3 <head><title>Preferences</title></head>
6 <p><strong>Preferences</strong></p>
7 <p>There are four tabs in the Preferences dialog box:
9 <li>The <a href="#visual"><strong>"Visual"</strong> Preferences</a>
10 tab allows you to configure the default display for a new alignment window.
13 href="#connections"><strong>"Connections"</strong> Preferences</a>
14 tab allows you to change the links made from Jalview to your default web browser.
16 <li>The <a href="#output"><strong>"Output"</strong> Preferences</a>
17 tab contains settings affecting the export of sequence alignments and EPS
19 <li>The <a href="#editing"><strong>"Editing"</strong> Preferences</a>
20 tab contains settings affecting the export of sequence alignments and EPS
22 <li>The <a href="#editing"><strong>"DAS Settings"</strong> Preferences</a>
23 tab allows you to select which DAS sources to use when fetching DAS Features.</li>
26 <p><strong><a name="visual">Visual</a> Preferences tab</strong></p>
27 <p><em>Maximise Window</em> - If this is selected, a new alignment window will stretch
28 to fit the available space.</p>
29 <p><em>Open Overview Window</em> - When this is selected, the <a
30 href="overview.html">alignment overview</a> panel is opened by
31 default for a new alignment window.</p>
32 <p><em>Show Annotations</em> - If this is selected the new window will display an annotation
33 panel below the sequences. This annotation panel may have several rows describing
34 the whole alignment. The 3 standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
35 may be shown or hidden by default.</p>
36 <p><em>Full Sequence ID</em> - If selected the ID panel will display the name of a sequence
37 plus the start and end residues in the format name/start-end. If not selected,
38 the displayed ID will be the name of the sequence.</p>
39 <p><em>Right Align IDs</em> - select to align all sequence IDs to the
40 left-hand edge of the sequence alignment, rather than the left-hand
41 edge of the alignment display window.</p>
42 <p><em>Font</em> - The default font name, size and style can be set for a new
43 alignment window. </p>
44 <p><em>Sequence Name Italics</em> - select to apply the italicised
45 vbersion of the font to sequence labels.</p>
46 <p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster rendering
48 <p><em>Wrap Alignment</em> - Select whether to open new alignment windows in wrapped
50 <p><em>Gap Symbol</em> - The default gap symbol may be set to either "-" or "."</p>
51 <p><em>Colour</em> - The default colour scheme for a new alignment window. If
52 the chosen option is "User Defined" then the last User Defined Colour
53 loaded or saved via the User Defined Colours panel will be loaded. </p>
54 <p><em>Sort by</em> - When the alignment is loaded in, it will can be sorted by
55 Id or pairwise identity.</p>
56 <p><em>Open file</em> - If this is selected then the default alignment file will
57 be opened when Jalview is started. You can change the default file by clicking
58 on file name and either typing in the file path or selecting it from the file
60 <p><a name="connections"><strong>"Connections" Preferences tab</strong></a></p>
61 <p><em>URL Link From Sequence ID</em><br>
62 Right click a sequence id to see a popup menu with "Link" as one of
63 the items. By default the item "SRS" is added to this link menu. This
64 link will show a web page in your default browser with the selected sequence
65 id as part of the URL.<br>
66 Jalview allows you to add your own custom links to other web pages. Click new
67 to add a new link. You can name the link, this will be displayed on a new menu
68 item under the "Link" menu when you right click on a sequence id.
70 You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen
71 sequence id when you click on it. </p>
73 UniRef100 = http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100<br>
74 Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$
76 Links will also be made for any database cross references
77 associated with the sequence where the database name exactly
78 matches a URL link name. In this case, the $SEQUENCE_ID$ string will be replaced with
79 the accession string for the database cross-reference, rather than the
80 sequence ID for the sequence (<em>since Jalview 2.4</em>).
82 <strong>Regular Expression Substitution</strong><br>
83 A url may contain a string of the form $SEQUENCE_ID=/<em>regular expression</em>/=$. In this case, the regular expression will be applied to the full sequence ID string and the resulting match will be inserted into the URL.
84 Groups of parentheseses can be used to specify which regions of the regular expression will be used to generate the URL:
86 <li>Each top level parenthesis will yield a URL containing the text matched within that parenthesis.
88 <li>Regions matching sub-parentheseses within a top-level parenthesis will be concatenated to form the text inserted into the URL for the top-level parenthesis.</li>
90 <ul><li>The regular expressions supported by Jalview are those provided by the <a href="www.javaregex.com">Stevesoft javaregex package</a>.
91 </li><li>Some characters must be escaped when specifying them as a match within a regular expression.</li></ul>
92 <br>Many Thanks to Bernd Brand of the Free University of Amsterdam for testing this new regular-expression expansion feature!
97 <p><em>Default Browser (Unix)</em><br>
98 Its difficult in Java to detect the default web browser for Unix users. If Jalview
99 can't find your default web browser, enter the name or full path to your web
100 browser application. </p>
101 <p><em>Proxy Server</em><br>
102 If you normally use a proxy server for using the internet, you must tick the
103 box "Use a Proxy Server" and enter the address and port details as
104 necessary. Web Services will not work if you are using a proxy server and do
105 not enter the settings here.</p>
106 <p><a name="output"><strong>Output Preferences tab</strong></a></p>
107 <p><em>EPS Rendering Style</em><br>
108 This is a selection box which allows the
109 user to set a default rendering style for EPS export:
110 <ul><li>"Lineart"<br>EPS files will accurately
111 reproduce the alignment view in Jalview and all characters will be
112 converted into line art. Files generated in this way are large and are
113 not easily editable, but have no font table dependencies.</li>
114 <li>"Text"<br>EPS files will be a mixture of text and
115 lineart. This produces compact files that can be edited easily in
116 programs like Microsoft Word and Adobe Illustrator, but can be
117 problematic if the fonts available to jalview are not accessible by
118 the program reading the EPS file.
119 <li>"Prompt each time"<br>Choose this to be asked select between Lineart and Text each time you make an EPS file.</li>
122 <p><em>Sequence//Start-End Numbering</em><br>
123 The output tab also has a group of checkboxes for each file format. If these
124 are ticked, then Jalview will write files with the start and end sequence positions
125 appended to each sequence id:
130 <p>If the boxes are left unchecked for a particular format, the sequence limits
131 will not be appended to the sequence id. </p>
133 <p><em>Use Modeller Output</em></p>
134 <p>This option only applies to PIR format output. Jalview
135 automatically reads PIR files with sequence descriptions compatible
137 href="http://salilab.org/modeller/">Modeller</a>.
138 If this option is selected <a href="../io/modellerpir.html">Jalview will write Modeller style PIR
139 files</a> with correct start/end numbering and PDB file association (if
140 available). The Jalview id/start-end option is ignored if Modeller output is selected.
141 <p><a name="editing"><strong>Editing Preferences tab</strong></a></p>
142 <p>There are currently 2 options available which can be selected / deselected.
144 <p><em>AutoCalculate Consensus</em> - For large alignments it can be useful to
145 deselect "Autocalculate Consensus" when editing. This prevents lengthy
146 calculations which are performed after each sequence edit. New alignment windows
147 will have their "Autocalculate Consensus" option set according to
149 <p><em>Pad gaps when editing</em> - New alignment windows will "Pad Gaps"
150 according to this setting.</p>
151 <p><a name="editing"><strong>DAS Settings </strong></a></p>
152 <p>See <a href="dassettings.html">DAS Settings</a></p>