+++ /dev/null
-<html>
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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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- *
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- * Jalview is free software: you can redistribute it and/or
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- * of the License, or (at your option) any later version.
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- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Hidden Regions</title>
-</head>
-<body>
- <p>
- <strong>Hidden Regions</strong>
- </p>
- <p>Use the keyboard key "H" to hide / reveal selected
- columns and sequences. To hide / reveal only selected sequences, use
- "Shift H", to hide / reveal only selected columns, use
- "Control H". You can also use "Shift" and
- "Control" together to hide everything but the currently
- selected region.</p>
- <p>
- <strong><em>Hiding Sequences</em></strong><br> To hide selected
- sequences in an alignment, use the <strong>"View ->
- Hide -> Selected Sequences"</strong> menu item or simply select <strong>"Hide
- Sequences"</strong> from the Popup menu after a right click on the
- sequence Ids.
- </p>
- <p>Hidden sequences will not be used in any calculations, editing
- or web service alignments performed on visible sequences.</p>
- <p>
- <strong><em>Hidden Sequences Representatives</em></strong><br>
- A more advanced hide involves a right-mouse click on a sequence,
- then selecting <strong>"SequenceID -> Represent
- Group with SequenceId"</strong>. Using this method of hiding
- sequences, any edits performed on the visible group representative
- will be propagated to all the sequences in that group. <br> The
- hidden representative sequences will not be used in any calculations
- or web service alignments (<em>nb. this may change in the
- future</em>).
- <p>
- <strong><em>Hidden Sequence Representatives and
- Multiple Views</em></strong><br> <em>A word of warning: hidden
- representative sequence groups are (still) only partly implemented
- in the Jalview 2.5 release, and we hope to deal with the following
- issues in the future.</em><br> Currently, represented hidden
- groups are only made correctly if there is just one alignment view.
- When multiple views on an alignment exist, then the represented
- group will be displayed correctly in the view in which it was made,
- but in other views, both representative and hidden sequences will be
- visible, but will behave as if they are grouped. <br> Hidden
- representatives are propagated correctly to a new view if they exist
- in the current view. However, if the represented sequences are
- revealed in any one view, then in all other views they will simply
- be marked as hidden, and their association with the representative
- sequence will be lost.<br>
- </blockquote>
- </p>
- <p>
- <strong><em>Hiding Columns</em></strong><br> To hide selected
- columns in an alignment, use the <strong>"View ->
- Hide -> Selected Columns"</strong> menu item, or right click within
- a region of selected columns in the scale above the alignment (only
- available in non wrapped mode) and select <strong>"Hide
- Columns"</strong>.
- </p>
- <p>When an alignment view contains hidden columns, certain
- constraints apply:
- <ul>
- <li>Editing the alignment is bound by the hidden columns, <em>i.e.</em>
- you cannot move residues across a hidden column boundary.
- </li>
- <li><strong><a href="../calculations/tree.html">Tree</a></strong>,
- <strong><a href="../calculations/pairwise.html">pairwise
- alignment</a></strong> and <strong><a
- href="../calculations/pca.html">PCA</a></strong> calculations will
- only be performed using the <em>visible</em> parts of the
- alignment.</li>
- <li><a href="../webServices/msaclient.html">Multiple
- Sequence Alignments</a> are performed locally on on each visible
- chunk of the input, and concatenated with the hidden regions to
- form the final result.
- </p></li>
- </ul>
- <p>
- <strong>Column Separability</strong><br> Calculations where
- hidden columns are excluded, and a single analysis performed on the
- result, are termed <em>column-separable</em>. The simple Tree and
- PCA calculations are column separable because essentially the same
- results would be obtained if the excluded hidden columns were
- replaced by gaps as the input to the calculation.
- </p>
- <p>Multiple Sequence alignment and secondary structure prediction
- are both non-column-separable, and so the exclusion of hidden
- regions leads to only 'locally optimal' results - sometimes
- different to that obtained when using the full alignment.</p>
- <p> </p>
- <p> </p>
- <p> </p>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff