X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=95dcad838c9f562f3ef5ab4a38a7c69b439c21f1;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=a7cb733d856154ee6f042de9e3348951b309f245;hpb=87fa9a883d14416ba0e7f778bad69de813048b9c;p=jalview.git

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index a7cb733..95dcad8 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -62,18 +62,16 @@
 						Select the format of the text by selecting one of the following
 						menu items.</em>
 					<ul>
-						<li><strong>FASTA</strong> <em></em>
-						</li>
-						<li><strong>MSF</strong>
-						</li>
-						<li><strong>CLUSTAL</strong>
-						</li>
-						<li><strong>BLC</strong>
-						</li>
-						<li><strong>PIR</strong>
-						</li>
-						<li><strong>PFAM</strong>
-						</li>
+						<li><strong>FASTA</strong> </li>
+						<li><strong>MSF</strong></li>
+						<li><strong>CLUSTAL</strong></li>
+						<li><strong>BLC</strong></li>
+						<li><strong>PIR</strong></li>
+						<li><strong>PFAM</strong></li>
+						<li><strong>PileUp</strong></li>
+						<li><strong>AMSA</strong></li>
+						<li><strong>STH</strong></li>
+						<li><strong>Phylip</strong></li>
 					</ul></li>
 				<li><strong>Print (Control P)<br> </strong><em>Jalview
 						will print the alignment using the current fonts and colours of
@@ -203,9 +201,9 @@
 						the last redundancy deletion.</em>
 				</li>
 				<li><strong>Pad Gaps<br> </strong><em>When selected,
-						the alignment will be kept at minimal width (so there no empty
+						the alignment will be kept at minimal width (so there are no empty
 						columns before or after the first or last aligned residue) and all
-						sequences will be padded with gap characters to the before and
+						sequences will be padded with gap characters before and
 						after their terminating residues.<br> This switch is useful
 						when making a tree using unaligned sequences and when working with
 						alignment analysis programs which require 'properly aligned
@@ -279,39 +277,6 @@
 						selected, the view will automatically scroll to display the
 						highlighted sequence position corresponding to the position under
 						the mouse pointer in a linked alignment or structure view.</em></li>
-				<li><strong>Show Annotations<br> </strong><em>If this
-						is selected the &quot;Annotation Panel&quot; will be displayed
-						below the alignment. The default setting is to display the
-						conservation calculation, quality calculation and consensus values
-						as bar charts. </em>
-				</li>
-			  <li><strong>Show All Annotations</strong><em><br>
-			    Show all available annotations on the alignment. You can selectively hide these from the <a href="./popupMenu.html">Popup</a> 
-			    or <a href="../features/annotation.html">Annotation</a> menus. (Since Jalview 2.8.2)</em></li>
-			  <li><strong>Hide All Annotations</strong><em><br>
-			    Hide all annotations on the alignment. (Since Jalview 2.8.2)</em></li>
-				<li><strong>Autocalculated Annotation<br> </strong><em>Settings
-					for the display of autocalculated annotation.</em>
-					<ul>
-						<li><strong>Apply to all groups<br> </strong><em> When
-							ticked, any modification to the current settings will be applied
-							to all autocalculated annotation.</em></li>
-						<li><strong>Show Consensus Histogram<br> </strong><em>
-							Enable or disable the display of the histogram above the
-							consensus sequence.</em></li>
-						<li><strong>Show Consensus Logo<br> </strong><em> Enable
-							or disable the display of the Consensus Logo above the consensus
-							sequence.</em></li>
-						<li><strong>Normalise Consensus Logo<br>
-						</strong><em>When enabled, scales all logo stacks to the same height,
-								making it easier to compare symbol diversity in highly variable
-								regions.</em></li>
-						<li><strong>Group Conservation<br> </strong><em> When
-							ticked, display a conservation row for all groups (only available
-							for protein alignments).</em></li>
-						<li><strong>Apply to all groups<br> </strong><em> When
-							ticked, display a consensus row for all groups.</em></li>
-					</ul></li>
 				<li><strong>Show Sequence Features</strong><br> <em>Show
 						or hide sequence features on this alignment.</em>
 				</li>
@@ -338,6 +303,61 @@
 						using the mouse. </em>
 				</li>
 			</ul></li>
+		<li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
+			<ul>
+			  <li><strong>Show Annotations<br> </strong><em>If this
+						is selected the &quot;Annotation Panel&quot; will be displayed
+						below the alignment. The default setting is to display the
+						conservation calculation, quality calculation and consensus values
+						as bar charts. </em>
+			  </li>
+			  <li><strong>Show Alignment Related</strong><em><br>
+			    Show all annotations that are for the alignment as a whole (for example, Consensus, 
+			    or secondary structure prediction from alignment).</em></li>
+			  <li><strong>Hide Alignment Related</strong><em><br>
+			    Hide all annotations that are for the alignment as a whole.</em></li>
+			  <li><strong>Show Sequence Related</strong><em><br>
+			    Show all annotations that are for individual sequences.</em></li>
+			  <li><strong>Hide Sequence Related</strong><em><br>
+			    Hide all annotations that are for individual sequences.</em></li>
+			  <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a> 
+			    or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
+			  <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
+			  (and within that, by label).</em></li>
+			  <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
+			  (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
+			  allowing you to make a manual ordering of the annotations.</em></li>
+			  <li><strong>Autocalculated Annotation<br> </strong><em>Settings
+					for the display of autocalculated annotation.</em>
+					<ul>
+					    <li><strong>Show first<br></strong><em>
+					      Show autocalculated annotations above sequence-specific annotations.
+					      Note this also applies to other annotations for the alignment, for example secondary
+					      structure prediction from alignment.</em></li>
+					    <li><strong>Show last<br></strong><em>
+					      Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
+						<li><strong>Apply to all groups<br> </strong><em> When
+							ticked, any modification to the current settings will be applied
+							to all autocalculated annotation.</em></li>
+						<li><strong>Show Consensus Histogram<br> </strong><em>
+							Enable or disable the display of the histogram above the
+							consensus sequence.</em></li>
+						<li><strong>Show Consensus Logo<br> </strong><em> Enable
+							or disable the display of the Consensus Logo above the consensus
+							sequence.</em></li>
+						<li><strong>Normalise Consensus Logo<br>
+						</strong><em>When enabled, scales all logo stacks to the same height,
+								making it easier to compare symbol diversity in highly variable
+								regions.</em></li>
+						<li><strong>Group Conservation<br> </strong><em> When
+							ticked, display a conservation row for all groups (only available
+							for protein alignments).</em></li>
+						<li><strong>Group Consensus<br> </strong><em> When
+							ticked, display a consensus row for all groups.</em></li>
+					</ul>
+				</li>
+			</ul>
+		</li>
 		<li><strong>Alignment Window Format Menu</strong>
 			<ul>
 				<li><strong>Font...<br> </strong><em>Opens the