2 <head><title>Hidden Regions</title></head>
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4 <p><strong>Hidden Regions</strong> </p>
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5 <p>Use the keyboard key "H" to hide / reveal selected columns and sequences.
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6 To hide / reveal only selected sequences, use "Shift H", to hide /
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7 reveal only selected columns, use "Control H".</p>
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8 <p><strong><em>Hiding Sequences</em></strong><br>
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9 To hide selected sequences in an alignment, use the <strong>"View
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10 -> Hide -> Selected Sequences"</strong> menu item or simply select <strong>"Hide
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11 Sequences"</strong> from the Popup menu after a right click on the sequence Ids.
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13 <p>Hidden sequences will not be used in any calculations, editing or web service
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14 alignments performed on visible sequences. </p>
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15 <p><strong><em>Hidden Sequences Representatives</em></strong><br>
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16 A more advanced hide involves a right-mouse click on a sequence, then selecting
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17 <strong>"SequenceID -> Represent Group with SequenceId"</strong>. Using this method
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18 of hiding sequences, any edits performed on the visible group representative
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19 will be propogated to all the sequences in that group. <br>
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20 The hidden representative sequences will not be used in any
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21 calculations or web service alignments (<em>nb. this may change in
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24 <p><strong><em>Hiding Columns</em></strong><br>
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25 To hide selected columns in an alignment, use the <strong>"View
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26 -> Hide -> Selected Columns"</strong> menu item, or right click within a region
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27 of selected columns in the scale above the alignment (only available in non
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28 wrapped mode) and select <strong>"Hide Columns"</strong>. </p>
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29 <p>When an alignment view contains hidden columns, certain constraints
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30 apply:<ul><li>Editing the alignment is bound by the hidden columns, <em>i.e.</em> you cannot move residues
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31 across a hidden column boundary.</li>
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32 <li><strong>Tree</strong>, <strong>pairwise alignment</strong> and <strong>PCA</strong> calculations will only be
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33 performed using the <em>visible</em> parts of the alignment.
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36 href="../webservices/msaclient.html">Multiple Sequence
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37 Alignments</a> are performed locally on on each visible chunk of
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38 the input, and concatenated with the hidden regions to form the
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42 <p>The analysis and web service calculations where hidden columns are
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43 excluded are termed <em>column-separable</em>. Calculations which
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44 are not column-separable will be performed on the whole alignmnent
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45 or sequence set, not just the visible regions.</p>
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