From c78133920a45e1b5b0b1bea5807f3ae880425914 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 26 Sep 2011 15:37:31 +0100
Subject: [PATCH] updated documentation table of contents, menus and whats new
 for 2.7

---
 help/help.jhm                    |    1 +
 help/helpTOC.xml                 |    6 +-
 help/html/menus/desktopMenu.html |    2 +
 help/html/releases.html          |  147 +++++++++++++++++++-------------------
 help/html/whatsNew.html          |  104 +++++++++++++++++++--------
 5 files changed, 157 insertions(+), 103 deletions(-)

diff --git a/help/help.jhm b/help/help.jhm
index 6ed0d7b..261d6d0 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -17,6 +17,7 @@
    <mapID target="msaservice" url="html/webServices/msaclient.html"/>
    <mapID target="jnet" url="html/webServices/jnet.html"/>
    <mapID target="shmrws" url="html/webServices/shmr.html"/>
+   <mapID target="newsreader" url="html/webServices/newsreader.html"/>
    <mapID target="seqfetch" url="html/features/seqfetch.html"/>
    <mapID target="dbreffetcher" url="html/webservices/dbreffetcher.html"/>
    <mapID target="seqmappings" url="html/features/seqmappings.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index a1cf057..6da4490 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -20,10 +20,12 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="true">
-      <tocitem text="Jaba Web Services" target="jabaws"/>
       <tocitem text="Enhanced Jmol/Jalview interaction" target="pdbjmol"/>
           <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
-      <tocitem text="Default Colouring preferences" target=""/>
+          <tocitem text="Jalview News Reader" target="newsreader"/>
+          <tocitem text="Sort alignments associated with tree" target="treeviewer"/>
+      <tocitem text="Default Annotation preferences" target="colours.annotation"/>
+      <tocitem text="Jaba Web Services" target="jabaws"/>
 	</tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>	
     <tocitem text="Cursor Mode" target="cursor"/>
diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index e108ded..03502f5 100755
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -68,6 +68,8 @@
 		</em></li>
 		<li><strong>Java Console<br/></strong>
 		<em>Toggles the display of a the Jalview Java Console window. This setting will be remembered in your user preferences.</em></li>
+		<li><strong>Jalview News<br/></strong>
+		<em>Opens the <a href="../webServices/newsreader.html">Jalview News</a> dialog box. </em></li>
 		<li><strong>Groovy Console...<em> (only available if groovy is on the classpath)</em><br></strong>
 		<em>Open's the <a href="../groovy.html">Groovy Console</a> for interactive scripting.</em><strong><br></strong></li>
 		
diff --git a/help/html/releases.html b/help/html/releases.html
index 19ff3e7..b67b69b 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -37,163 +37,166 @@
 			<td>
 				<div align="center">
 					<strong><a name="Jalview2.7">2.7</a>
-					</strong><br> <em>20/09/2011</em>
+					</strong><br> <em>27/09/2011</em>
 				</div></td>
 			<td><em>Application</em>
 				<ul>
-					<li>tweaked default layout of web services menu</li>
-					<li>view/alignment association menu to enable user to easily
+					<li>Jalview Desktop News Reader</li>
+					<li>Tweaked default layout of web services menu</li>
+					<li>View/alignment association menu to enable user to easily
 						specify which alignment a multi-structure view takes its
 						colours/correspondences from</li>
-					<li>allow properties file location to be specified as URL </li>
-						<li>extend jalview project to preserve associations between
+					<li>Allow properties file location to be specified as URL </li>
+						<li>Extend jalview project to preserve associations between
 							many alignment views and a single Jmol display</li>
 						<li>Store annotation row height in jalview project file</li>
-						<li>annotation row column label formatting attributes stored
+						<li>Annotation row column label formatting attributes stored
 							in project file</li>
-						<li>annotation row order for auto-calculated annotation rows
+						<li>Annotation row order for auto-calculated annotation rows
 							preserved in jalview project file</li>
-						<li>visual progress indication when Jalview state is saved
+						<li>Visual progress indication when Jalview state is saved
 							using Desktop window menu</li>
-						<li>visual indication that command line arguments are still
+						<li>Visual indication that command line arguments are still
 							being processed</li>
-						<li>groovy script execution from URL</li>
-						<li>colour by annotation default min and max colours in
+						<li>Groovy script execution from URL</li>
+						<li>Colour by annotation default min and max colours in
 							preferences</li>
-						<li>automatically associate PDB files dragged onto an
+						<li>Automatically associate PDB files dragged onto an
 							alignment with sequences that have high similarity and matching
 							IDs</li>
-						<li>update JGoogleAnalytics to latest release (0.3)</li>
+						<li>Update JGoogleAnalytics to latest release (0.3)</li>
 						<li>&#39;view structures&#39; option to open many structures
 							in same window</li>
 						<li>Sort associated views menu option for tree panel</li>
-						<li>group all JABA and non-JABA services for a particular
+						<li>Group all JABA and non-JABA services for a particular
 							analysis function in its own submenu</li>
 				</ul> <em>Applet</em>
 			<ul>
-					<li>userdefined and autogenerated annotation rows for groups</li>
-					<li>adjustment of alignment annotation pane height</li>
-					<li>annotation scrollbar for annotation panel</li>
-					<li>drag to reorder annotation rows in annotation panel</li>
+					<li>Userdefined and autogenerated annotation rows for groups</li>
+					<li>Adjustment of alignment annotation pane height</li>
+					<li>Annotation scrollbar for annotation panel</li>
+					<li>Drag to reorder annotation rows in annotation panel</li>
 					<li>&#39;automaticScrolling&#39; parameter</li>
-					<li>allow sequences with partial ID string matches to be
+					<li>Allow sequences with partial ID string matches to be
 						annotated from GFF/jalview features files</li>
-					<li>sequence logo annotation row in applet</li>
+					<li>Sequence logo annotation row in applet</li>
 					<li>Absolute paths relative to host server in applet
 						parameters are treated as such</li>
 					<li>New in the JalviewLite javascript API:
 						<ul>
-							<li>jalviewLite.js javascript library</li>
+							<li>JalviewLite.js javascript library</li>
 							<li>Javascript callbacks for
 								<ul>
-									<li>applet initialisation</li>
-									<li>sequence/alignment mouse-overs and selections</li>
+									<li>Applet initialisation</li>
+									<li>Sequence/alignment mouse-overs and selections</li>
 								</ul>
 							</li>
 							<li>scrollTo row and column alignment scrolling functions</li>
-							<li>select sequence/alignment regions from javascript</li>
+							<li>Select sequence/alignment regions from javascript</li>
 							<li>javascript structure viewer harness to pass messages
 								between Jmol and Jalview when running as distinct applets</li>
 							<li>sortBy method</li>
-							<li>set of applet and application examples shipped with
+							<li>Set of applet and application examples shipped with
 								documentation</li>
-							<li>new example to demonstrate jalviewLite and Jmol
+							<li>New example to demonstrate jalviewLite and Jmol
 								javascript message exchange</li>
 						</ul>
 				</ul> <em>General</em>
 				<ul>
-					<li>enable Jmol displays to be associated with multiple
+					<li>Enable Jmol displays to be associated with multiple
 						multiple alignments</li>
 					<li>Option to automatically sort alignment with new tree</li>
-					<li>user configurable link to enable redirects to a
+					<li>User configurable link to enable redirects to a
 						www.jalview.org mirror</li>
 					<li>Jmol colours option for Jmol displays</li>
-					<li>configurable newline string when writing alignment and
+					<li>Configurable newline string when writing alignment and
 						other flat files</li>
 					<li>Allow alignment annotation description lines to contain
 						html tags</li>
 				</ul> <em>Documentation and Development</em>
 				<ul>
-					<li>add groovy test harness for bulk load testing to examples
+					<li>Add groovy test harness for bulk load testing to examples
 					</li>
-					<li>groovy script to load and align a set of sequences using a
+					<li>Groovy script to load and align a set of sequences using a
 						web service before displaying the result in the Jalview desktop</li>
-					<li>restructured javascript and applet api documentation</li>
-					<li>ant target to publish example html files with applet archive</li>
-					<li>netbeans project for building jalview from source</li>
+					<li>Restructured javascript and applet api documentation</li>
+					<li>Ant target to publish example html files with applet archive</li>
+					<li>Netbeans project for building jalview from source</li>
 					<li>ant task to create online javadoc for jalview source</li>
 				</ul></td>
 			<td><em>Application</em>
 				<ul>
-					<li>user defined colourscheme throws exception when current
+					<li>User defined colourscheme throws exception when current
 						built in colourscheme is saved as new scheme</li>
 					<li>AlignFrame-&gt;Save in application pops up save dialog for
 						valid filename/format</li>
-					<li>cannot view associated structure for uniprot sequence</li>
-					<li>pdb file association breaks for Uniprot sequence P37173</li>
-					<li>associate PDB from file dialog does not tell you which
+					<li>Cannot view associated structure for Uniprot sequence</li>
+					<li>PDB file association breaks for Uniprot sequence P37173</li>
+					<li>Associate PDB from file dialog does not tell you which
 						sequence is to be associated with the file</li>
-					<li>find All raises null pointer exception when query only
+					<li>Find All raises null pointer exception when query only
 						matches sequence IDs</li>
-					<li>pre 2.6 jalview project cannot be loaded into v2.6</li>
+					<li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
 					<li>Jalview project with Jmol views created with Jalview 2.4
 						cannot be loaded</li>
-					<li>filetype associations not installed for webstart launch</li>
-					<li>two or more chains in a single PDB file associated with
+					<li>Filetype associations not installed for webstart launch</li>
+					<li>Two or more chains in a single PDB file associated with
 						sequences in different alignments do not get coloured by their
 						associated sequence</li>
-					<li>visibility status of autocalculated annotation row not
+					<li>Visibility status of autocalculated annotation row not
 						preserved when project is loaded</li>
-					<li>tree bootstraps are not preserved when saved as a jalview
+					<li>Annotation row height and visibility attributes not stored
+						in jalview project</li>
+					<li>Tree bootstraps are not preserved when saved as a jalview
 						project</li>
-					<li>envision2 workflow tooltips are corrupted</li>
-					<li>enabling show group conservation also enables colour by
+					<li>Envision2 workflow tooltips are corrupted</li>
+					<li>Enabling show group conservation also enables colour by
 						conservation</li>
-					<li>duplicate group associated conservation or consensus
+					<li>Duplicate group associated conservation or consensus
 						created on new view</li>
-					<li>annotation scrollbar not displayed after &#39;show all
+					<li>Annotation scrollbar not displayed after &#39;show all
 						hidden annotation rows&#39; option selected</li>
-					<li>alignment quality not updated after alignment annotation
+					<li>Alignment quality not updated after alignment annotation
 						row is hidden then shown</li>
-					<li>preserve colouring of structures coloured by sequences in pre
+					<li>Preserve colouring of structures coloured by sequences in pre
 						jalview 2.7 projects</li>
 					<li>Web service job parameter dialog is not laid out properly
 					</li>
-					<li>web services menu not refreshed after &#39;reset
+					<li>Web services menu not refreshed after &#39;reset
 						services&#39; button is pressed in preferences</li>
-					<li>annotation off by one in jalview v2_3 example project</li>
-					<li>structures imported from file and saved in project get
+					<li>Annotation off by one in jalview v2_3 example project</li>
+					<li>Structures imported from file and saved in project get
 						name like jalview_pdb1234.txt when reloaded</li>
 					<li>Jalview does not always retrieve progress of a JABAWS job
 						execution in full once it is complete</li>
 				</ul> <em>Applet</em>
 				<ul>
-					<li>alignment height set incorrectly when lots of annotation
+					<li>Alignment height set incorrectly when lots of annotation
 						rows are displayed</li>
-					<li>relative URLs in feature HTML text not resolved to
+					<li>Relative URLs in feature HTML text not resolved to
 						codebase</li>
-					<li>view follows highlighting does not work for positions in
+					<li>View follows highlighting does not work for positions in
 						sequences</li>
 					<li>&lt;= shown as = in tooltip</li>
-					<li>export features raises exception when no features exist</li>
-					<li>separator string used for serialising lists of ids for
+					<li>Export features raises exception when no features exist</li>
+					<li>Separator string used for serialising lists of IDs for
 						javascript api is modified when separator string provided as
 						parameter</li>
-					<li>null pointer exception when selecting tree leaves for
+					<li>Null pointer exception when selecting tree leaves for
 						alignment with no existing selection</li>
-					<li>relative URLs for datasources assumed to be relative to
+					<li>Relative URLs for datasources assumed to be relative to
 						applet&#39;s codebase</li>
-					<li>status bar not updated after finished searching and search
+					<li>Status bar not updated after finished searching and search
 						wraps around to first result</li>
 					<li>StructureSelectionManager instance shared between several
 						jalview applets causes race conditions and memory leaks</li>
-					<li>hover tooltip and mouseover of position on structure not
+					<li>Hover tooltip and mouseover of position on structure not
 						sent from Jmol in applet</li>
-					<li>certain sequences of javascript method calls to applet API
+					<li>Certain sequences of javascript method calls to applet API
 						fatally hang browser</li>
 				</ul> <em>General</em>
 				<ul>
-					<li>view follows structure mouseover scrolls beyond position
+					<li>View follows structure mouseover scrolls beyond position
 						with wrapped view and hidden regions</li>
 					<li>Find sequence position moves to wrong residue with/without
 						hidden columns</li>
@@ -201,24 +204,22 @@
 						off by 1</li>
 					<li>InvalidNumberFormat exceptions thrown when trying to
 						import PDB like structure files</li>
-					<li>positional search results are only highlighted between
+					<li>Positional search results are only highlighted between
 						user-supplied sequence start/end bounds</li>
-					<li>end attribute of sequence is not validated</li>
+					<li>End attribute of sequence is not validated</li>
 					<li>Find dialog only finds first sequence containing a given
 						sequence position</li>
-					<li>sequence numbering not preserved in MSF alignment output</li>
+					<li>Sequence numbering not preserved in MSF alignment output</li>
 					<li>Jalview PDB file reader does not extract sequence from
 						nucleotide chains correctly</li>
-					<li>annotation row height and visibility attributes not stored
-						in jalview project</li>
-					<li>structure colours not updated when tree partition changed
+					<li>Structure colours not updated when tree partition changed
 						in alignment</li>
-					<li>sequence associated secondary structure not correctly
+					<li>Sequence associated secondary structure not correctly
 						parsed in interleaved stockholm</li>
-					<li>colour by annotation dialog does not restore current state
+					<li>Colour by annotation dialog does not restore current state
 					</li>
 					<li>Hiding (nearly) all sequences doesn&#39;t work properly</li>
-					<li>sequences containing lowercase letters are not properly
+					<li>Sequences containing lowercase letters are not properly
 						associated with their pdb files</li>
 				</ul> <em>Documentation and Development</em>
 				<ul>
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 44e0961..88e8ee9 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -20,36 +20,84 @@
 <title>What's new ?</title>
 </head>
 <body>
-<p><strong>What's new ?</strong></p>
-<p>The Jalview 2.6.1 release fixes a number of minor bugs affecting
-Jalview operation, including issues affecting the import and export of
-PIR files and working with multiple multiple structure superpositions.
-For full details see the <a href="releases.html#Jalview2.6.1">Jalview
-2.6.1 release history</a>.</p>
-<p><strong>Highlights in Jalview Version 2.6</strong></p>
-<ul>
-	<li><a href="webServices/JABAWS.html">JABA Web Services</a> for
-	multiple alignment using:
+	<p>
+		<strong>What's new ?</strong>
+	</p>
+	<p>
+		The Jalview 2.7 release features new web services, and important
+		improvements to the way in which Jalview handles alignments and
+		associated PDB structures, as well as numerous minor improvements and
+		bug fixes. Version 2.7 of the JalviewLite applet also features a
+		significantly enhanced Javascript API enabling it to be more easily
+		integrated with javascript based web applications. <br /> For full
+		details see the <a href="releases.html#Jalview2.7">Jalview 2.7
+			release history</a>.
+	</p>
+	<p>
+		<strong>Highlights in Jalview Desktop Version 2.7</strong>
+	</p>
 	<ul>
-		<li>ClustalW</li>
-		<li>MAFFT</li>
-		<li>Muscle</li>
-		<li>ProbCons</li>
-		<li>T-COFFEE</li>
+		<li>New <a href="features/viewingpdbs.html">structure viewer
+				options</a>:
+			<ul>
+				<li>Colour and superimpose 3D structures of complexes and
+					multi-domain chains using several different alignments</li>
+				<li>Drag and drop to associate PDB files with sequences that
+					have the same name</li>
+				<li>Open and superimpose all associated structures for the
+					current selection</li>
+			</ul>
+		<li>New web services for <a href="webServices/shmr.html">alignment
+				analysis</a></li>
+		<li>Improved graphical user interface for <a
+			href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>services.
+		</li>
+		<li>Sort associated alignment views option in tree viewer</li>
+		<li>Default colours for <a
+			href="colourSchemes/annotationColouring.html">shading alignment
+				by quantitative annotation</a>.
+		</li>
+		<li><a href="webServices/newsreader.html">Jalview Desktop RSS
+				reader</a> - following important updates at <a
+			href="http://www.jalview.org/feeds/desktop/rss">http://www.jalview.org/feeds/desktop/rss</a>
 	</ul>
-	</li>
-	<li>User modifiable alignment service parameters</li>
-	<li>Visualization of superposed structures associated with protein
-	or nucleotide sequence alignments.</li>
-	<li>Export coordinates and projection as CSV from PCA viewer</li>
-</ul>
 
-<p><strong>Issues Resolved (a select list - see release
-history for details)</strong></p>
-<ul>
-
-</ul>
-<p>See the <a href="releases.html">Release History</a> page for
-details of all new features and resolved issues.</p>
+	<p>
+		<strong>Issues Resolved (a select list - see the <a
+			href="releases.html#Jalview2.7">release history</a> for full details)
+		</strong>
+	</p>
+	<p>
+		<strong>Issues in the Jalview Desktop</strong>
+	<ul>
+		<li>Problems viewing associated structures for sequences
+			retrieved from UNIPROT</li>
+		<li>Problems viewing Jalview projects from older versions in
+			version 2.6</li>
+		<li>Preservation of hidden annotation rows and tree bootstrap
+			values in projects</li>
+		<li>Newly added JABAWS servers not always visible in web services
+			menu</li>
+	</ul>
+	<strong>Issues specific to the JalviewLite Applet</strong>
+	<ul>
+		<li>Layout problems when lots of annotation rows are displayed</li>
+		<li>&lt;= shown as = in annotation row tooltip</li>
+		<li>export features raises exception when no features exist</li>
+		<li>relative URLs not handled properly when used in parameters
+			and annotation files</li>
+	</ul>
+	<strong>Issues affecting both applet and application</strong>
+	<ul>
+		<li>sequence numbering not preserved in MSF alignment output</li>
+		<li>sequence associated secondary structure not correctly parsed
+			in interleaved stockholm</li>
+		<li>sequences containing lowercase letters are not properly
+			associated with their pdb files</li>
+		<li>Jalview PDB file reader does not extract sequence from deoxy
+			nucleotide chains correctly</li>
+		<li>Sequence length given in alignment properties window is off
+			by 1</li>
+	</ul>
 </body>
 </html>
-- 
1.7.10.2