+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<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 alt, option or 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
- "Control" key ("Cmd" key on OSX) 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.
- <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