* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
---!>
-<head>
-<title>Preferences</title>
-</head>
-
-<body>
-<p><strong>Preferences</strong></p>
-<p>There are four tabs in the Preferences dialog box:
-<ul>
- <li>The <a href="#visual"><strong>"Visual"</strong>
- Preferences</a> tab allows you to configure the default display for a new
- alignment window.</li>
- <li>The <a href="#connections"><strong>"Connections"</strong>
- Preferences</a> tab allows you to change the links made from Jalview to
- your default web browser.</li>
- <li>The <a href="#output"><strong>"Output"</strong>
- Preferences</a> tab contains settings affecting the export of sequence
- alignments and EPS files.</li>
- <li>The <a href="#editing"><strong>"Editing"</strong>
- Preferences</a> tab contains settings affecting the export of sequence
- alignments and EPS files.</li>
- <li>The <a href="dassettings.html"><strong>"DAS
- Settings"</strong> Preferences</a> tab allows you to select which DAS sources
- to use when fetching DAS Features.</li>
-</ul>
-</p>
-<p><strong><a name="visual">Visual</a> Preferences tab</strong></p>
-<p><em>Maximise Window</em> - If this is selected, a new alignment
-window will stretch to fit the available space.</p>
-<p><em>Open Overview Window</em> - When this is selected, the <a
- href="overview.html">alignment overview</a> panel is opened by default
-for a new alignment window.</p>
-<p><em>Show Annotations</em> - If this is selected the new window
-will display an annotation panel below the sequences. This annotation
-panel may have several rows describing the whole alignment. The 3
-standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
-for the alignment may be shown or hidden by default using the checkboxes
-below.</p>
-<p><em>Show group: Conservation and Consensus</em> controls the
-display of per-group automatic annotation.</p>
-<p><em>Consensus: Histogram and Logo</em> checkboxes control the
-display of the consensus histogram and sequence logo for consensus
-annotation rows.</p>
-<p><em>Full Sequence ID</em> - If selected the ID panel will display
-the name of a sequence plus the start and end residues in the format
-name/start-end. If not selected, the displayed ID will be the name of
-the sequence.</p>
-<p><em>Right Align IDs</em> - select to align all sequence IDs to
-the left-hand edge of the sequence alignment, rather than the left-hand
-edge of the alignment display window.</p>
-<p><em>Font</em> - The default font name, size and style can be set
-for a new alignment window.</p>
-<p><em>Sequence ID Tooltip</em>: Control the display of Database
-References and Non-positional annotation in the tooltip displayed when
-the mouse is over a sequence's ID.</p>
-<p><em>Sequence Name Italics</em> - select to apply the italicised
-vbersion of the font to sequence labels.</p>
-<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
-rendering of the alignment.</p>
-<p><em>Wrap Alignment</em> - Select whether to open new alignment
-windows in wrapped mode or not.</p>
-<p><em>Gap Symbol</em> - The default gap symbol may be set to either
-"-" or "."</p>
-<p><em>Colour</em> - The default colour scheme for a new alignment
-window. If the chosen option is "User Defined" then the last
-User Defined Colour loaded or saved via the User Defined Colours panel
-will be loaded.</p>
-<p><em>Sort by</em> - When the alignment is loaded in, it will can
-be sorted by Id or pairwise identity.</p>
-<p><em>Open file</em> - If this is selected then the default
-alignment file will be opened when Jalview is started. You can change
-the default file by clicking on file name and either typing in the file
-path or selecting it from the file chooser window.</p>
-<p><a name="connections"><strong>"Connections"
-Preferences tab</strong></a></p>
-<p><em>URL Link From Sequence ID</em><br>
-These definitions are used to generate URLs from a sequence's ID or
-database cross references. Read more about <a
- href="../webServices/urllinks.html#urllinks">configuring URL links
-here</a>.</p>
-<p><em>Default Browser (Unix)</em><br>
-Its difficult in Java to detect the default web browser for Unix users.
-If Jalview can't find your default web browser, enter the name or full
-path to your web browser application.</p>
-<p><em>Proxy Server</em><br>
-If you normally use a proxy server for using the internet, you must tick
-the box "Use a Proxy Server" and enter the address and port
-details as necessary. Web Services will not work if you are using a
-proxy server and do not enter the settings here.</p>
-<p><em>Usage statistics, Questionnaire and Version checks</em><br>
-Uncheck these options to prevent Jalview from submitting usage
-statistics to google analytics, checking for jalview questionnaires or
-retrieving details of the latest release version (at www.jalview.org).
-See the <a href="../privacy.html">user privacy statement</a> for more
-information.</p>
-<p><a name="output"><strong>Output Preferences tab</strong></a></p>
-<p><em>EPS Rendering Style</em><br>
-This is a selection box which allows the user to set a default rendering
-style for EPS export:
-<ul>
- <li>"Lineart"<br>
- EPS files will accurately reproduce the alignment view in Jalview and
- all characters will be converted into line art. Files generated in this
- way are large and are not easily editable, but have no font table
- dependencies.</li>
- <li>"Text"<br>
- EPS files will be a mixture of text and lineart. This produces compact
- files that can be edited easily in programs like Microsoft Word and
- Adobe Illustrator, but can be problematic if the fonts available to
- jalview are not accessible by the program reading the EPS file.
- <li>"Prompt each time"<br>
- Choose this to be asked select between Lineart and Text each time you
- make an EPS file.</li>
-</ul>
-</p>
-<p><em>Sequence//Start-End Numbering</em><br>
-The output tab also has a group of checkboxes for each file format. If
-these are ticked, then Jalview will write files with the start and end
-sequence positions appended to each sequence id: <pre>
- >ID/1-10
- AACDEAAFEA
-</pre>
-<p>If the boxes are left unchecked for a particular format, the
-sequence limits will not be appended to the sequence id.</p>
-</p>
-<p><em>Use Modeller Output</em></p>
-<p>This option only applies to PIR format output. Jalview
-automatically reads PIR files with sequence descriptions compatible with
-the program <a href="http://salilab.org/modeller/">Modeller</a>. If this
-option is selected <a href="../io/modellerpir.html">Jalview will
-write Modeller style PIR files</a> with correct start/end numbering and PDB
-file association (if available). The Jalview id/start-end option is
-ignored if Modeller output is selected.
-<p><a name="editing"><strong>Editing Preferences tab</strong></a></p>
-<p>There are currently 2 options available which can be selected /
-deselected.</p>
-<p><em>AutoCalculate Consensus</em> - For large alignments it can be
-useful to deselect "Autocalculate Consensus" when editing.
-This prevents lengthy calculations which are performed after each
-sequence edit. New alignment windows will have their "Autocalculate
-Consensus" option set according to this setting.</p>
-<p><em>Pad gaps when editing</em> - New alignment windows will
-"Pad Gaps" according to this setting.</p>
-<p> </p>
-<p> </p>
-</body>
-</html>
+-->
git://source.jalview.org / jalview.git / blobdiff