+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Preferences</title>
-</head>
-
-<body>
- <p>
- <strong>Preferences</strong>
- </p>
- <p>
- The preferences panel is opened from the Jalview Desktop’s <strong><em>Tools</em></strong>
- menu.
- </p>
- <p>There are eight 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="#colours"><strong>"Colours"</strong>
- Preferences</a> tab allows you to configure default colourschemes
- for a new alignment window.
- </li>
- <li>The <a href="#overview"><strong>"Overview"</strong>
- Preferences</a> tab configures defaults for the overview window.
- </li>
- <li>The <a href="#structure"><strong>"Structure"</strong>
- Preferences</a> tab allows you to configure options for obtaining
- and displaying structure information.
- </li>
- <li>The <a href="#connections"><strong>"Connections"</strong>
- Preferences</a> tab allows you to configure Jalview's internet
- settings and specify your default web browser.
- </li>
- <li>The <a href="#links"><strong>"Links"</strong>
- Preferences</a> tab shows the currently configured <em>URL
- Links</em> shown in the <strong>Link</strong> submenu in the Sequence
- ID popup menu.
- </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 behaviour when editing alignments.
- </li>
- <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>
- </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 4
- standard annotations <em>Conservation</em>, <em>Quality</em>,
- <em>Occupancy</em> and <em>Consensus</em> for the alignment may
- be shown or hidden by default using the checkboxes adjacent and
- 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>Show Unconserved</em> - When this is selected, all consensus
- sequence symbols will be rendered as a '.', highlighting mutations
- in highly conserved alignments.
- </p>
- <p>
- <em>Sequence Name Italics</em> - select to apply the italicised
- version 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>Gap Symbol</em> - The default gap symbol may be set to either
- "-" or "."
- </p>
- <p>
- <em>Wrap Alignment</em> - Select whether to open new alignment
- windows in wrapped mode or not.
- </p>
- <p>
- <em>Sort alignment by</em> - When the alignment is loaded in, it can
- be ordered as read (No sort), or sorted by Id or pairwise identity.
- </p>
- <p>
- <em>Sort annotations by</em> - Annotations can be unsorted, sorted
- by the order of the related sequences in the alignment, or by label.
- Autocalculated annotations (e.g. Consensus) can be shown either last
- (below sequence annotations) or first (above sequence annotations).
- <em>Since Jalview 2.8.2.</em>
- </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.<br /> <em>Note:
- The default example alignment is updated periodically to
- demonstrate new features in Jalview.</em>
- </p>
- <p>
- <a name="colours"><strong>"Colours"
- Preferences tab</strong>
- </p>
- <p>
- <em>Alignment 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>Annotation Shading Default</em> - set the default minimum and
- maximum colours used when <a
- href="../colourSchemes/annotationColouring.html">Colour
- by Annotation...</a> is selected from the alignment window's colours
- menu.
- </p>
- <p>
- <a name="overview"><strong>"Overview"
- Preferences tab</strong>
- </p>
- <p>
- <em>Use legacy gap colouring (gaps are white)</em> - when enabled,
- Jalview's overview shows gaps as white, and sequences with no
- colourscheme applied as grey.
- </p>
- <p>
- <em>Show Hidden regions when opening overview</em> - default setting
- for inclusion of hidden regions.
- </p>
- <p>
- <em>Gap Colour</em> - When legacy gap colouring is not enabled, this
- configures the default colour for gaps in the overview.
- </p>
- <p>
- <em>Hidden Colour</em> - colour used to highlight regions in the
- overview that are hidden in the alignment.
- </p>
- <p>
- <em>Gap 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>
- <a name="structure"><strong>"Structure"
- Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
- </p>
- <p>
- <em>Process secondary structure from PDB</em> - if selected, then
- structure information read from PDB will be processed and annotation
- added to associated sequences.
- <p>
- <em>Use RNAView for secondary structure</em> - if selected, the
- pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
- will be called to derive secondary structure information for RNA
- chains.
- <p>
- <em>Add secondary structure annotation to alignment</em> - if
- selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
- implementation DSSP</a> will be used to add annotation to polypeptide
- chains in the structure.
- <p>
- <em>Add Temperature Factor annotation to alignment</em> - if
- selected, values extracted from the Temperature Factor column for
- the backbone atoms in the PDB file will be extracted as annotation
- lines shown on the alignment.
- <p>
- <em>Default structure viewer</em> - choose Jmol or CHIMERA for
- viewing 3D structures.
- <p>
- <em>Path to Chimera program</em> - Optional, as Jalview will search
- standard installation paths for Windows, Linux or MacOS. If you have
- installed Chimera in a non-standard location, you can specify it
- here, by entering the full path to the Chimera executable program.
- Double-click this field to open a file chooser dialog.
- <p>
- <a name="connections"><strong>"Connections"
- Preferences tab</strong></a>
- </p>
- <p>
- <em>Default Browser (Unix)</em><br> It's 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="links"><strong>The "Links" Preferences
- tab</strong></a>
- </p>
- <p>
- This panel shows a table, and two sections - <em>Edit</em> and <em>Filter</em>.
- The table shows the available URL link definitions (consisting of a
- database, Name, and URL template string), a checkbox <em>In
- Menu</em> which indicates if the link is enabled, and <em>Double
- Click</em> which marks the link that will be opened if a sequence's ID
- is double clicked. The table can be sorted by clicking on the column headers.
- </p>
- <p><em>Edit Links</em><br /> This section contains three buttons,
- <em>New</em>, <em>Edit</em> and <em>Delete</em>, which allow you to
- create, modify and remove user-defined URL links from the Sequence
- ID's links submenu.
- </p>
- <p>
- <em>Filter</em><br /> The <em>Filter text</em> box allows you to
- quickly show rows in the table containing a particular text string.
- The <em>Custom only</em> button limits the entries in the table to
- just those you have configured yourself <em>via</em> the <em>Edit
- Links</em> buttons. Press <em>Show all</em> to clear any filters.
- </p>
- <p>The links table is prepopulated with persistent URLs for many common
- bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
- the <em>identifiers.org</em> website, and the names and URLs are not
- user editable.
- <a href="../webServices/urllinks.html#urllinks">Read more about configuring
- URL links.</a>
- </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>"Prompt each time"<br> Choose this to be
- asked to select between Lineart and Text each time you make an EPS
- file.
- </li>
- <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.
- </ul>
- <p>
- <em>Automatically set ID width</em><br> 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>
- <p>
- <em>Figure ID column width</em><br> 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.
- </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>
- <em>Embed BioJSON to HTML export</em>
- </p>
- <p>
- When this option is enabled, Jalview embeds <a
- href="bioJsonFormat.html">BioJSON</a> data within HTML files
- exported from Jalview at generation time. This enables the exported
- HTML files to be extracted and imported back into the Jalview
- desktop application at a later time.
- <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 three 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>
- <em>Sort with New Tree</em> - When selected, any trees calculated or
- loaded onto the alignment will automatically sort the alignment.
- </p>
- <p> </p>
- <p> </p>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff