<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<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>
+ <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