help/html/menus/popupMenu.html

   1 <html>
   2 <head>
   3 <title>Popup Menu</title>
   4 </head>
   5
   6 <body>
   7 <p><strong>Popup Menu</strong><br>
   8 <em>This menu is visible when right clicking either within a
   9 selected region on the alignment or on a selected sequence name. It may
  10 not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
  11 <ul>
  12         <li><strong>Selection</strong>
  13         <ul>
  14                 <li><strong>Edit </strong>
  15                 <ul>
  16                         <li><strong>Copy</strong><br>
  17                         <em>Copys the selected region. In the applet version, the copied
  18                         sequences are not available to the system clipboard.</em></li>
  19                         <li><strong>Cut<br>
  20                         </strong><em>Cuts the selected region from the alignment. In the applet
  21                         version, the copied sequences are not available to the system
  22                         clipboard.</em></li>
  23                         <li><strong>To Upper Case</strong><em><strong><br>
  24                         </strong><em>Changes the case of selected region to lower case.</em> </em></li>
  25                         <li><strong>To Lower Case<br>
  26                         </strong><em>Changes the case of selected region to upper case.</em><strong>
  27                         </strong></li>
  28                         <li><strong>Toggle Case</strong><br>
  29                         <em>Switches the case of all residues within the selected
  30                         region.</em></li>
  31                 </ul>
  32                 </li>
  33                 <li><strong>Output to Textbox<br>
  34                 </strong><em>The selection area will be output to a a text window in the
  35                 selected alignment format. </em></li>
  36                 <li><strong><a href="../features/creatinFeatures.html">Create
  37                 Sequence Feature...</a></strong><br>
  38                 <em>Opens the dialog box for creating sequence features over the
  39                 currently selected region on each selected sequence.</em></li>
  40                 <li><strong>Group</strong><br>
  41                 <em>Group Operations</em>
  42                 <ul>
  43                         <li><strong>Group</strong><em>This will display a window
  44                         asking for the name of the currently selected group. Click OK to set
  45                         the name, cancel to use the default group name. </em></li>
  46                         <li><strong>Remove Group<br>
  47                         </strong><em>This will undefine the selected group. </em><strong> </strong></li>
  48                         <li><strong>Group Colour<br>
  49                         </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> of
  50                         the group.</em><strong> </strong></li>
  51                         <li><strong>Boxes<br>
  52                         </strong><em>If selected the background of a residue within the selected
  53                         group will be coloured according to the assigned colour scheme.</em><strong>
  54                         </strong></li>
  55                         <li><strong>Text<br>
  56                         </strong><em>If selected the selected group will display text. </em></li>
  57                         <li><strong>Colour Text<br>
  58                         </strong><em>If selected the selected group will display text in a colour
  59                         slightly darker than the background colour of that residue.</em></li>
  60                         <li><strong>Border Colour <br>
  61                         </strong><em>Selecting this will display a &quot;Colour Chooser&quot;
  62                         window. Select a colour than press OK to set the border colour of a
  63                         group.</em></li>
  64                 </ul>
  65                 </li>
  66         </ul>
  67         </li>
  68         <li><strong>Sequence Id<br>
  69         </strong><em>This menu is only visible if you right-click on a sequence
  70         name. </em>
  71         <ul>
  72                 <li><strong>Edit Name/Description<br>
  73                 </strong><em>You may edit the name and description of each sequence. A
  74                 window will be displayed asking for a new sequence name and sequence
  75                 description to be entered. Press OK to accept your edit. To save
  76                 sequence descriptions, you must save in Fasta, PIR or Jalview File
  77                 format.</em></li>
  78                 <li><strong>Associate Structure with Sequence</strong>
  79                 <ul>
  80                         <li><strong>From File<br>
  81                         </strong><em>Load a PDB file from local disk which will be associated
  82                         with this sequence. This file will be used if the user subsequently
  83                         clicks on &quot;View PDB Structure&quot; menu item.</em></li>
  84                         <li><strong>Enter PDB id<br>
  85                         </strong><em>Enter the PDB id from an input window. This PDB id will be
  86                         used by the service WSDBFetch, provided by the EBI, to fetch the PDB
  87                         file if the user subsequently clicks on &quot;View PDB
  88                         Structure&quot; menu item. </em></li>
  89                         <li><strong>Discover PDB ids<br>
  90                         </strong><em>This will use the service WSDBFetch, provided by the EBI, to
  91                         retrieve all PDB ids associated with the sequences in the alignment
  92                         if the sequences have valid Uniprot names or accession ids. </em></li>
  93                 </ul>
  94                 </li>
  95                 <li><strong>View PDB Structure<br>
  96                 </strong><em> If the sequence has an associated PDB file added by one of
  97                 the methods described above, Jalview will display a 3D interactive
  98                 viewer of the file.<br>
  99                 This entry is only present if the sequence has an <a
 100                         href="../features/viewingpdbs.html">associated PDB structure</a>. </em></li>
 101                 <li><strong>Represent Group With (Sequence Id)</strong><br>
 102                 <em>All sequences in the current selection group will be hidden,
 103                 apart from (Sequence Id). Any edits performed on the visible
 104                 representative sequence will be propagated to the hidden sequences. </em></li>
 105                 <li><strong>Link</strong><br>
 106                 <em>This menu item lists all links which have been set up in the
 107                 <a href="../features/preferences.html">Preferences</a> Connections
 108                 tab.</em><strong><br>
 109                 </strong></li>
 110         </ul>
 111         </li>
 112         <li><strong>Hide Sequences</strong><br>
 113         <em>This menu item lists all links which have been set up in the <a
 114                 href="../features/preferences.html">Preferences</a> Connections tab.
 115         It is only displayed when you right click (Apple click) on a sequence
 116         id. </em><strong><br>
 117         <br>
 118         </strong></li>
 119 </ul>
 120 </body>
 121 </html>