help/html/menus/alwannotation.html

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  22 <head>
  23 <title>Alignment Window Menus</title>
  24 </head>
  25
  26 <body>
  27 <p><strong>Alignment Window Annotations Menu</strong> (Since Jalview 2.8.2)</p>
  28 <ul>
  29                           <li><strong>Show Alignment Related</strong><em><br>
  30                             Show all annotations that are for the alignment as a whole (for example, Consensus,
  31                             or secondary structure prediction from alignment)).</em></li>
  32                           <li><strong>Hide Alignment Related</strong><em><br>
  33                             Hide all annotations that are for the alignment as a whole.</em></li>
  34                           <li><strong>Show Sequence Related</strong><em><br>
  35                             Show all annotations that are for individual sequences.</em></li>
  36                           <li><strong>Hide Sequence Related</strong><em><br>
  37                             Hide all annotations that are for individual sequences.</em></li>
  38                           <li><strong>Show Alignment Related</strong><em><br>
  39                             Show all annotations that are for the alignment as a whole (for example, Consensus).</em></li>
  40                           <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
  41                             or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
  42                           <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
  43                           (and within that, by label).</em></li>
  44                           <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
  45                           (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
  46                           allowing you to make a manual ordering of the annotations.</em></li>
  47                           <li><strong>Autocalculated Annotation<br> </strong><em>Settings
  48                                         for the display of autocalculated annotation.</em>
  49                                         <ul>
  50                                             <li><strong>Show first<br></strong><em>
  51                                               Show autocalculated annotations above sequence-specific annotations.
  52                                               Note this also applies to other annotations for the alignment, for example secondary
  53                                               structure prediction from alignment.</em></li>
  54                                             <li><strong>Show last<br></strong><em>
  55                                               Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
  56                                                 <li><strong>Apply to all groups<br> </strong><em> When
  57                                                         ticked, any modification to the current settings will be applied
  58                                                         to all autocalculated annotation.</em></li>
  59                                                 <li><strong>Show Consensus Histogram<br> </strong><em>
  60                                                         Enable or disable the display of the histogram above the
  61                                                         consensus sequence.</em></li>
  62                                                 <li><strong>Show Consensus Logo<br> </strong><em> Enable
  63                                                         or disable the display of the Consensus Logo above the consensus
  64                                                         sequence.</em></li>
  65                                                 <li><strong>Normalise Consensus Logo<br>
  66                                                 </strong><em>When enabled, scales all logo stacks to the same height,
  67                                                                 making it easier to compare symbol diversity in highly variable
  68                                                                 regions.</em></li>
  69                                                 <li><strong>Group Conservation<br> </strong><em> When
  70                                                         ticked, display a conservation row for all groups (only available
  71                                                         for protein alignments).</em></li>
  72                                                 <li><strong>Group Consensus<br> </strong><em> When
  73                                                         ticked, display a consensus row for all groups.</em></li>
  74                                         </ul>
  75                                 </li>
  76 </ul>
  77 <p>&nbsp;</p>
  78 </body>
  79 </html>