+++ /dev/null
-<html>
-<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>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 will display a window
- asking for the name of the currently selected group. Click OK to set
- the name, cancel to use the default group name. </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>
- </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><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>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 PDB 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>
- This entry is only present if the sequence has an <a
- href="../features/viewingpdbs.html">associated PDB structure</a>. </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><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.</em><strong><br>
- </strong></li>
- </ul>
- </li>
- <li><strong>Hide Sequences</strong><br>
- <em>Hides the currently selected seuqences in this alignment view.</em><strong><br>
- <br>
- </strong></li>
-</ul>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff