--- /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>Popup Menu</title>
+</head>
+
+<body>
+ <p>
+ <strong>Popup Menu</strong><br> <em>This menu is visible
+ when right clicking either within a selected region on the
+ alignment or on a selected sequence name. It may not be accessible
+ when in 'Cursor Mode' (toggled with the F2 key).</em><br /> <em><strong>Mac
+ Users:</strong> pressing CTRL whilst clicking the mouse/track pad is the
+ same as a right-click. See your system's settings to configure
+ your track-pad's corners to generate right-clicks.</em>
+ </p>
+ <ul>
+ <li><strong>Selection</strong>
+ <ul>
+ <li><a name="sqreport"><strong>Sequence
+ Details...<br>
+ </strong></a><em>(Since Jalview 2.8)<br>Open an <a
+ href="../io/exportseqreport.html">HTML report
+ containing the annotation and database cross references</a> normally
+ shown in the sequence's tooltip.
+ </em></li>
+ <li><strong>Show Annotations...<br>
+ </strong><em>Choose to show (unhide) either All or a selected type
+ of annotation for the selected sequences. (Since Jalview
+ 2.8.2)</em></li>
+ <li><strong>Hide Annotations...<br>
+ </strong><em>Choose to hide either All or a selected type of
+ annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+ <li><a name="addrefannot"><strong>Add
+ Reference Annotations<br>
+ </strong><em>Add to the alignment window any annotations on the
+ selected sequences which have been read from reference
+ sources or calculated (for example, secondary structure
+ derived from 3D structure). (Since Jalview 2.8.2)</em></li>
+ <li><strong>Edit </strong>
+ <ul>
+ <li><strong>Copy</strong><br> <em>Copies the
+ selected region. In the applet version, the copied
+ sequences are not available to the system clipboard.</em></li>
+ <li><strong>Cut<br>
+ </strong><em>Cuts the selected region from the alignment. In the
+ applet version, the copied sequences are not available
+ to the system clipboard.</em></li>
+ <li><strong>Edit Sequence</strong><br> <em>Edit
+ the selected sequence(s) directly. Spaces will be
+ converted to the current gap character.</em></li>
+ <li><strong>To Upper Case</strong><em><strong><br>
+ </strong><em>Changes the case of selected region to lower
+ case.</em> </em></li>
+ <li><strong>To Lower Case<br>
+ </strong><em>Changes the case of selected region to upper case.</em><strong>
+ </strong></li>
+ <li><strong>Toggle Case</strong><br> <em>Switches
+ the case of all residues within the selected region.</em></li>
+ </ul></li>
+ <li><strong>Output to Textbox<br>
+ </strong><em>The selection area will be output to a a text window in
+ the selected alignment format. </em></li>
+ <li><strong><a
+ href="../features/creatinFeatures.html">Create
+ Sequence Feature...</a></strong><br> <em>Opens the dialog box
+ for creating sequence features over the currently selected
+ region on each selected sequence.</em></li>
+ <li><strong>Create Group<br>
+ </strong><em>This will define a new group from the current
+ selection.</em><strong> </strong></li>
+ <li><strong>Remove Group<br>
+ </strong><em>This will undefine the selected group. </em><strong>
+ </strong></li>
+ <li><strong>Edit (New) Group</strong><br> <em>Group
+ Editing Menu</em> <br />Options in this menu modify the name and
+ display properties of the currently selected group, or a new
+ group defined using the current selection.
+ <ul>
+ <li><strong>Name: <Group></strong> or <strong>Edit
+ name and description</strong><br> <em>The first entry
+ in the menu displays the name for the currently selected
+ group, if it has one. Selecting this option opens a
+ window allowing the name and description for this group
+ to be edited. Click OK to set the new name and
+ decription, and cancel to leave the existing name and
+ description unchanged.</em></li>
+ <li><strong>Group Colour<br>
+ </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
+ of the group.
+ </em><strong> </strong></li>
+ <li><strong>Boxes<br>
+ </strong><em>If selected the background of a residue within the
+ selected group will be coloured according to the
+ assigned colour scheme.</em><strong> </strong></li>
+ <li><strong>Text<br>
+ </strong><em>If selected the selected group will display text. </em></li>
+ <li><strong>Colour Text<br>
+ </strong><em>If selected the selected group will display text in
+ a colour slightly darker than the background colour of
+ that residue.</em></li>
+ <li><strong>Border Colour <br>
+ </strong><em>Selecting this will display a "Colour
+ Chooser" window. Select a colour than press OK to
+ set the border colour of a group.</em></li>
+ <li><strong>Show Unconserved<br>
+ </strong><em>When this is selected, all symbols in the group
+ matching the consensus sequence at that column will be
+ rendered as a '.', highlighting mutations in the group
+ area. </em></li>
+ </ul></li>
+
+ </ul></li>
+ <li><strong>Sequence Id<br>
+ </strong><em>This menu is only visible if you right-click on a sequence
+ name. </em>
+ <ul>
+ <li><a name="sqreport"><strong>Sequence
+ Details ...<br>
+ </strong></a><em>(Since Jalview 2.8)<br>Open an <a
+ href="../io/exportseqreport.html">HTML report
+ containing the annotation and database cross references</a>
+ normally shown in the sequence's tooltip.
+ </em></li>
+ <li><strong>Edit Name/Description<br>
+ </strong><em>You may edit the name and description of each sequence.
+ A window will be displayed asking for a new sequence name
+ and sequence description to be entered. Press OK to accept
+ your edit. To save sequence descriptions, you must save in
+ Fasta, PIR or Jalview File format.</em></li>
+ <li><strong>Add <a
+ href="../features/annotation.html#seqannots">Reference
+ Annotations</a></strong><br> <em>When enabled, copies any
+ available alignment annotation for this sequence to the
+ current view.</em></li>
+ <li><strong>Set as Reference</strong> or <strong>Unmark
+ as Reference</strong><br /> Sets or unsets the reference sequence
+ for the the alignment.</li>
+
+ <li><strong>Represent Group With (Sequence Id)</strong><br>
+ <em>All sequences in the current selection group will be
+ hidden, apart from (Sequence Id). Any edits performed on the
+ visible representative sequence will be propagated to the
+ hidden sequences. </em></li>
+ <li><a name="sqid.popup"><strong>Link</strong><br>
+ <em>This menu item lists all links which have been set
+ up in the <a href="../features/preferences.html">Preferences</a>
+ Connections tab.<br> Since Jalview 2.4, links will
+ also be made for database cross references (where the
+ database name exactly matches the link name set up in <a
+ href="../features/preferences.html">Preferences</a>).
+ <br>Since Jalview 2.5, links are also shown for
+ non-positional sequence features attached to the sequence,
+ and any regular-expression based URL links that matched
+ the description line.
+ </em><strong><br> </strong></li>
+ </ul></li>
+ <li><strong>3D Structure Data...</strong> </strong><em>This menu is
+ visible when you right-click on a sequence name. When this
+ option is clicked, Jalview will open the <a
+ href="../features/structurechooser.html">'Structure Chooser'
+ </a>, which allows you to discover and view 3D structures for the
+ current selection. For more info, see <a
+ href="../features/viewingpdbs.html">viewing PDB structures</a>.
+ </em></li>
+ <li><strong>VARNA 2D Structure</strong><br /> <em> If the
+ sequence or alignment has RNA structure, then <strong>VARNA
+ 2D Structure</strong> entries will also be present enabling you to open
+ a linked view of the RNA structure in <a
+ href="../features/varna.html">VARNA</a>.
+ </em></li>
+ <li><a name="hideinserts"><strong>Hide Insertions</strong></a><br />
+ <em>Hides columns containing gaps in both the current
+ sequence and selected region, and reveals columns not including
+ gaps. (before 2.10.2, this option hid or revealed columns
+ according to gaps in just the current sequence)</em></li>
+ <li><strong>Hide Sequences</strong><br> <em>Hides the
+ currently selected sequences in this alignment view.</em><strong><br>
+ </strong></li>
+ </ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff