* 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/>.
---!>
-<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></p>
-<ul>
- <li><strong>Selection</strong>
- <ul>
- <li><strong>Edit </strong>
- <ul>
- <li><strong>Copy</strong><br>
- <em>Copys 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>Group</strong><br>
- <em>Group Operations</em>
- <ul>
- <li><strong>Group</strong><em>This is the first entry in the
- menu, and will display the currently selected group's
- name. Selecting it displays 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>Remove Group<br>
- </strong><em>This will undefine the selected group. </em><strong>
- </strong></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>
- <li><strong>Group Links<br>
- </strong><em>This menu is only visible if there are group links available for the current selection.
- </em>
- <ul>
- <li><em>ID links</em> allow you to send IDs associated with the current selection to a web server.</li>
- <li><em>Sequence links</em> allow you to send the sequences in the currently selected region to a web server.</li>
- <li><em>Sequence and ID links</em> allow you to send sets of IDs and sequences associated with the current selection to a web server.</li>
- </ul>
- <em>Group Links were added in Jalview 2.5</em></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><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><em> </em></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>Structure</strong>
- </strong><em>This menu is only visible if you right-click on a sequence name.
- </em>
- <ul>
- <li><strong>Associate Structure with Sequence</strong>
- <ul>
- <li><strong>From File<br>
- </strong><em>Load a PDB file from local disk which will be associated
- with this sequence. This file will be used if the user subsequently
- clicks on "View PDB Structure" menu item.</em></li>
- <li><strong>Enter PDB id<br>
- </strong><em>Enter the PDB id from an input window. This PDB id will
- be used by the service WSDBFetch, provided by the EBI, to fetch the
- PDB file if the user subsequently clicks on "View PDB Structure"
- menu item. </em></li>
- <li><strong>Discover PDB ids<br>
- </strong><em>This will use the service WSDBFetch, provided by the
- EBI, to retrieve all PDB ids associated with the sequences in the
- alignment if the sequences have valid Uniprot names or accession ids.
- </em></li>
- </ul>
- </li>
- <li><strong>View Structure<br>
- </strong><em> If the sequence has an associated PDB file added by one
- of the methods described above, Jalview will display a 3D interactive
- viewer of the file.<br>
- These entries will only be present if the sequence has <a
- href="../features/viewingpdbs.html">associated PDB structures</a>.</em><br>
- </li>
- </ul>
- </li>
- <li><strong>Hide Sequences</strong><br>
- <em>Hides the currently selected sequences in this alignment view.</em><strong><br>
- <br>
- </strong></li>
-</ul>
-</body>
-</html>
+-->
git://source.jalview.org / jalview.git / blobdiff