From 5ba0be3c2257b380e292c53d47993b78ece4892d Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 8 May 2007 16:51:47 +0000
Subject: [PATCH] formatting

---
 help/html/menus/alwformat.html |  111 ++++++++++++++++++++--------------------
 1 file changed, 55 insertions(+), 56 deletions(-)
diff --git a/help/html/menus/alwformat.html b/help/html/menus/alwformat.html
index d7224b3..3a13e02 100644
--- a/help/html/menus/alwformat.html
+++ b/help/html/menus/alwformat.html
@@ -1,56 +1,55 @@
-<html>
-<head>
-<p><strong>Alignment Window Format Menu</strong></p>
-<ul>
-  <li><strong>Font...</strong><br>
-    <em>Opens the &quot;Choose Font&quot; dialog box, in order to change the font 
-    of the display and enable or disable 'smooth fonts' (anti-aliasing) for faster 
-    alignment rendering. </em></em></li>
-  <li><strong>Wrap<br>
-    </strong><em>When ticked, the alignment display is &quot;<a
-		href="../features/wrap.html">wrapped</a>&quot; to the width of the alignment 
-    window. This is useful if your alignment has only a few sequences to view 
-    its full width at once.<br>
-    Additional options for display of sequence numbering and scales are also visible 
-    in wrapped layout mode:</em>
-    <ul>
-      <li><strong>Scale Left</strong><br>
-        <em>Show the sequence position for the first aligned residue in each row 
-        in the left column of the alignment.</em></li>
-      <li><strong>Scale Right</strong><br>
-        <em>Show the sequence position for the last aligned residue in each row 
-        in the right-most column of the alignment.</em></li>
-    </ul>
-  
-  <li><strong>Scale Above</strong><br>
-    <em>Show the alignment column position scale.</em></li>
-  <li><strong>Show Sequence Limits<br>
-    </strong><em>If this box is selected the sequence name will have the start 
-    and end position of the sequence appended to the name, in the format NAME/START-END</em></li>
-  <li><strong>Right Align Sequence ID<br>
-    </strong> <em>If this box is selected then the sequence names displayed in 
-    the sequence label area will be aligned against the left-hand edge of the 
-    alignment display, rather than the left-hand edge of the alignment window.</em></li>
-  <li><strong>Show Hidden Markers<br>
-    </strong><em>When this box is selected, positions in the alignment where rows 
-    and columns are hidden will be marked by blue arrows.</em></li>
-  <li><strong>Boxes</strong><em><br>
-    If this is selected the background of a residue will be coloured using the 
-    selected background colour. Useful if used in conjunction with &quot;Colour 
-    Text.&quot; </em></li>
-  <li><strong>Text<br>
-    </strong><em>If this is selected the residues will be displayed using the 
-    standard 1 character amino acid alphabet.</em></li>
-  <li><strong>Colour Text<br>
-    </strong><em>If this is selected the residues will be coloured according to 
-    the background colour associated with that residue. The colour is slightly 
-    darker than background so the amino acid symbol remains visible. </em></li>
-  <li><strong>Show Gaps<br>
-    </strong><em>When this is selected, gap characters will be displayed as &quot;.&quot; 
-    or &quot;-&quot;. If unselected, then gap characters will appear as blank 
-    spaces. <br>
-    You may set the default gap character in <a
-		href="../features/preferences.html">preferences</a>.</em></li>
-</ul>
-</body>
-</html>
+<html>
+<head>
+<p><strong>Alignment Window Format Menu</strong></p>
+<ul>
+  <li><strong>Font...</strong><br>
+    <em>Opens the &quot;Choose Font&quot; dialog box, in order to change the font 
+    of the display and enable or disable 'smooth fonts' (anti-aliasing) for faster 
+    alignment rendering. </em></em></li>
+  <li><strong>Wrap<br>
+    </strong><em>When ticked, the alignment display is &quot;<a
+		href="../features/wrap.html">wrapped</a>&quot; to the width of the alignment 
+    window. This is useful if your alignment has only a few sequences to view 
+    its full width at once.<br>
+    Additional options for display of sequence numbering and scales are also visible 
+    in wrapped layout mode:</em>
+    <ul>
+      <li><strong>Scale Left</strong><br>
+        <em>Show the sequence position for the first aligned residue in each row 
+        in the left column of the alignment.</em></li>
+      <li><strong>Scale Right</strong><br>
+        <em>Show the sequence position for the last aligned residue in each row 
+        in the right-most column of the alignment.</em></li>
+      <li><strong>Scale Above</strong><br>
+        <em>Show the alignment column position scale.</em></li>
+    </ul>
+  <li><strong>Show Sequence Limits<br>
+    </strong><em>If this box is selected the sequence name will have the start 
+    and end position of the sequence appended to the name, in the format NAME/START-END</em></li>
+  <li><strong>Right Align Sequence ID<br>
+    </strong> <em>If this box is selected then the sequence names displayed in 
+    the sequence label area will be aligned against the left-hand edge of the 
+    alignment display, rather than the left-hand edge of the alignment window.</em></li>
+  <li><strong>Show Hidden Markers<br>
+    </strong><em>When this box is selected, positions in the alignment where rows 
+    and columns are hidden will be marked by blue arrows.</em></li>
+  <li><strong>Boxes</strong><em><br>
+    If this is selected the background of a residue will be coloured using the 
+    selected background colour. Useful if used in conjunction with &quot;Colour 
+    Text.&quot; </em></li>
+  <li><strong>Text<br>
+    </strong><em>If this is selected the residues will be displayed using the 
+    standard 1 character amino acid alphabet.</em></li>
+  <li><strong>Colour Text<br>
+    </strong><em>If this is selected the residues will be coloured according to 
+    the background colour associated with that residue. The colour is slightly 
+    darker than background so the amino acid symbol remains visible. </em></li>
+  <li><strong>Show Gaps<br>
+    </strong><em>When this is selected, gap characters will be displayed as &quot;.&quot; 
+    or &quot;-&quot;. If unselected, then gap characters will appear as blank 
+    spaces. <br>
+    You may set the default gap character in <a
+		href="../features/preferences.html">preferences</a>.</em></li>
+</ul>
+</body>
+</html>
-- 
1.7.10.2

