From 7fd07d9b6a64aa33e3dcab2fa2f8bc20be189f2f Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 3 Jun 2014 14:28:44 +0100
Subject: [PATCH] JAL-1503 gui changes (score models, flanking regions, trim
 retrieved sequences)

---
 help/html/menus/alignmentMenu.html |   38 +++++++++++++++++++++++++-----------
 help/html/menus/wsmenu.html        |   35 +++++++++++++++++++++------------
 2 files changed, 50 insertions(+), 23 deletions(-)

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index d4ffc50..fdaa023 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -484,14 +484,15 @@
 						<li><strong>Neighbour Joining Using Blosum62<br>
 						</strong></li>
 					</ul>
+					<strong>Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu.</strong>
 				</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>.</em><br>
 				</li>
 				<li><strong>Principal Component Analysis</strong><br> <em>Shows
-						a spatial clustering of the sequences based on the BLOSUM62 scores
-						in the alignment. See <a href="../calculations/pca.html">Principal
+						a spatial clustering of the sequences based on similarity scores calculated with
+						the alignment. See <a href="../calculations/pca.html">Principal
 							Component Analysis</a>.</em> <br>
 				</li>
 				<li><strong>Extract Scores ... (optional)</strong><br> <em>This
@@ -509,21 +510,36 @@
 				<li><strong>Sort With New Tree</strong><br> <em>When
 						enabled, Jalview will automatically sort the alignment when a new
 						tree is calculated or loaded onto it.</em> <br></li>
-			</ul></li>
+			<li><strong>Show Flanking Regions</strong><br> <em>Opens
+					a new alignment window showing any additional sequence data either
+					side of the current alignment. Useful in conjunction with 'Fetch
+					Database References' when the 'Trim Retrieved Sequences' option is
+					disabled to retrieve full length sequences for a set of aligned
+					peptides. </em></li>
+		</ul></li>
 
 		<li><strong>Web Service Menu</strong><br /> <em>This menu
 				is dynamic, and may contain user-defined web service entries in
 				addition to any of the following ones:</em>
 			<ul>
 				<li><strong>Fetch DB References</strong><br> <em>This
-						will use any of the database services that Jalview is aware of
-						(e.g. DAS sequence servers and the WSDBFetch service provided by
-						the EBI) to verify the sequence and retrieve all database cross
-						references and PDB ids associated with all or just the selected
-						sequences in the alignment. <br />'Standard Databases' will check
-						sequences against the EBI databases plus any active DAS sequence
-						sources, or you can verify against a specific source from one of
-						the sub-menus.</em><br></li>
+        submenu contains options for accessing any of the database services
+        that Jalview is aware of (e.g. DAS sequence servers and the
+        WSDBFetch service provided by the EBI) to verify sequence start/end
+        positions and retrieve all database cross references and PDB ids
+        associated with all or just the selected sequences in the alignment.
+        <ul>
+          <li>'Trim Retrieved Sequences' - when checked, Jalview will
+            discard any additional sequence data for accessions associated with
+            sequences in the alignment. <br> <strong>Note: Disabling this
+              could cause out of memory errors when working with genomic
+              sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
+        </li>
+          <li>'Standard Databases' will check sequences against the EBI
+            databases plus any active DAS sequence sources<</li>
+        </ul> Other sub-menus allow you to pick a specific source to query -
+        sources are listed alphabetically according to their nickname.
+    </em><br></li>
 			</ul>
 			<p>Selecting items from the following submenus will start a
 				remote service on compute facilities at the University of Dundee, or
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index f3a4102..0e050b1 100755
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -23,18 +23,29 @@
 		<p><strong>Web Service Menu</strong><br /> <em>This menu
 				is dynamic, and may contain user-defined web service entries in
 				addition to any of the following ones:</em>
-			<ul>
-				<li><strong>Fetch DB References</strong><br> <em>This
-						will use any of the database services that Jalview is aware of
-						(e.g. DAS sequence servers and the WSDBFetch service provided by
-						the EBI) to verify the sequence and retrieve all database cross
-						references and PDB ids associated with all or just the selected
-						sequences in the alignment. <br />'Standard Databases' will check
-						sequences against the EBI databases plus any active DAS sequence
-						sources, or you can verify against a specific source from one of
-						the sub-menus.</em><br></li>
-			</ul>
-			<p>Selecting items from the following submenus will start a
+			
+	<ul>
+		<li><strong>Fetch DB References</strong><br> <em>This
+				submenu contains options for accessing any of the database services
+				that Jalview is aware of (e.g. DAS sequence servers and the
+				WSDBFetch service provided by the EBI) to verify sequence start/end
+				positions and retrieve all database cross references and PDB ids
+				associated with all or just the selected sequences in the alignment.
+				<ul>
+					<li>'Retrieve full Sequence' - when checked, Jalview will
+						retrieve the full sequence for any accessions associated with
+						sequences in the alignment. <br> <strong>Note: This
+							could cause out of memory errors when working with genomic
+							sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
+		    </li>
+					<li>'Standard Databases' will check sequences against the EBI
+						databases plus any active DAS sequence sources<</li>
+				</ul> Other submenus allow you to pick a specific source to query -
+				sources are listed alphabetically according to their nickname.
+		</em>
+	</li>
+	</ul>
+	<p>Selecting items from the following submenus will start a
 				remote service on compute facilities at the University of Dundee, or
 				elsewhere. You need a continuous network connection in order to use
 				these services through Jalview.
-- 
1.7.10.2