-<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 2.9.0b1)
+ * Copyright (C) 2015 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
+ either "Control" key (or the "Alt;" on OSX if
+ "Control" does not work) 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