<p>Use the keyboard key "H" to hide / reveal selected columns and sequences. \r
To hide / reveal only selected sequences, use "Shift H", to hide / \r
reveal only selected columns, use "Control H".</p>\r
-<p> </p>\r
-<p>To <strong>hide selected sequences </strong>from an alignment, use the "View \r
- -> Hide -> Selected Sequences" menu item or simply select "Hide \r
- Sequences" from the Popup menu after a right click on the sequence Ids. \r
+<p><strong><em>Hiding Sequences</em></strong><br>\r
+To hide selected sequences in an alignment, use the <strong>"View \r
+ -> Hide -> Selected Sequences"</strong> menu item or simply select <strong>"Hide \r
+ Sequences"</strong> from the Popup menu after a right click on the sequence Ids. \r
</p>\r
<p>Hidden sequences will not be used in any calculations, editing or web service \r
alignments performed on visible sequences. </p>\r
-<p>A more advanced hide involves a right-mouse click on a sequence, then selecting \r
- "SequenceID -> Represent Group with SequenceId". Using this method \r
+<p><strong><em>Hidden Sequences Representatives</em></strong><br>\r
+A more advanced hide involves a right-mouse click on a sequence, then selecting \r
+ <strong>"SequenceID -> Represent Group with SequenceId"</strong>. Using this method \r
of hiding sequences, any edits performed on the visible group representative \r
will be propogated to all the sequences in that group. <br>\r
- The hidden sequences will not be used in any calculations or web service alignments. \r
+ The hidden representative sequences will not be used in any\r
+ calculations or web service alignments (<em>nb. this may change in\r
+ the future</em>)\r
</p>\r
-<p> </p>\r
-<p>To <strong>hide selected columns</strong> from an alignment, use the "View \r
- -> Hide -> Selected Columns" menu item, or right click within a region \r
+<p><strong><em>Hiding Columns</em></strong><br>\r
+To hide selected columns in an alignment, use the <strong>"View \r
+ -> Hide -> Selected Columns"</strong> menu item, or right click within a region \r
of selected columns in the scale above the alignment (only available in non \r
- wrapped mode) and select "Hide Columns". </p>\r
-<p>Hidden columns will not be used in any calculations. This allows you to eg. \r
- create trees from the visible alignment and ignore any poorly aligned sections \r
- of the alignment, without cutting and deleting them permanently from your alignment.<br>\r
- It is possible to retrieve the input data to any trees, PCA analysis windows \r
- which were created from alignments containing hidden columns by using the "File \r
- -> Input Data..." menu item from the tree window. </p>\r
-<p> Editing the alignment is bound by the hidden columns, ie you cannot move residues \r
- across a hidden column boundary.</p>\r
-<p>Any web service alignments performed on sequences which contain hidden columns \r
- send the alignment as a series of chunks delimited by the hidden columns. </p>\r
+ wrapped mode) and select <strong>"Hide Columns"</strong>. </p>\r
+<p>When an alignment view contains hidden columns, certain constraints\r
+apply:<ul><li>Editing the alignment is bound by the hidden columns, <em>i.e.</em> you cannot move residues \r
+ across a hidden column boundary.</li>\r
+<li><strong>Tree</strong>, <strong>pairwise alignment</strong> and <strong>PCA</strong> calculations will only be\r
+performed using the <em>visible</em> parts of the alignment.\r
+</li>\r
+<li><a\r
+ href="../webservices/msaclient.html">Multiple Sequence\r
+ Alignments</a> are performed locally on on each visible chunk of\r
+ the input, and concatenated with the hidden regions to form the\r
+ final result.</p>\r
+</li>\r
+</ul>\r
+<p>The analysis and web service calculations where hidden columns are\r
+ excluded are termed <em>column-separable</em>. Calculations which\r
+ are not column-separable will be performed on the whole alignmnent\r
+ or sequence set, not just the visible regions.</p>\r
<p> </p>\r
<p> </p>\r
<p> </p>\r
git://source.jalview.org / jalview.git / blobdiff