<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<title>Sequence Feature Settings Dialog Box</title>
</head>
<body>
-<p><strong>Sequence Feature Settings Dialog Box</strong></p>
-<p>Select <strong>View→Feature Settings...</strong> menu entry
-in an alignment window to open the feature settings dialog box, which
-allows you to precisely control the presence and appearance of sequence
-features for the current alignment.</p>
-<center><img src="featureSettings.gif" width="400" height="452">
-<br>
-Sequence Feature Settings for the Jalview Application</img></center>
-<p>The top section of the dialog box lists all the sequence feature
-groups, along with a tickbox for each that controls whether its features
-are displayed. The table in the middle lists all the features in the
-currently selected groups, along with their display style and whether
-they are currently being displayed (only the ticked features and groups
-are displayed). <strong><em>You can change the colour or
-shading style used for a feature in the associated alignment by clicking
-on its colour box.</em></strong></p>
- <p>
- <a name="selectbyfeature"><strong><em>Selecting
- alignment columns by feature</em></strong></a><br> <strong>Double-clicking
- a feature type</strong> in the <strong>Feature
- Settings</strong> dialog allows you to select columns in the
- alignment that contain (or do not contain) features of that type. If a
- region of the alignment is currently selected, then only features in
- the current selection will be searched. The following keys affect the
- way in which selections are made:<ul>
- <li>Hold down <strong>Alt</strong> to select columns not
- containing features of a particular type.
- </li>
- <li>Hold down <strong>Shift</strong> to add columns to the
- current selection.
- </li>
- <li>Press <strong>Command/Windows key</strong> to toggle column
- selection state (XOR)
- </li>
- </ul>
- Options are also provided in the feature's pop-up menu (see below).
- <br />
- <em>Select columns by feature was added in Jalview 2.8.1</em>
- </p>
- <p><strong><em>Feature settings pop-up menu</em></strong><br>
-<strong>Right-click</strong> on a feature to open a pop-up menu that
-allows you to sort the alignment or current selection using that feature
-type (see below), or toggle the type of colouring used for the feature.
-Features may be highlighted with either a single colour or a <a
- href="featureschemes.html">feature colourscheme</a> based on either the
-scores associated with that feature or from the feature's description
-(e.g. to distinguish different names associated with a DOMAIN feature).</p>
-<p><strong>Ordering alignment by features</strong><br>
-The 'Seq Sort by Score' and 'Seq Sort by Density' buttons will sort the
-alignment based on the average score or total number of currently active
-features and groups on each sequence. To order the alignment using a
-specific feature type, use the <em>sort by ..</em> entries in the pop-up
-menu for that type.<br>
-<em>Feature sorting and graduated feature colouring was introduced
-in jalview 2.5</em></p>
+ <p>
+ <strong>Sequence Feature Settings Dialog Box</strong>
+ </p>
+ <p>
+ Select <strong>View→Feature Settings...</strong> menu entry in
+ an alignment window to open the feature settings dialog box, which
+ allows you to precisely control the presence and appearance of
+ sequence features for the current alignment.
+ </p>
+ <center>
+ <img src="featureSettings.gif" width="400" height="452"> <br>
+ Sequence Feature Settings for the Jalview Application</img>
+ </center>
+ <p>
+ The top section of the dialog box lists all the sequence feature
+ groups, along with a tickbox for each that controls whether its
+ features are displayed. The table in the middle lists all the
+ features in the currently selected groups, along with their display
+ style and whether they are currently being displayed (only the
+ ticked features and groups are displayed). <strong><em>You
+ can change the colour or shading style used for a feature in the
+ associated alignment by clicking on its colour box.</em></strong>
+ </p>
+ <p>
+ <a name="selectbyfeature"><strong><em>Selecting
+ alignment columns by feature</em></strong></a><br> <strong>Double-clicking
+ a feature type</strong> in the <strong>Feature Settings</strong> dialog
+ allows you to select columns in the alignment that contain (or do
+ not contain) features of that type. If a region of the alignment is
+ currently selected, then only features in the current selection will
+ be searched. The following keys affect the way in which selections
+ are made:
+ <ul>
+ <li>Hold down <strong>Alt</strong> to select columns not
+ containing features of a particular type.
+ </li>
+ <li>Hold down <strong>Shift</strong> to add columns to the
+ current selection.
+ </li>
+ <li>Press <strong>Command/Windows key</strong> to toggle column
+ selection state (XOR)
+ </li>
+ </ul>
+ Options are also provided in the feature's pop-up menu (see below).
+ <br />
+ <em>Select columns by feature was added in Jalview 2.8.1</em>
+ </p>
+ <p>
+ <strong><em>Feature settings pop-up menu</em></strong><br> <strong>Right-click</strong>
+ on a feature to open a pop-up menu that allows you to sort the
+ alignment or current selection using that feature type (see below),
+ or toggle the type of colouring used for the feature. Features may
+ be highlighted with either a single colour or a <a
+ href="featureschemes.html"
+ >feature colourscheme</a> based on either the scores associated with
+ that feature or from the feature's description (e.g. to distinguish
+ different names associated with a DOMAIN feature).
+ </p>
+ <p>
+ <strong>Ordering alignment by features</strong><br> The 'Seq
+ Sort by Score' and 'Seq Sort by Density' buttons will sort the
+ alignment based on the average score or total number of currently
+ active features and groups on each sequence. To order the alignment
+ using a specific feature type, use the <em>sort by ..</em> entries
+ in the pop-up menu for that type.<br> <em>Feature sorting
+ and graduated feature colouring were introduced in Jalview 2.5</em>
+ </p>
-<p><strong>Transparency and Feature Ordering</strong></p>
-<p>It is important to realise that sequence features are often not
-distinct and often overlap (for example, a metal binding site feature
-may be attached to one position along a stretch of sequence marked with
-a secondary structure feature).</p>
-<p>The ordering of the sequence features in the dialog box list is
-the order used by jalview for rendering sequence features. A feature at
-the bottom of the list is rendered <em>below</em> a feature higher up in
-the list.<br>
-<em><strong>You can change the order of a feature by
-dragging it up and down the list with the mouse</strong></em>.</p>
-<p>The <strong><em>Optimise order</em></strong> button (currently
-only available in the application) will re-order the feature render
-ordering based on the average length of each feature type.</p>
-<p>The <strong><em>transparency slider setting</em></strong>
-(currently only available in the application version) controls the
-visibility of features rendered below other features. Reducing the
-transparency will mean that features at the top of the list can obscure
-features lower down, and increasing it allows the user to 'see through'
-the upper layers of a set of features.</p>
-<p><strong><em>You can save all features, with their
-current colours and visibility in a Jalview format file. </em></strong></p>
+ <p>
+ <strong>Transparency and Feature Ordering</strong>
+ </p>
+ <p>It is important to realise that sequence features are often not
+ distinct and often overlap (for example, a metal binding site
+ feature may be attached to one position along a stretch of sequence
+ marked with a secondary structure feature).</p>
+ <p>
+ The ordering of the sequence features in the dialog box list is the
+ order used by Jalview for rendering sequence features. A feature at
+ the bottom of the list is rendered <em>below</em> a feature higher
+ up in the list.<br> <em><strong>You can change
+ the order of a feature by dragging it up and down the list with
+ the mouse</strong></em>.
+ </p>
+ <p>
+ The <strong><em>Optimise order</em></strong> button (currently only
+ available in the application) will re-order the feature render
+ ordering based on the average length of each feature type.
+ </p>
+ <p>
+ The <strong><em>transparency slider setting</em></strong> (currently
+ only available in the application version) controls the visibility
+ of features rendered below other features. Reducing the transparency
+ will mean that features at the top of the list can obscure features
+ lower down, and increasing it allows the user to 'see through' the
+ upper layers of a set of features.
+ </p>
+ <p>
+ <strong><em>You can save all features, with their
+ current colours and visibility in a Jalview format file. </em></strong>
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff