3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
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11 * of the License, or (at your option) any later version.
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14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Editing</title>
27 <strong>Editing</strong>
30 There are two major ways to edit alignments - in 'Normal mode', gaps
31 are inserted and deleted at the mouse pointer in various ways by
32 clicking the left mouse button and pressing a combination of either
33 shift and control (or the alt, option or apple key on Macs) and
34 dragging the mouse. Pressing <em>F2</em> toggles the alternative <a
35 href="../features/cursorMode.html">'Cursor mode'</a> keyboard
36 editing facility, where the space bar and delete keys add and remove
37 gaps at the current editing position. The key strokes for both these
38 modes are summarised in the <a href="../keys.html">keystrokes
42 <strong>Tip:</strong> For large alignments, deselect "Calculate
43 -> Autocalculate Consensus" to prevent the alignment
44 performing lengthy calculations after every edit.
47 <em>Inserting / removing gaps</em> - hold down the "Shift"
48 key. Click on a residue with the mouse and drag it to the left or
49 right to insert gaps and remove gaps.<br> If the current
50 selection is a group over all sequences in the alignment, or a group
51 over some sequences or all columns in the alignment, then hold down
52 "Control" key ("Cmd" key on OSX) and drag the residue
53 left or right to edit all sequences in the defined group at once.
56 <em>Copy/paste/cut/delete</em> - any sequences which are in the
57 current selection box (indicated in red) may be cut and / or copied
58 to a new alignment or deleted.
61 <em>Undo / redo</em> - editing of sequences (insertion/removal of
62 gaps, removal of sequences, trimming sequences etc) may be undone or
63 redone at any time using the appropriate menu items from the edit
66 <em>Trimming alignment</em> - First select a column by clicking the
67 scale indicator (above the sequences) The alignment may then be
68 trimmed to the left or right of this column. If multiple columns are
69 selected, the alignment is trimmed to the right of the rightmost
70 selected column (or to the left of the leftmost selected column)
73 <em>Remove gapped columns</em> - Removes columns within the
74 alignment which contain only space characters ("-" or
75 "." or " ")
78 <em>Removing gaps</em> - Removes all gaps from the alignment. Gaps
79 are "-" or "." or " ".
82 <em>Set gap character</em> - Switches the gap character between
83 "." and "-". If the "Render Gaps"
84 option from the "View" menu is unticked all gaps will
85 appear as blank spaces.
89 <strong>Editing In Selection Areas</strong>
91 Editing can be restricted to the current selection area. This allows
92 the user to "Lock" the alignment either side of the
93 selection area. Any gap insertions or deletions will only affect the
94 current selection area.
96 <img src="editing.jpg" width="428" height="186" align="top">
98 <p>In this example, if Sequence IL2RA_MACMU has gaps removed from
99 position 98-104, the same number of gaps will be inserted at
100 position 116, (between M and L).</p>
102 <em>Locked selection area based editing was introduced in