-<html>\r
-<head><title>Alignment Window Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Alignment Window Calculate Menu</strong></p>\r
-<ul>\r
- <li><strong>Sort </strong> \r
- <ul>\r
- <li><strong>by ID</strong><em><br>\r
- This will sort the sequences according to sequence name. If the sort is \r
- repeated, the order of the sorted sequences will be inverted. </em></li>\r
- <li><strong>by Group</strong><strong><br>\r
- </strong><em>This will sort the sequences according to sequence name. \r
- If the sort is repeated, the order of the sorted sequences will be inverted. \r
- </em><strong></strong></li>\r
- <li><strong>by Pairwise Identity<br>\r
- </strong><em>This will sort the selected sequences by their percentage \r
- identity to the consensus sequence. The most similar sequence is put at \r
- the top. </em></li>\r
- <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have \r
- some additional options if you have just done a multiple alignment calculation, \r
- or opened a tree viewer window.</em><br>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong>Calculate Tree </strong> <br>\r
- <em>Functions for calculating trees on the alignment or the currently selected \r
- region. See <a\r
- href="../calculations/tree.html">calculating trees</a>.</em> \r
- <ul>\r
- <li><strong>Average Distance Using % Identity</strong></li>\r
- <li><strong>Neighbour Joining Using % Identity</strong></li>\r
- <li><strong>Average Distance Using Blosum62</strong></li>\r
- <li><strong>Neighbour Joining Using Blosum62<br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Pairwise Alignments</strong><br>\r
- <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise \r
- alignments</a>.</em><br>\r
- </li>\r
- <li><strong>Principal Component Analysis</strong><br>\r
- <em>Shows a spatial clustering of the sequences based on the BLOSUM62 scores \r
- in the alignment. See <a href="../calculations/pca.html">Principal Component \r
- Analysis</a>.</em> <br>\r
- </li>\r
- <li><strong>Autocalculate Consensus</strong><br>\r
- <em>For large alignments it can be useful to deselect "Autocalculate \r
- Consensus" when editing. This prevents lengthy calculations which are \r
- performed after each sequence edit.</em> <br>\r
- </li>\r
-</ul>\r
- </body>\r
-</html>\r
+#-------------------------------------------------------------------------------
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+#
+# This file is part of Jalview.
+#
+# Jalview is free software: you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Jalview is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+# PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<head><title>Alignment Window Menus</title></head>
+
+<body>
+<p><strong>Alignment Window Calculate Menu</strong></p>
+<ul>
+ <li><strong>Sort </strong>
+ <ul>
+ <li><strong>by ID</strong><em><br>
+ This will sort the sequences according to sequence name. If the sort is
+ repeated, the order of the sorted sequences will be inverted. </em></li>
+ <li><strong>by Length</strong><em><br>
+ This will sort the sequences according to their length (excluding gap characters). If the sort is
+ repeated, the order of the sorted sequences will be inverted. </em></li>
+ <li><strong>by Group</strong><strong><br>
+ </strong><em>This will sort the sequences according to sequence name.
+ If the sort is repeated, the order of the sorted sequences will be inverted.
+ </em><strong></strong></li>
+ <li><strong>by Pairwise Identity<br>
+ </strong><em>This will sort the selected sequences by their percentage
+ identity to the consensus sequence. The most similar sequence is put at
+ the top. </em></li>
+ <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have
+ some additional options if the alignment has any associated
+ score annotation, or you have just done a multiple alignment calculation
+ or opened a tree viewer window.</em><br>
+ </li>
+ </ul>
+ </li>
+ <li><strong>Calculate Tree </strong> <br>
+ <em>Functions for calculating trees on the alignment or the currently selected
+ region. See <a
+ href="../calculations/tree.html">calculating trees</a>.</em>
+ <ul>
+ <li><strong>Average Distance Using % Identity</strong></li>
+ <li><strong>Neighbour Joining Using % Identity</strong></li>
+ <li><strong>Average Distance Using Blosum62</strong></li>
+ <li><strong>Neighbour Joining Using Blosum62<br>
+ </strong></li>
+ </ul>
+ </li>
+ <li><strong>Pairwise Alignments</strong><br>
+ <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
+ alignments</a>.</em><br>
+ </li>
+ <li><strong>Principal Component Analysis</strong><br>
+ <em>Shows a spatial clustering of the sequences based on the BLOSUM62 scores
+ in the alignment. See <a href="../calculations/pca.html">Principal Component
+ Analysis</a>.</em> <br>
+ </li>
+ <li><strong>Extract Scores ... (optional)</strong><br>
+ <em>This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.<br>
+ When selected, these numbers are parsed into sequence associated annotation which can
+ then be used to sort the alignment via the Sort by→Score menu.</em> <br>
+ </li>
+
+ <li><strong>Autocalculate Consensus</strong><br>
+ <em>For large alignments it can be useful to deselect "Autocalculate
+ Consensus" when editing. This prevents the sometimes lengthy calculations
+ performed after each sequence edit.</em> <br>
+ </li>
+</ul>
+ </body>
+</html>
git://source.jalview.org / jalview.git / blobdiff