From b5fd4f62a35039495e03fc69c82a0920d848e587 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 28 Apr 2010 10:23:26 +0000
Subject: [PATCH] 2.5 updates...

---
 help/html/releases.html |   28 +++++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index fcb9534..e7ab682 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -30,7 +30,9 @@
 			<li>Linked viewing of nucleic acid sequences and structures</li>
 			<li>Automatic Scrolling option in View menu to display the
 			currently highlighted region of an alignment.</li>
-			<li>Optionally scale multi-character column labels to fit within each column of annotation row<!-- todo for applet --></li>
+			<li>Order an alignment in order of average feature score or
+			total feature count</li>
+			<li>Shading features by score or associated description</li>
 			<!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
 		</ul>
 		<em>Vamsas Capabilities</em>
@@ -54,29 +56,36 @@
 			references in sequence ID tooltip from View menu in application.</li>
 	<!--			<li>New hidden columns and rows and representatives capabilities
 			in annotations file (in progress - not yet fully implemented)</li> -->
-			<li>Order an alignment in order of average feature score or
-			total feature count</li>
-			<li>Shading features by score or associated description</li>
-			<li>Group-associated automatic and user-defined alignment
-			annotation</li>
+			<li>Group-associated consensus, sequence logos and conservation plots</li>
 			<li>Symbol distributions for each column can be exported and
 			visualized as sequence logos</li>
+			<li>Optionally scale multi-character column labels to fit within each column of annotation row<!-- todo for applet --></li>
 			<li>Optional automatic sort of associated alignment view when a
 			new tree is opened.</li>
 			<li>Jalview Java Console</li>
 			<li>New preference items for sequence ID tooltip and consensus annotation</li>
+			<li>Client to submit sequences and IDs to <a href="webServices/index.html#envision2">Envision2</a> Workflows</li>
 		</ul>
 		<em>Applet</em>
 		<ul>
 			<li>Middle button resizes annotation row height</li>
-			<li>parameter to enable automatic sort of associated alignment view when a
-			new tree is opened.</li>
-		<li>Non-positional features displayed in sequence ID tooltip</li>
+			<li>New Parameters
+			<ul>
+			 <li>sortByTree (true/false) - automatically sort the associated alignment view by the tree when a new tree is opened.</li>
+			 <li>showTreeBootstraps (true/false) - show or hide branch bootstraps (default is to show them if available)</li>
+			 <li>showTreeDistances (true/false) - show or hide branch lengths (default is to show them if available)</li>
+			 <li>showUnlinkedTreeNodes (true/false) - indicate if unassociated nodes should be highlighted in the tree view</li>
+			 <li>heightScale and widthScale (1.0 or more) - increase the height or width of a cell in the alignment grid relative to the current font size.</li>
+			</ul>
+			</li>
+			<li>Non-positional features displayed in sequence ID tooltip</li>
+		<li></li>
 		</ul>
 		<em>Other</em>
 		<ul>
 			<li>Features format: graduated colour definitions and
 			specification of feature scores</li>
+			<li>Alignment Annotations format: new keywords for group associated annotation (GROUP_REF) and annotation row display properties (ROW_PROPERTIES)</li>
 			<li>XML formats extended to support graduated feature colourschemes, group associated annotation, and profile visualization settings.</li>
 		</td>
 		<td>
@@ -93,6 +102,7 @@
 			ID and sequence string and query strings do not have to be in upper
 			case to match case-insensitively.</li>
 			<li>AMSA files only contain first column of multi-character column annotation labels</li>
+			<li>Jalview Annotation File generation/parsing consistent with documentation (e.g. Stockholm annotation can be exported and re-imported)</li>
 			<li>PDB files without embedded PDB IDs given a friendly name</li>
 			<li>Applet:
 			<ul>
-- 
1.7.10.2