updated menus and rearranged seqfeatures (again)

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

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index d0f1052..ee8661f 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -146,10 +146,14 @@
         the current alignment) exceeds this value then one of the sequences (the \r
         shorter) is discarded. Press the "Apply" button to remove redundant \r
         sequences. The &quot;Undo&quot; button will undo the last redundancy deletion.</em></li>\r
-      <li><strong>Pad Gaps<br>\r
-        </strong><em>Adds gaps to the end of all the sequences so they are all \r
-        the same length. This is useful for making a tree using unaligned sequences.<br>\r
-        You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+  <li><strong>Pad Gaps<br>\r
+    </strong><em>When selected, the alignment will be kept at minimal\r
+    width (no empty columns before or after the first or last aligned\r
+    residue). This is useful when making a tree using unaligned\r
+    sequences and when working with alignment analysis programs which\r
+    require 'properly aligned sequences' to be all the same length.<br>\r
+    You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+    </em></li>\r
         </em><br>\r
       </li>\r
     </ul>\r
@@ -158,7 +162,8 @@
     <ul>\r
       <li><strong>Find<br>\r
         </strong><em>Select this to <a href="../features/search.html">search</a> \r
-        for residues, sequence name or residue position within the alignment. \r
+        for residues, sequence name or residue position within the\r
+        alignment and create new sequence features from the queries. \r
         <br>\r
         </em></li>\r
     </ul>\r
@@ -168,6 +173,10 @@
       <li><strong>Font<br>\r
         </strong><em>Change the font of the display from the &quot;Choose Font&quot; \r
         dialog box, which is shown when this item is selected. </em></li>\r
+      <li><strong>Smooth Fonts</strong><em><br>\r
+      If selected, the alignment will be drawn with anti-aliasing on which looks \r
+      better, but performace is reduced.\r
+      </em></li>\r
       <li><strong>Wrap<br>\r
         </strong><em>When ticked, the alignment display is &quot;<a href="../features/wrap.html">wrapped</a>&quot; \r
         to the width of the alignment window. This is useful if your alignment \r
@@ -201,7 +210,7 @@
         be displayed below the alignment. The default setting is to display the \r
         conservation calculation, quality calculation and consensus values as \r
         bar charts. </em></li>\r
-      <li><strong>Sequence Features<br>\r
+      <li><strong>Fetch Sequence Features<br>\r
         </strong><em>If the sequence names are Swissprot entries Jalview will \r
         use the names to retrieve <a href="../features/seqfeatures.html">sequence \r
         features</a> from the EBI. Features which are 1 residue in length are \r
@@ -210,11 +219,13 @@
         <br>\r
         Note: The retrieved information will update the sequence start and end \r
         labels if they are incorrect. </em></li>\r
-      <li><strong>Seqence Settings </strong><br>\r
-        <em>If features have been added to the alignment then the priority of \r
-        rendering the features can be altered so that overlapping features can \r
-        be displayed or hidden. See <a href="features/seqfeatures.html">Sequence \r
-        Features</a>.</em></li>\r
+        <li><strong>Show Sequence Features</strong><br><em>Show or\r
+        hide sequence features on this alignment.</em></li>\r
+    <li><strong>Seqence Feature Settings...</strong><em><br>\r
+      <em>Control the colour and display of sequence features on the\r
+      alignment. See <a\r
+      href="../features/featuresettings.html">Sequence Feature Settings</a>.</em><br>\r
+      </em></li>\r
       <li><strong><a href="../features/overview.html">Overview Window</a><br>\r
         </strong><em>A scaled version of the alignment will be displayed in a \r
         small window. A red box will indicate the currently visible area of the \r
@@ -245,6 +256,10 @@
         </strong><em>Use this to set the threshold value for colouring above Identity. \r
         Useful if the window has been closed. <br>\r
         </em></li>\r
+    <li><strong>By Annotation</strong><br>\r
+      <em>Colours the alignment on a per-column value from a specified annotation. \r
+      See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>\r
+    </li>\r
     </ul>\r
   </li>\r
   <li><strong>Calculate</strong> \r