-<html>\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><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
-<p><em>Undo / redo</em> - editing of sequences (insertion/removal of gaps, removal\r
- of sequences, trimming sequences etc) may be undone or redone at any time using\r
- the appropriate menu items from the edit menu. The undo history list only allows\r
- a maximum of 10 actions.\r
-<p><em>Trimming alignment</em> - First select a column by clicking the scale indicator\r
- (above the sequences) The alignment may then be trimmed to the left or right\r
- of this column. If multiple columns are selected, the alignment is trimmed to\r
- the right of the rightmost selected column (or to the left of the leftmost selected\r
- column)</p>\r
-<p><em>Remove gapped columns</em> - Removes columns within the alignment which\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
- menu is unticked all gaps will appear as blank spaces.</p>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<head><title>Editing</title></head>
+<body>
+<p><strong>Editing</strong></p>
+<p>There are two major ways to edit alignments - in 'Normal mode',
+gaps are inserted and deleted at the mouse pointer in various ways by
+clicking the left mouse button and pressing a combination of either
+shift and control (or the apple key on Macs) and dragging the mouse. Pressing
+<em>F2</em> toggles the alternative <a href="../features/cursorMode.html">'Cursor
+mode'</a> keyboard editing facility, where the space bar and delete
+keys add and remove gaps at the current editing position. The key
+strokes for both these modes are summarised in the <a
+href="../keys.html">keystrokes table</a>.</p>
+<p><strong>Tip:</strong> For large alignments, deselect "Calculate ->
+ Autocalculate Consensus" to prevent the alignment performing lengthy calculations
+ after every edit. </p>
+<p><em>Inserting / removing gaps</em> - hold down the
+ "Shift" key. Click on a residue with the mouse and drag it
+ to the left or right to insert gaps and remove gaps.<br>
+ If the current selection is a group over all sequences in the
+ alignment, or a group over some sequences or all columns in the
+ alignment, then hold down either "Control"
+ key and drag the residue left or right to edit all sequences in the defined
+ group at once.</p>
+<p><em>Copy/paste/cut/delete</em> - any sequences which are in the current selection
+ box (indicated in red) may be cut and / or copied to a new alignment or deleted.
+</p>
+<p><em>Undo / redo</em> - editing of sequences (insertion/removal of gaps, removal
+ of sequences, trimming sequences etc) may be undone or redone at any time using
+ the appropriate menu items from the edit menu. The undo history list only allows
+ a maximum of 10 actions.
+<p><em>Trimming alignment</em> - First select a column by clicking the scale indicator
+ (above the sequences) The alignment may then be trimmed to the left or right
+ of this column. If multiple columns are selected, the alignment is trimmed to
+ the right of the rightmost selected column (or to the left of the leftmost selected
+ column)</p>
+<p><em>Remove gapped columns</em> - Removes columns within the alignment which
+ contain only space characters ("-" or "." or " ")</p>
+<p><em>Removing gaps</em> - Removes all gaps from the alignment. Gaps are "-"
+ or "." or " ".</p>
+<p><em>Set gap character</em> - Switches the gap character between "."
+ and "-". If the "Render Gaps" option from the "View"
+ menu is unticked all gaps will appear as blank spaces.</p>
+<p> </p>
+<p><strong>Editing In Selection Areas</strong></p>
+Editing 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><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>
+<p> </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff