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added sorting alignments documentation.
authorjprocter <Jim Procter>
Tue, 24 May 2005 08:51:43 +0000 (08:51 +0000)
committerjprocter <Jim Procter>
Tue, 24 May 2005 08:51:43 +0000 (08:51 +0000)
help/help.jhm patch | blob | history
help/helpTOC.xml patch | blob | history
help/html/calculations/sorting.html [new file with mode: 0755] patch | blob

diff --git a/help/help.jhm b/help/help.jhm
index c843321..4081a57 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -14,7 +14,8 @@
    \r
    <mapID target="io" url="html/io/index.html"/>\r
    <mapID target="edit" url="html/editing/index.html"/>\r
-   \r
+\r
+   <mapID target="sorting" url="html/calculations/sorting.html"/>\r
    <mapID target="trees" url="html/calculations/tree.html"/>\r
    <mapID target="pca" url="html/calculations/pca.html"/>\r
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>\r
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index b60a46c..0bcf3e6 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -30,6 +30,7 @@
                <tocitem text="By conservation" target="colours.conservation"/>\r
        </tocitem>\r
        <tocitem text="Calculations" expand="false">\r
+                <tocitem text="Sorting alignments" target="sorting"/>\r
                <tocitem text="Calculating trees" target="trees"/>\r
                <tocitem text="Principal Component Analysis" target="pca"/>\r
                <tocitem text="Pairwise Alignments" target="pairwise"/>\r
diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
new file mode 100755 (executable)
index 0000000..c3414bc
--- /dev/null
+++ b/help/html/calculations/sorting.html
@@ -0,0 +1,41 @@
+<html>
+<head>
+<title>Sorting Sequences</title>
+</head>
+<body>
+<p><strong>Sorting Sequences</strong></p>
+<p>Any group of selected sequences may be reordered by pressing the
+up or down arrow keys. The whole alignment may also be reordered by
+the use of the functions in the Sort menu (Calculate->Sort):
+</p>
+<ul>
+<li><strong>Sort by ID</strong>
+<p>Orders the sequences by the alphanumeric (0-9A-Za-z)
+precedence of their names.</p>
+</li>
+<li><strong>Sort by Group</string>
+<p>Places sequences in the same group adjacent to eachother.</p>
+</li>
+<li><strong>Sort by Pairwise Identity</strong> 
+<p>Places pairs of sequences together that align with the greatest
+fraction of conserved residues. 
+</p>
+</li><strong>Sort by Tree Order</strong>
+<p>The leaf ordering of a particular phylogenetic tree is used to
+order the sequences corresponding to those leaves in the
+alignment.<br>
+If a tree has been calculated from or associated with the current
+alignment, its name will appear in the submenu 'Sort->By Tree Order->'.<p>
+</li>
+<li><strong>Sort by alignment ordering</strong>
+<p>Multiple alignment methods often order the sequences in their
+alignments by some measure of sequence identity.<br>
+If the current alignment has been generated by one of the Jalview
+alignment web services, the alignment ordering can be recovered by
+its corresponding entry in the 'Sort->By ..' menu.
+</p>
+</li>
+</ul>
+
+</body>
+</html>