3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Preferences</title>
24 <p><strong>Preferences</strong></p>
25 <p>The preferences panel is opened from the Jalview Desktop’s <strong><em>Tools</em></strong> menu.</p>
26 <p>There are six tabs in the Preferences dialog box:
28 <li>The <a href="#visual"><strong>"Visual"</strong>
29 Preferences</a> tab allows you to configure the default display for a new
30 alignment window.</li>
31 <li>The <a href="#colours"><strong>"Colours"</strong>
32 Preferences</a> tab allows you to configure default colourschemes for a new
33 alignment window.</li>
34 <li>The <a href="#connections"><strong>"Connections"</strong>
35 Preferences</a> tab allows you to change the links made from Jalview to
36 your default web browser.</li>
37 <li>The <a href="#output"><strong>"Output"</strong>
38 Preferences</a> tab contains settings affecting the export of sequence
39 alignments and EPS files.</li>
40 <li>The <a href="#editing"><strong>"Editing"</strong>
41 Preferences</a> tab contains settings affecting the export of sequence
42 alignments and EPS files.</li>
43 <li>The <a href="dassettings.html"><strong>"DAS
44 Settings"</strong> Preferences</a> tab allows you to select which DAS sources
45 to use when fetching DAS Features.</li>
46 <li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web Service"</strong> Preferences</a> tab allows you to configure the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a> servers that Jalview uses, and change the layout of the alignment's Web Services menu.</li>
49 <p><strong><a name="visual">Visual</a> Preferences tab</strong></p>
50 <p><em>Maximise Window</em> - If this is selected, a new alignment
51 window will stretch to fit the available space.</p>
52 <p><em>Open Overview Window</em> - When this is selected, the <a
53 href="overview.html">alignment overview</a> panel is opened by default
54 for a new alignment window.</p>
55 <p><em>Show Annotations</em> - If this is selected the new window
56 will display an annotation panel below the sequences. This annotation
57 panel may have several rows describing the whole alignment. The 3
58 standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
59 for the alignment may be shown or hidden by default using the checkboxes
61 <p><em>Show group: Conservation and Consensus</em> controls the
62 display of per-group automatic annotation.</p>
63 <p><em>Consensus: Histogram and Logo</em> checkboxes control the
64 display of the consensus histogram and sequence logo for consensus
66 <p><em>Full Sequence ID</em> - If selected the ID panel will display
67 the name of a sequence plus the start and end residues in the format
68 name/start-end. If not selected, the displayed ID will be the name of
70 <p><em>Right Align IDs</em> - select to align all sequence IDs to
71 the left-hand edge of the sequence alignment, rather than the left-hand
72 edge of the alignment display window.</p>
73 <p><em>Font</em> - The default font name, size and style can be set
74 for a new alignment window.</p>
75 <p><em>Sequence ID Tooltip</em>: Control the display of Database
76 References and Non-positional annotation in the tooltip displayed when
77 the mouse is over a sequence's ID.</p>
78 <p><em>Sequence Name Italics</em> - select to apply the italicised
79 vbersion of the font to sequence labels.</p>
80 <p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
81 rendering of the alignment.</p>
82 <p><em>Wrap Alignment</em> - Select whether to open new alignment
83 windows in wrapped mode or not.</p>
84 <p><em>Gap Symbol</em> - The default gap symbol may be set to either
85 "-" or "."</p>
86 <p><em>Sort by</em> - When the alignment is loaded in, it will can
87 be sorted by Id or pairwise identity.</p>
88 <p><em>Open file</em> - If this is selected then the default
89 alignment file will be opened when Jalview is started. You can change
90 the default file by clicking on file name and either typing in the file
91 path or selecting it from the file chooser window.<br/><em>Note: The default example alignment is updated periodically to demonstrate new features in Jalview.</em></p>
92 <p><a name="colours"><strong>"Colours" Preferences tab</strong></p>
93 <p><em>Alignment Colour</em> - The default colour scheme for a new alignment
94 window. If the chosen option is "User Defined" then the last
95 User Defined Colour loaded or saved via the User Defined Colours panel
98 <em>Annotation Shading Default</em> - set the default minimum
99 and maximum colours used when <a
100 href="../colourSchemes/annotationColouring.html">Colour by
101 Annotation ..</a> is selected from the alignment window's colours menu.
105 <p><a name="connections"><strong>"Connections"
106 Preferences tab</strong></a></p>
107 <p><em>URL Link From Sequence ID</em><br>
108 These definitions are used to generate URLs from a sequence's ID or
109 database cross references. Read more about <a
110 href="../webServices/urllinks.html#urllinks">configuring URL links
112 <p><em>Default Browser (Unix)</em><br>
113 Its difficult in Java to detect the default web browser for Unix users.
114 If Jalview can't find your default web browser, enter the name or full
115 path to your web browser application.</p>
116 <p><em>Proxy Server</em><br>
117 If you normally use a proxy server for using the internet, you must tick
118 the box "Use a Proxy Server" and enter the address and port
119 details as necessary. Web Services will not work if you are using a
120 proxy server and do not enter the settings here.</p>
121 <p><em>Usage statistics, Questionnaire and Version checks</em><br>
122 Uncheck these options to prevent Jalview from submitting usage
123 statistics to google analytics, checking for jalview questionnaires or
124 retrieving details of the latest release version (at www.jalview.org).
125 See the <a href="../privacy.html">user privacy statement</a> for more
127 <p><a name="output"><strong>Output Preferences tab</strong></a></p>
128 <p><em>EPS Rendering Style</em><br>
129 This is a selection box which allows the user to set a default rendering
130 style for EPS export:
132 <li>"Lineart"<br>
133 EPS files will accurately reproduce the alignment view in Jalview and
134 all characters will be converted into line art. Files generated in this
135 way are large and are not easily editable, but have no font table
137 <li>"Text"<br>
138 EPS files will be a mixture of text and lineart. This produces compact
139 files that can be edited easily in programs like Microsoft Word and
140 Adobe Illustrator, but can be problematic if the fonts available to
141 jalview are not accessible by the program reading the EPS file.
142 <li>"Prompt each time"<br>
143 Choose this to be asked select between Lineart and Text each time you
144 make an EPS file.</li>
147 <p><em>Automatically set ID width</em><br>
148 When enabled, the column containing sequence and annotation labels at the left hand side of an exported figure will be made large enough to display each sequence ID and annotation label in its own line. Enable this if you have particularly long sequence IDs and need to generate EPS or PNG figures or web pages.</p>
149 <p><em>Figure ID column width</em><br>
150 Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if <em>"Automatically set ID width"</em> is set.
152 <p><em>Sequence//Start-End Numbering</em><br>
153 The output tab also has a group of checkboxes for each file format. If
154 these are ticked, then Jalview will write files with the start and end
155 sequence positions appended to each sequence id: <pre>
159 <p>If the boxes are left unchecked for a particular format, the
160 sequence limits will not be appended to the sequence id.</p>
162 <p><em>Use Modeller Output</em></p>
163 <p>This option only applies to PIR format output. Jalview
164 automatically reads PIR files with sequence descriptions compatible with
165 the program <a href="http://salilab.org/modeller/">Modeller</a>. If this
166 option is selected <a href="../io/modellerpir.html">Jalview will
167 write Modeller style PIR files</a> with correct start/end numbering and PDB
168 file association (if available). The Jalview id/start-end option is
169 ignored if Modeller output is selected.
170 <p><a name="editing"><strong>Editing Preferences tab</strong></a></p>
171 <p>There are currently 2 options available which can be selected /
173 <p><em>AutoCalculate Consensus</em> - For large alignments it can be
174 useful to deselect "Autocalculate Consensus" when editing.
175 This prevents lengthy calculations which are performed after each
176 sequence edit. New alignment windows will have their "Autocalculate
177 Consensus" option set according to this setting.</p>
178 <p><em>Pad gaps when editing</em> - New alignment windows will
179 "Pad Gaps" according to this setting.</p>
git://source.jalview.org / jalview.git / blob