<mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>\r
<mapID target="features.fileformat" url="html/features/featuresFormat.html"/> \r
<mapID target="edit" url="html/editing/index.html"/>\r
- <mapID target="editInSelArea" url="html/editing/selectionAreas.html"/>\r
+ <mapID target="edit.selareas" url="html/editing/selectionAreas.html"/>\r
<mapID target="jalarchive" url="html/features/jalarchive.html"/>\r
<mapID target="trees" url="html/calculations/tree.html"/>\r
<mapID target="sorting" url="html/calculations/sorting.html"/>\r
<tocitem text="What's new" target="new" expand="false">\r
<tocitem text="Cursor Mode" target="cursor"/>\r
<tocitem text="Selection Area Based Editing"\r
- target="editInSelArea"/>\r
+ target="edit.selareas"/>\r
<tocitem text="User Defined Sequence Features" target="search"/>\r
<tocitem text="Sequence Feature Groups" target="seqfeatures"/>\r
<tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
<p><strong>Tip:</strong> For large alignments, deselect "Calculate -> \r
Autocalculate Consensus" to prevent the alignment performing lengthy calculations \r
after every edit. </p>\r
-<p><em>Inserting / removing gaps</em> - hold down the "Shift" key. Click\r
- a residue with the mouse and drag the residue to the right to insert gaps or\r
- to the left to remove gaps.<br>\r
- If the residue selected is within a defined group, hold down either "Control" \r
+<p><em>Inserting / removing gaps</em> - hold down the\r
+ "Shift" key. Click on a residue with the mouse and drag it\r
+ to the left or right to insert gaps and remove gaps.<br>\r
+ If the current selection is a group over all sequences in the\r
+ alignment, or a group over some sequences or all columns in the\r
+ alignment, then hold down either "Control" \r
key and drag the residue left or right to edit all sequences in the defined \r
- group at once. </p>\r
+ group at once.</p>\r
<p><em>Copy/paste/cut/delete</em> - any sequences which are in the current selection\r
box (indicated in red) may be cut and / or copied to a new alignment or deleted.\r
</p>\r
--- /dev/null
+<html>
+<head>
+<title>Editing In Selection Areas</title>
+</head>
+<body>
+<p><strong>Editing In Selection Areas</strong></p>
+ <a href="index.html">Editing</a> can be restricted to the current
+ selection area. This allows the user to "Lock" the alignment either
+ side of the selection area. Any gap insertions or deletions will only affect
+ the current selection area. </p>
+<p><img src="editing.jpg" width="428" height="186" align="top"></p>
+<p>In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104,
+ the same number of gaps will be inserted at position 116, (between M and L).
+</p>
+
+<p><em>Locked selection area based editing was introduced in Jalview 2.08</em></p>
+</body>
+</html>
--- /dev/null
+<html>
+<head>
+<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="appFeatureSettings.gif" align="center"><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
+ colour and whether they are currently being displayed (only the
+ ticked features and groups are displayed). <strong><em>You can change the
+ colour used for a feature in the associated alignment by clicking on
+ its colour box.</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>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 / commitdiff