-<html>\r
-<head>\r
-<title>Popup Menu</title>\r
-</head>\r
-\r
-<body>\r
-<p><strong>Popup Menu</strong><br>\r
-<em>This menu is visible when right clicking either within a\r
-selected region on the alignment or on a selected sequence name. It may\r
-not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>\r
-<ul>\r
- <li><strong>Selection</strong> \r
- <ul>\r
- <li><strong>Edit </strong> \r
- <ul>\r
- <li><strong>Copy</strong><br>\r
- <em>Copys the selected region. In the applet version, the copied sequences \r
- are not available to the system clipboard.</em></li>\r
- <li><strong>Cut<br>\r
- </strong><em>Cuts the selected region from the alignment. In the applet \r
- version, the copied sequences are not available to the system clipboard.</em></li>\r
- <li><strong>Edit Sequence</strong><br>\r
- <em>Edit the selected sequence(s) directly. Spaces will be converted \r
- to current gap character.</em></li>\r
- <li><strong>To Upper Case</strong><em><strong><br>\r
- </strong><em>Changes the case of selected region to lower case.</em> \r
- </em></li>\r
- <li><strong>To Lower Case<br>\r
- </strong><em>Changes the case of selected region to upper case.</em><strong> \r
- </strong></li>\r
- <li><strong>Toggle Case</strong><br>\r
- <em>Switches the case of all residues within the selected region.</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Output to Textbox<br>\r
- </strong><em>The selection area will be output to a a text window in the \r
- selected alignment format. </em></li>\r
- <li><strong><a href="../features/creatinFeatures.html">Create Sequence Feature...</a></strong><br>\r
- <em>Opens the dialog box for creating sequence features over the currently \r
- selected region on each selected sequence.</em></li>\r
- <li><strong>Group</strong><br>\r
- <em>Group Operations</em> \r
- <ul>\r
- <li><strong>Group</strong><em>This will display a window asking for \r
- the name of the currently selected group. Click OK to set the name, \r
- cancel to use the default group name. </em></li>\r
- <li><strong>Remove Group<br>\r
- </strong><em>This will undefine the selected group. </em><strong> \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> </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
- </strong></li>\r
- <li><strong>Text<br>\r
- </strong><em>If selected the selected group will display text. </em></li>\r
- <li><strong>Colour Text<br>\r
- </strong><em>If selected the selected group will display text in a \r
- colour slightly darker than the background colour of that residue.</em></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 \r
- a group.</em></li>\r
- </ul>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Sequence Id<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></li>\r
- <li><em> </em></li>\r
- <li><strong>Represent Group With (Sequence Id)</strong><br>\r
- <em>All sequences in the current selection group will be hidden, apart \r
- from (Sequence Id). Any edits performed on the visible representative \r
- sequence will be propagated to the hidden sequences. </em></li>\r
- <li><strong>Link</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.</em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Structure</strong> \r
- <ul>\r
- <li><strong>Associate Structure with Sequence</strong> \r
- <ul>\r
- <li><strong>From File<br>\r
- </strong><em>Load a PDB file from local disk which will be associated \r
- with this sequence. This file will be used if the user subsequently \r
- clicks on "View PDB Structure" menu item.</em></li>\r
- <li><strong>Enter PDB id<br>\r
- </strong><em>Enter the PDB id from an input window. This PDB id will \r
- be used by the service WSDBFetch, provided by the EBI, to fetch the \r
- PDB file if the user subsequently clicks on "View PDB Structure" \r
- menu item. </em></li>\r
- <li><strong>Discover PDB ids<br>\r
- </strong><em>This will use the service WSDBFetch, provided by the \r
- EBI, to retrieve all PDB ids associated with the sequences in the \r
- alignment if the sequences have valid Uniprot names or accession ids. \r
- </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>View Structure<br>\r
- </strong><em> If the sequence has an associated PDB file added by one \r
- of the methods described above, Jalview will display a 3D interactive \r
- viewer of the file.<br>\r
- This entry is only present if the sequence has an <a\r
- href="../features/viewingpdbs.html">associated PDB structure</a>.</em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Hide Sequences</strong><br>\r
- <em>Hides the currently selected seuqences in this alignment view.</em><strong><br>\r
- <br>\r
- </strong></li>\r
-</ul>\r
-</body>\r
-</html>\r
+<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>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>
+ </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><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><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>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 / commitdiff