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
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
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.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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"
36 >'Cursor mode'</a> keyboard editing facility, where the space bar and
37 delete keys add and remove gaps at the current editing position. The
38 key strokes for both these modes are summarised in the <a
40 >keystrokes table</a>.
43 <strong>Tip:</strong> For large alignments, deselect "Calculate
44 -> Autocalculate Consensus" to prevent the alignment
45 performing lengthy calculations after every edit.
48 <em>Inserting / removing gaps</em> - hold down the "Shift"
49 key. Click on a residue with the mouse and drag it to the left or
50 right to insert gaps and remove gaps.<br> If the current
51 selection is a group over all sequences in the alignment, or a group
52 over some sequences or all columns in the alignment, then hold down
53 either "Control" key (or the "Alt;" on OSX if
54 "Control" does not work) and drag the residue left or
55 right to edit all sequences in the defined group at once.
58 <em>Copy/paste/cut/delete</em> - any sequences which are in the
59 current selection box (indicated in red) may be cut and / or copied
60 to a new alignment or deleted.
63 <em>Undo / redo</em> - editing of sequences (insertion/removal of
64 gaps, removal of sequences, trimming sequences etc) may be undone or
65 redone at any time using the appropriate menu items from the edit
66 menu. The undo history list only allows a maximum of 10 actions.
68 <em>Trimming alignment</em> - First select a column by clicking the
69 scale indicator (above the sequences) The alignment may then be
70 trimmed to the left or right of this column. If multiple columns are
71 selected, the alignment is trimmed to the right of the rightmost
72 selected column (or to the left of the leftmost selected column)
75 <em>Remove gapped columns</em> - Removes columns within the
76 alignment which contain only space characters ("-" or
77 "." or " ")
80 <em>Removing gaps</em> - Removes all gaps from the alignment. Gaps
81 are "-" or "." or " ".
84 <em>Set gap character</em> - Switches the gap character between
85 "." and "-". If the "Render Gaps"
86 option from the "View" menu is unticked all gaps will
87 appear as blank spaces.
91 <strong>Editing In Selection Areas</strong>
93 Editing can be restricted to the current selection area. This allows
94 the user to "Lock" the alignment either side of the
95 selection area. Any gap insertions or deletions will only affect the
96 current selection area.
98 <img src="editing.jpg" width="428" height="186" align="top">
100 <p>In this example, if Sequence IL2RA_MACMU has gaps removed from
101 position 98-104, the same number of gaps will be inserted at
102 position 116, (between M and L).</p>
104 <em>Locked selection area based editing was introduced in