JAL-2189 format help

[jalview.git] / help / html / menus / alwcalculate.html

diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 34e8d75..8032348 100755 (executable)
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -75,14 +75,14 @@
       </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>.
+        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 similarity scores
         calculated over the alignment.. See <a
-        href="../calculations/pca.html"
-      >Principal Component Analysis</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
@@ -91,27 +91,28 @@
         parsed into sequence associated annotation which can then be
         used to sort the alignment via the Sort by&#8594;Score menu.
     </em> <br></li>
-    <li><strong>Translate as cDNA</strong> (not applet)<br>
-    <em>This option is visible for nucleotide alignments. Selecting
-        this option shows the DNA's calculated protein product in a new
-        <a href="../features/splitView.html">split frame</a> window.
-        Note that the translation is not frame- or intron-aware; it
-        simply translates all codons in each sequence, using the
-        standard <a href="../misc/geneticCode.html">genetic code</a>
-        (any incomplete final codon is discarded). You can perform this
-        action on the whole alignment, or selected rows, columns, or
-        regions.
+    <li><strong>Translate as cDNA</strong> (not applet)<br> <em>This
+        option is visible for nucleotide alignments. Selecting this
+        option shows the DNA's calculated protein product in a new <a
+        href="../features/splitView.html">split frame</a> window. Note
+        that the translation is not frame- or intron-aware; it simply
+        translates all codons in each sequence, using the standard <a
+        href="../misc/geneticCode.html">genetic code</a> (any incomplete
+        final codon is discarded). You can perform this action on the
+        whole alignment, or selected rows, columns, or regions.
     </em> <br></li>
     <li><strong>Reverse, Reverse Complement</strong> (not applet)<br>
-    <em>These options are visible for nucleotide alignments. Selecting them adds the reverse (or reverse complement)
-    of the sequences (or selected region) as new sequences in the alignment. To try this out, add this sequence and
-    perform 'Reverse Complement' followed by 'Translate as cDNA':
-    <br><small>
-    Seq GTCATTTGCGCGTGTTGATTATTCGGACCGCTCCACTTCCCTTTACTCGTGCGTTCAATTGATTTAATCCTC
-    TGGGGGGGCTCTGGTTTACATAGCTTAAATCTATTCCATTCAAGGAAGCTCATG</small>
+      <em>These options are visible for nucleotide alignments.
+        Selecting them adds the reverse (or reverse complement) of the
+        sequences (or selected region) as new sequences in the
+        alignment. To try this out, add this sequence and perform
+        'Reverse Complement' followed by 'Translate as cDNA': <br>
+      <small> Seq
+          GTCATTTGCGCGTGTTGATTATTCGGACCGCTCCACTTCCCTTTACTCGTGCGTTCAATTGATTTAATCCTC
+          TGGGGGGGCTCTGGTTTACATAGCTTAAATCTATTCCATTCAAGGAAGCTCATG</small>
     </em> <br></li>
     <li><strong>Get Cross-References</strong> (not applet)<br>
-    <em>This option is visible where sequences have
+      <em>This option is visible where sequences have
         cross-references to other standard databases; for example, an
         EMBL entry may have cross-references to one or more UNIPROT
         entries. Select the database to view all cross-referenced