<html>
-<head><title>Hidden Regions</title></head>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
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+ * This file is part of Jalview.
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+ * of the License, or (at your option) any later version.
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+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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".</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 propogated 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>
-<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>Tree</strong>, <strong>pairwise alignment</strong> and <strong>PCA</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