-<html>\r
-<head><title>Popup Menu</title></head>\r
-\r
-<body>\r
-<p><strong>Popup Menu</strong><br>\r
- <em>This menu is visible when right clicking either within a selected region \r
- on the alignment or on a selected sequence name.</em></p>\r
-<ul>\r
- <li><strong>Define </strong> \r
- <ul>\r
- <li><strong>Group<br>\r
- </strong><em>This will display a window asking for the name of the currently \r
- selected group. Click OK to set the name, cancel to use the default group \r
- name. </em><strong><br>\r
- </strong></li>\r
- <li><strong>Remove Group<br>\r
- </strong><em>This will undefine the selected group. </em><strong> <br>\r
- </strong></li>\r
- <li><strong>Group Colour<br>\r
- </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> \r
- of the group.</em><strong> <br>\r
- </strong></li>\r
- <li><strong>Boxes<br>\r
- </strong><em>If selected the background of a residue within the selected \r
- group will be coloured according to the assigned colour scheme.</em><strong> \r
- <br>\r
- </strong></li>\r
- <li><strong> Text<br>\r
- </strong><em>If selected the selected group will display text. </em><strong><br>\r
- </strong></li>\r
- <li><strong>Colour Text<br>\r
- </strong><em>If selected the selected group will display text in a colour \r
- slightly darker than the background colour of that residue.</em><strong><br>\r
- </strong></li>\r
- <li><strong>Border Colour <br>\r
- </strong><em>Selecting this will display a "Colour Chooser" \r
- window. Select a colour than press OK to set the border colour of a group.</em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Sequence <br>\r
- </strong><em>This menu is only visible if you right-click on a sequence name. \r
- </em> \r
- <ul>\r
- <li><strong>Edit Name/Description<br>\r
- </strong><em>You may edit the name and description of each sequence. A \r
- window will be displayed asking for a new sequence name and sequence description \r
- to be entered. Press OK to accept your edit. To save sequence descriptions, \r
- you must save in Fasta, PIR or Jalview File format.</em><strong><br>\r
- </strong></li>\r
- <li><strong>View PDB Structure<br>\r
- </strong><em>\r
- If the sequence has a PDB file associated with it Jalview will display \r
- a 3D interactive viewer of the file.<br>\r
-This entry is only present if the sequence has an\r
- <a href="../features/viewingpdbs.html">associated PDB structure</a>.\r
- If you can't see this entry for your sequence, and the sequence name\r
- is a uniprot identifier, then try enabling the "View \r
- -> Sequence Features" and opening the popup menu again.</em>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong><em>Link</em></strong><br>\r
- <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> \r
- Connections tab. It is only displayed when you right click (Apple click) on \r
- a sequence id. </em><strong><br>\r
- <br>\r
- </strong></li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<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>
+<!-- not available in 2.5 yet
+ <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 open a 3D interactive
+ view 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