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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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="#structure"><strong>"Structure"</strong>
45 Preferences</a> tab allows you to configure options for obtaining
46 and displaying structure information.
48 <li>The <a href="#connections"><strong>"Connections"</strong>
49 Preferences</a> tab allows you to configure Jalview's internet
50 settings and specify your default web browser.
52 <li>The <a href="#links"><strong>"Links"</strong>
53 Preferences</a> tab shows the currently configured <em>URL
54 Links</em> shown in the <strong>Link</strong> submenu in the Sequence
57 <li>The <a href="#output"><strong>"Output"</strong>
58 Preferences</a> tab contains settings affecting the export of
59 sequence alignments and EPS files.
61 <li>The <a href="#editing"><strong>"Editing"</strong>
62 Preferences</a> tab contains settings affecting the export of
63 sequence alignments and EPS files.
65 <li>The <a href="dassettings.html"><strong>"DAS
66 Settings"</strong> Preferences</a> tab allows you to select which DAS
67 sources to use when fetching DAS Features.
69 <li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web
70 Service"</strong> Preferences</a> tab allows you to configure the <a
71 href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
72 servers that Jalview uses, and change the layout of the
73 alignment's Web Services menu.
78 <strong><a name="visual">Visual</a> Preferences tab</strong>
81 <em>Maximise Window</em> - If this is selected, a new alignment
82 window will stretch to fit the available space.
85 <em>Open Overview Window</em> - When this is selected, the <a
86 href="overview.html">alignment overview</a> panel is opened
87 by default for a new alignment window.
90 <em>Show Annotations</em> - If this is selected the new window will
91 display an annotation panel below the sequences. This annotation
92 panel may have several rows describing the whole alignment. The 4
93 standard annotations <em>Conservation</em>, <em>Quality</em>,
94 <em>Occupancy</em> and <em>Consensus</em> for the alignment may
95 be shown or hidden by default using the checkboxes adjacent and
99 <em>Show group: Conservation and Consensus</em> controls the display
100 of per-group automatic annotation.
103 <em>Consensus: Histogram and Logo</em> checkboxes control the
104 display of the consensus histogram and sequence logo for consensus
108 <em>Full Sequence ID</em> - If selected the ID panel will display
109 the name of a sequence plus the start and end residues in the format
110 name/start-end. If not selected, the displayed ID will be the name
114 <em>Right Align IDs</em> - select to align all sequence IDs to the
115 left-hand edge of the sequence alignment, rather than the left-hand
116 edge of the alignment display window.
119 <em>Font</em> - The default font name, size and style can be set for
120 a new alignment window.
123 <em>Sequence ID Tooltip</em>: Control the display of Database
124 References and Non-positional annotation in the tooltip displayed
125 when the mouse is over a sequence's ID.
128 <em>Show Unconserved</em> - When this is selected, all consensus
129 sequence symbols will be rendered as a '.', highlighting mutations
130 in highly conserved alignments.
133 <em>Sequence Name Italics</em> - select to apply the italicised
134 version of the font to sequence labels.
137 <em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
138 rendering of the alignment.
141 <em>Gap Symbol</em> - The default gap symbol may be set to either
142 "-" or "."
145 <em>Wrap Alignment</em> - Select whether to open new alignment
146 windows in wrapped mode or not.
149 <em>Sort alignment by</em> - When the alignment is loaded in, it can
150 be ordered as read (No sort), or sorted by Id or pairwise identity.
153 <em>Sort annotations by</em> - Annotations can be unsorted, sorted
154 by the order of the related sequences in the alignment, or by label.
155 Autocalculated annotations (e.g. Consensus) can be shown either last
156 (below sequence annotations) or first (above sequence annotations).
157 <em>Since Jalview 2.8.2.</em>
160 <em>Open file</em> - If this is selected then the default alignment
161 file will be opened when Jalview is started. You can change the
162 default file by clicking on file name and either typing in the file
163 path or selecting it from the file chooser window.<br /> <em>Note:
164 The default example alignment is updated periodically to
165 demonstrate new features in Jalview.</em>
168 <a name="colours"><strong>"Colours"
169 Preferences tab</strong>
172 <em>Alignment Colour</em> - The default colour scheme for a new
173 alignment window. If the chosen option is "User Defined"
174 then the last User Defined Colour loaded or saved via the User
175 Defined Colours panel will be loaded.
178 <em>Annotation Shading Default</em> - set the default minimum and
179 maximum colours used when <a
180 href="../colourSchemes/annotationColouring.html">Colour
181 by Annotation...</a> is selected from the alignment window's colours
185 <a name="structure"><strong>"Structure"
186 Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
189 <em>Process secondary structure from PDB</em> - if selected, then
190 structure information read from PDB will be processed and annotation
191 added to associated sequences.
193 <em>Use RNAView for secondary structure</em> - if selected, the
194 pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
195 will be called to derive secondary structure information for RNA
198 <em>Add secondary structure annotation to alignment</em> - if
199 selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
200 implementation DSSP</a> will be used to add annotation to polypeptide
201 chains in the structure.
203 <em>Add Temperature Factor annotation to alignment</em> - if
204 selected, values extracted from the Temperature Factor column for
205 the backbone atoms in the PDB file will be extracted as annotation
206 lines shown on the alignment.
208 <em>Default structure viewer</em> - choose JMOL or CHIMERA for
209 viewing 3D structures.
211 <em>Path to Chimera program</em> - Optional, as Jalview will search
212 standard installation paths for Windows, Linux or MacOS. If you have
213 installed Chimera in a non-standard location, you can specify it
214 here, by entering the full path to the Chimera executable program.
215 Double-click this field to open a file chooser dialog.
217 <a name="connections"><strong>"Connections"
218 Preferences tab</strong></a>
221 <em>Default Browser (Unix)</em><br> Its difficult in Java to
222 detect the default web browser for Unix users. If Jalview can't find
223 your default web browser, enter the name or full path to your web
227 <em>Proxy Server</em><br> If you normally use a proxy server
228 for using the internet, you must tick the box "Use a Proxy
229 Server" and enter the address and port details as necessary.
230 Web Services will not work if you are using a proxy server and do
231 not enter the settings here.
234 <em>Usage statistics, Questionnaire and Version checks</em><br>
235 Uncheck these options to prevent Jalview from submitting usage
236 statistics to google analytics, checking for Jalview questionnaires
237 or retrieving details of the latest release version (at
238 www.jalview.org). See the <a href="../privacy.html">user privacy
239 statement</a> for more information.
242 <a name="links"><strong>The "Links" Preferences
246 This panel shows a table, and two sections - <em>Edit</em> and <em>Filter</em>.
247 The table shows the available URL link definitions (consisting of a
248 database, Name, and URL template string), a checkbox <em>In
249 Menu</em> which indicates if the link is enabled, and <em>Double
250 Click</em> which marks the link that will be opened if a sequence's ID
251 is double clicked. The table can be sorted by clicking on the column headers.
253 <p><em>Edit Links</em><br /> This section contains three buttons,
254 <em>New</em>, <em>Edit</em> and <em>Delete</em>, which allow you to
255 create, modify and remove user-defined URL links from the Sequence
259 <em>Filter</em><br /> The <em>Filter text</em> box allows you to
260 quickly show rows in the table containing a particular text string.
261 The <em>Custom only</em> button limits the entries in the table to
262 just those you have configured yourself <em>via</em> the <em>Edit
263 Links</em> buttons. Press <em>Show all</em> to clear any filters.
265 <p>The links table is prepoulated with persistent URLs for many common
266 bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
267 the <em>identifiers.org</em> website, and the names and URLs are not
269 <a href="../webServices/urllinks.html#urllinks">Read more about configuring
273 <a name="output"><strong>Output Preferences tab</strong></a>
276 <em>EPS Rendering Style</em><br> This is a selection box which
277 allows the user to set a default rendering style for EPS export:
279 <li>"Prompt each time"<br> Choose this to be
280 asked select between Lineart and Text each time you make an EPS
283 <li>"Lineart"<br> EPS files will accurately
284 reproduce the alignment view in Jalview and all characters will be
285 converted into line art. Files generated in this way are large and
286 are not easily editable, but have no font table dependencies.
288 <li>"Text"<br> EPS files will be a mixture of
289 text and lineart. This produces compact files that can be edited
290 easily in programs like Microsoft Word and Adobe Illustrator, but
291 can be problematic if the fonts available to Jalview are not
292 accessible by the program reading the EPS file.
295 <em>Automatically set ID width</em><br> When enabled, the
296 column containing sequence and annotation labels at the left hand
297 side of an exported figure will be made large enough to display each
298 sequence ID and annotation label in its own line. Enable this if you
299 have particularly long sequence IDs and need to generate EPS or PNG
300 figures or web pages.
303 <em>Figure ID column width</em><br> Manually specify the width
304 of the left hand column where sequence IDs and annotation labels
305 will be rendered in exported alignment figures. This setting will be
306 ignored if <em>"Automatically set ID width"</em> is set.
309 <em>Sequence//Start-End Numbering</em><br> The output tab also
310 has a group of checkboxes for each file format. If these are ticked,
311 then Jalview will write files with the start and end sequence
312 positions appended to each sequence id:
317 <p>If the boxes are left unchecked for a particular format, the
318 sequence limits will not be appended to the sequence id.</p>
320 <em>Embed BioJSON to HTML export</em>
323 When this option is enabled, Jalview embeds <a
324 href="bioJsonFormat.html">BioJSON</a> data within HTML files
325 exported from Jalview at generation time. This enables the exported
326 HTML files to be extracted and imported back into the Jalview
327 desktop application at a later time.
329 <em>Use Modeller Output</em>
332 This option only applies to PIR format output. Jalview automatically
333 reads PIR files with sequence descriptions compatible with the
334 program <a href="http://salilab.org/modeller/">Modeller</a>. If this
335 option is selected <a href="../io/modellerpir.html">Jalview will
336 write Modeller style PIR files</a> with correct start/end numbering
337 and PDB file association (if available). The Jalview id/start-end
338 option is ignored if Modeller output is selected.
340 <a name="editing"><strong>e"Editinge" Preferences tab</strong></a>
342 <p>There are currently three options available which can be
343 selected / deselected.</p>
345 <em>AutoCalculate Consensus</em> - For large alignments it can be
346 useful to deselect "Autocalculate Consensus" when editing.
347 This prevents lengthy calculations which are performed after each
348 sequence edit. New alignment windows will have their
349 "Autocalculate Consensus" option set according to this
353 <em>Pad Gaps when Editing</em> - New alignment windows will
354 "Pad Gaps" according to this setting.
357 <em>Sort with New Tree</em> - When selected, any trees calculated or
358 loaded onto the alignment will automatically sort the alignment.