+++ /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