Edit</em> and <em>Filter</em>.
279 The table shows the available URL link definitions (consisting of a
280 database, Name, and URL template string), a checkbox <em>In
281 Menu</em> which indicates if the link is enabled, and <em>Double
282 Click</em> which marks the link that will be opened if a sequence's ID
283 is double clicked. The table can be sorted by clicking on the column headers.
285 <p><em>Edit Links</em><br /> This section contains three buttons,
286 <em>New</em>, <em>Edit</em> and <em>Delete</em>, which allow you to
287 create, modify and remove user-defined URL links from the Sequence
291 <em>Filter</em><br /> The <em>Filter text</em> box allows you to
292 quickly show rows in the table containing a particular text string.
293 The <em>Custom only</em> button limits the entries in the table to
294 just those you have configured yourself <em>via</em> the <em>Edit
295 Links</em> buttons. Press <em>Show all</em> to clear any filters.
297 <p>The links table is prepoulated with persistent URLs for many common
298 bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
299 the <em>identifiers.org</em> website, and the names and URLs are not
301 <a href="../webServices/urllinks.html#urllinks">Read more about configuring
305 <a name="output"><strong>Output Preferences tab</strong></a>
308 <em>EPS Rendering Style</em><br> This is a selection box which
309 allows the user to set a default rendering style for EPS export:
311 <li>"Prompt each time"<br> Choose this to be
312 asked select between Lineart and Text each time you make an EPS
315 <li>"Lineart"<br> EPS files will accurately
316 reproduce the alignment view in Jalview and all characters will be
317 converted into line art. Files generated in this way are large and
318 are not easily editable, but have no font table dependencies.
320 <li>"Text"<br> EPS files will be a mixture of
321 text and lineart. This produces compact files that can be edited
322 easily in programs like Microsoft Word and Adobe Illustrator, but
323 can be problematic if the fonts available to Jalview are not
324 accessible by the program reading the EPS file.
327 <em>Automatically set ID width</em><br> When enabled, the
328 column containing sequence and annotation labels at the left hand
329 side of an exported figure will be made large enough to display each
330 sequence ID and annotation label in its own line. Enable this if you
331 have particularly long sequence IDs and need to generate EPS or PNG
332 figures or web pages.
335 <em>Figure ID column width</em><br> Manually specify the width
336 of the left hand column where sequence IDs and annotation labels
337 will be rendered in exported alignment figures. This setting will be
338 ignored if <em>"Automatically set ID width"</em> is set.
341 <em>Sequence//Start-End Numbering</em><br> The output tab also
342 has a group of checkboxes for each file format. If these are ticked,
343 then Jalview will write files with the start and end sequence
344 positions appended to each sequence id:
349 <p>If the boxes are left unchecked for a particular format, the
350 sequence limits will not be appended to the sequence id.</p>
352 <em>Embed BioJSON to HTML export</em>
355 When this option is enabled, Jalview embeds <a
356 href="bioJsonFormat.html">BioJSON</a> data within HTML files
357 exported from Jalview at generation time. This enables the exported
358 HTML files to be extracted and imported back into the Jalview
359 desktop application at a later time.
361 <em>Use Modeller Output</em>
364 This option only applies to PIR format output. Jalview automatically
365 reads PIR files with sequence descriptions compatible with the
366 program <a href="http://salilab.org/modeller/">Modeller</a>. If this
367 option is selected <a href="../io/modellerpir.html">Jalview will
368 write Modeller style PIR files</a> with correct start/end numbering
369 and PDB file association (if available). The Jalview id/start-end
370 option is ignored if Modeller output is selected.
372 <a name="editing"><strong>e"Editinge" Preferences tab</strong></a>
374 <p>There are currently three options available which can be
375 selected / deselected.</p>
377 <em>AutoCalculate Consensus</em> - For large alignments it can be
378 useful to deselect "Autocalculate Consensus" when editing.
379 This prevents lengthy calculations which are performed after each
380 sequence edit. New alignment windows will have their
381 "Autocalculate Consensus" option set according to this
385 <em>Pad Gaps when Editing</em> - New alignment windows will
386 "Pad Gaps" according to this setting.
389 <em>Sort with New Tree</em> - When selected, any trees calculated or
390 loaded onto the alignment will automatically sort the alignment.
393 <a name="hmmer"><strong>"HMMER" Preferences tab</strong></a>
395 <p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),
396 then you should specify on this screen the location of the installation (the path to the folder
397 containing binary executable programs). Double-click in the input field to open a file browser.</p>
398 <p>When this path is configured, the <a href="../menus/alwhmmer.html">HMMER menu</a> will be
399 enabled in the Alignment window.</p>