<html>\r
-\r
+<head><title>Editing</title></head>\r
<body>\r
<p><strong>Editing</strong></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 "Alt"\r
- or "Control" key and drag the residue left or right to edit all sequences\r
- in the defined group at once. </p>\r
+<p>There are two major ways to edit alignments - in 'Normal mode',\r
+gaps are inserted and deleted at the mouse pointer in various ways by\r
+clicking the left mouse button and pressing a combination of either\r
+shift and control (or the apple key on Macs) and dragging the mouse. Pressing\r
+<em>F2</em> toggles the alternative <a href="../features/cursorMode.html">'Cursor\r
+mode'</a> keyboard editing facility, where the space bar and delete \r
+keys add and remove gaps at the current editing position. The key\r
+strokes for both these modes are summarised in the <a\r
+href="../keys.html">keystrokes table</a>.</p>\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\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
<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
contain only space characters ("-" or "." or " ")</p>\r
<p><em>Removing gaps</em> - Removes all gaps from the alignment. Gaps are "-"\r
or "." or " ".</p>\r
-<p><em>Set gap character</em> - Switches the gap character between "."\r
- and "-". If the "Render Gaps" option from the "View"\r
+<p><em>Set gap character</em> - Switches the gap character between "." \r
+ and "-". If the "Render Gaps" option from the "View" \r
menu is unticked all gaps will appear as blank spaces.</p>\r
<p> </p>\r
+<p><strong>Editing In Selection Areas</strong></p>\r
+<a href="index.html">Editing</a> can be restricted to the current selection area. \r
+This allows the user to "Lock" the alignment either side of the selection \r
+area. Any gap insertions or deletions will only affect the current selection area.\r
+<p><img src="editing.jpg" width="428" height="186" align="top"></p>\r
+<p>In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, \r
+ the same number of gaps will be inserted at position 116, (between M and L). \r
+</p>\r
+<p><em>Locked selection area based editing was introduced in Jalview 2.08</em></p>\r
+<p> </p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff