From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 30 Jan 2014 15:48:13 +0000 (+0000)
Subject: JAL-1432 'whats new' and release history
X-Git-Tag: Release_2_8_0b1~1^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8a3915baf2a22618346a5a2ecd38f7fbca5d4a44;p=jalview.git

JAL-1432 'whats new' and release history
---

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 5a92936..3c5b9c2 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -20,22 +20,9 @@
 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
-	<tocitem text="What's new" target="new" expand="true">
-    <tocitem text="Protein Disorder Prediction" target="disorder"/>
-    <tocitem text="Alignment Conservation Analysis" target="aacon"/>
-		<tocitem text="Viewing RNA structure" target="varna" />
-		<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
-		<tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
-		<tocitem text="HTML annotation report" target="io.seqreport"/>
-		<tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
-		<tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
-	  <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
-	  <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
-	  <tocitem text="DNA or Protein PCA calculation" target="pca"/>
-	  <tocitem text="Normalised sequence logo display" target="calcs.consensus"/>
-	</tocitem>
-    <tocitem text="Editing Alignments" target ="edit"/>	
-    <tocitem text="Cursor Mode" target="cursor"/>
+	<tocitem text="What's new" target="new" expand="false"/>
+  <tocitem text="Editing Alignments" target ="edit"/>	
+  <tocitem text="Cursor Mode" target="cursor"/>
 	<tocitem text="Key Strokes" target="keys"/>
 	<tocitem text="Input / Output" target="io"/>
   	<tocitem text="Making Figures" target="export"/>
diff --git a/help/html/releases.html b/help/html/releases.html
index e091da0..d436b34 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -34,6 +34,104 @@
 		<div align="center"><em><strong>Issues Resolved</strong></em></div>
 		</td>
 	</tr>
+	<tr>
+	<td><div align="center">
+	<strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
+	</div>
+	</td>
+      <td>
+        <ul>
+          <li>Trusted certificates for JalviewLite applet and
+            Jalview Desktop application<br />Certificate was donated by
+            <a href="https://www.certum.eu">Certum</a> to the Jalview
+            open source project).
+          </li>
+          <li>Jalview SRS links replaced by Uniprot and EBI-search
+          </li>
+          <li>Output in Stockholm format</li>
+          <li>Allow import of data from gzipped files</li>
+          <li>Export/import group and sequence associated line
+            graph thresholds</li>
+          <li>Nucleotide substitution matrix that supports RNA and
+            ambiguity codes</li>
+          <li>Allow disorder predictions to be made on the current
+            selection (or visible selection) in the same way that JPred
+            works</li>
+          <li>Groovy scripting for headless jalview operation</li>
+        </ul> <em>Other improvements</em>
+        <ul>
+          <li>Upgrade desktop installer to InstallAnywhere 2013</li>
+          <li>COMBINE statement uses current SEQUENCE_REF and
+            GROUP_REF scope to group annotation rows</li>
+          <li>Support &#39;&#39; style escaping of quotes in Newick
+            files</li>
+          <li>Group options for JABAWS service by command line name</li>
+          <li>Empty tooltip shown for JABA service options with a
+            link but no description</li>
+          <li>Select primary source when selecting authority in
+            database fetcher GUI</li>
+          <li>Add .mfa to FASTA file extensions recognised by
+            Jalview</li>
+          <li>Annotation label tooltip text wrap</li>
+        </ul>
+      </td>
+      <td>
+        <ul>
+          <li>Slow scrolling when lots of annotation rows are
+            displayed</li>
+          <li>Lots of NPE (and slowness) after creating RNA
+            secondary structure annotation line</li>
+          <li>Sequence database accessions not imported when
+            fetching alignments from Rfam</li>
+          <li>Incorrect SHMR submission for sequences with
+            identical IDs</li>
+          <li>View all structures does not always superpose
+            structures</li>
+          <li>Option widgets in service parameters not updated to
+            reflect user or preset settings</li>
+          <li>Null pointer exceptions for some services without
+            presets or adjustable parameters</li>
+          <li>Discover PDB IDs entry in structure menu doesn&#39;t
+            discover PDB xRefs</li>
+          <li>Exception encountered while trying to retrieve
+            features with DAS</li>
+          <li>Lowest value in annotation row isn&#39;t coloured
+            when colour by annotation (per sequence) is coloured</li>
+          <li>Keyboard mode P jumps to start of gapped region when
+            residue follows a gap</li>
+          <li>Jalview appears to hang importing an alignment with
+            Wrap as default or after enabling Wrap</li>
+          <li>&#39;Right click to add annotations&#39; message
+            shown in wrap mode when no annotations present</li>
+          <li>Disorder predictions fail with NPE if no automatic
+            annotation already exists on alignment</li>
+          <li>oninit javascript function should be called after
+            initialisation completes</li>
+          <li>Remove redundancy after disorder prediction corrupts
+            alignment window display</li>
+          <li>Example annotation file in documentation is invalid</li>
+          <li>Grouped line graph annotation rows are not exported
+            to annotation file</li>
+          <li>Multi-harmony analysis cannot be run when only two
+            groups created</li>
+          <li>Cannot create multiple groups of line graphs with
+            several &#39;combine&#39; statements in annotation file</li>
+          <li>Pressing return several times causes Number Format
+            exceptions in keyboard mode</li>
+          <li>Multi-harmony (SHMMR) method doesn&#39;t submit
+            correct partitions for input data</li>
+          <li>Translation from DNA to Amino Acids fails</li>
+          <li>Jalview fail to load newick tree with quoted label</li>
+          <li>--headless flag isn&#39;t understood</li>
+          <li>ClassCastException when generating EPS in headless
+            mode</li>
+          <li>Adjusting sequence-associated shading threshold only
+            changes one row&#39;s threshold</li>
+          <li>Preferences and Feature settings panel panel
+            doesn&#39;t open</li>
+        </ul>
+      </td>
+    </tr>
   <tr>
    <td><div align="center">
      <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index b81031d..79cf7c9 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -21,111 +21,52 @@
 <title>What's new ?</title>
 </head>
 <body>
- <p>
-  <strong>What's new ?</strong><br/>
-  Jalview 2.8 includes a number of enhancements and new features that
-  have been in development since July 2010. It is also the first Jalview
-  release to incorporate RNA visualization features developed by Lauren
-  Lui and Jan Engelhart during their Google Summer of Code projects
-  (http://code.google.com/soc/). As usual you can find the highlights
-  below, but to see the comprehensive list take a look at the look at
-  the <a href="releases.html#Jalview2.8">Jalview 2.8 Release Notes</a>.
- </p>
- <strong>Highlights in Jalview Version 2.8</strong>
- <ul>
-  <li><strong>Improved <a href="webServices/JABAWS.html">JABAWS</a>
-    client and new JABAWS 2.0 Services
-  </strong>
-   <ul>
-    <li><a href="webServices/AACon.html">AACon alignment
-      conservation</a></li>
-    <li><a href="webServices/proteinDisorder.html">Protein
-      disorder</a> - DisEMBL, RONN, GlobPlot and IUPred</li>
-    <li>Clustal Omega for creating huge protein alignments</li>
-   </ul></li>
-  <li><strong><a href="na/index.html">RNA</a></strong>
-   <ul>
-    <li>Import sequence and alignment associated WUSS or VIENNA
-     dot-bracket notation from files and the <strong>RFAM</strong>
-     database
-    </li>
-    <li>Interactive editing of RNA secondary structure annotation</li>
-    <li>Colour scheme for purine/pyrimidine and to highlight RNA
-     helices</li>
-    <li>RNA canonical <a
-     href="calculations/structureconsensus.html">base pair consensus
-      score</a> and sequence logo
-    </li>
-    <li>Embedded <a href="features/varna.html">VARNA</a> RNA
-     secondary structure viewer in the Desktop
-    </li>
-   </ul></li>
-  <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE
-    alignment quality scores</a> (thanks to Paolo di Tomasso of the Notredame
-   Group)
-  </li>
-  <li><a href="colourSchemes/annotationColouring.html">Per
-    sequence alignment annotation shading</a></li>
-  <li>Enhanced <a href="calculations/pca.html">PCA viewer</a>: more
-   export options, and switch between different PCA modes and residue
-   score models
-  </li>
-  <li>New Jalview Desktop <a href="webServices/dbreffetcher.html">database
-    fetcher</a> GUI
-  </li>
-  <li>Support for DAS 1.6 and DAS 2.0 sources (thanks to the new
-   JDAS Distributed Annotation client library (see
-   http://code.google.com/p/jdas))</li>
-  <li>Export sequence database annotation as an <a
-   href="io/exportseqreport.html">HTML report</a></li>
-  <li>Normalised <a href="calculations/consensus.html">Sequence
-    Logo Display</a></li>
- </ul>
- <p>
-  <strong>Issues resolved in the Jalview Desktop</strong>
- </p>
- <ul>
-  <li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
-   REST service</li>
-  <li>Stop windows being moved outside desktop on OSX</li>
-  <li>Jnet job queues forever if a very short sequence is submitted
-   for prediction</li>
-  <li>Structure view highlighting doesn't work on windows 7</li>
-  <li>Jalview desktop fails to launch with exception when using
-   proxy</li>
-  <li>DAS Sequence retrieval with range qualification results in
-   sequence xref which includes range qualification</li>
-  <li>Cannot close news reader when JABAWS server warning dialog is
-   shown</li>
-  <li>Edited sequence not submitted to web service</li>
-  <li>Jalview 2.7 InstallAnywhere installer doesn't unpack and run
-   on OSX Mountain Lion
-   <ul>
-    <li>If you use webstart then you may need to go into the
-     Security panel (<em>a.k.a</em> the gatekeeper) in your System
-     Settings, and select the 'allow any code to run' option.
-    </li>
-   </ul>
-  </li>
- </ul>
- <p>
-  <strong>Issues specific to the JalviewLite Applet</strong>
- </p>
- <ul>
-  <li>Sequence features are momentarily displayed before they are
-   hidden using hidefeaturegroups applet parameter</li>
-  <li>loading features via javascript API automatically enables
-   feature display</li>
-  <li>scrollToColumnIn javascript API method doesn't work</li>
- </ul>
- <p>
-  <strong>Issues affecting both applet and application</strong>
- </p>
- <ul>
-  <li>Redundancy removal fails for rna alignment</li>
-  <li>PCA window shows grey box when first opened on OSX</li>
-  <li>Letters coloured pink in sequence logo when alignment
-   coloured with clustalx</li>
- </ul>
+	<p>
+		<strong>What's new ?</strong><br /> Jalview 2.8.0b1 is a bugfix
+		release for Jalview version 2.8. <br /> As usual you can find the
+		highlights below, and the comprehensive list is given in the <a
+			href="releases.html#Jalview2.8.0b1">Jalview 2.8.0b1 Release Notes</a>.
+	</p>
+  <p>
+    This bug fix release includes numerous minor enhancements made over
+    the last 12 months. Importantly, it is also the first release that
+    provides Jalview as a trusted application, signed with a certificate
+    donated to us by <a href="certum.eu">Certum</a>.
+  </p>
+  <strong>Enhancements and new features</strong>
+	<ul>
+		<li>Allow disorder predictions to be made on the current
+			selection (or visible selection) in the same way that JPred works</li>
+		<li>allow import of data from gzipped files</li>
+    <li>Improved per-sequence 'colour-by-annotation' performance</li>
+		<li>Support &#39;&#39; style escaping of quotes in Newick files</li>
+		<li>group options for JABAWS service by command line name</li>
+		<li>Select primary source when selecting authority in database
+			fetcher GUI</li>
+    <li>COMBINE statement uses current SEQUENCE_REF and GROUP_REF
+      scope to group annotation rows</li>
+		<li>add .mfa to FASTA file extensions recognised by Jalview</li>
+		<li>groovy scripting for headless jalview operation</li>
+		<li>Output in Stockholm format</li>
+	</ul>
+	<strong>Bug fixes</strong>
+	<ul>
+		<li>Uniprot and PDB database cross-reference fetching works
+			properly</li>
+		<li>'View all structures' in the desktop is more reliable</li>
+		<li>Web services parameter dialog box shows the options enabled
+			for different presets</li>
+		<li>Interactive creation of RNA secondary structure works more
+			smoothly</li>
+		<li>Keyboard mode 'P' command jumps to the right place</li>
+		<li>Improved support for parsing database cross-references via
+			Stockholm and Rfam database</li>
+		<li>Improved semantics in annotation files for grouping
+			annotation rows associated with particular sequences and groups</li>
+		<li>More robust DNA->Amino acid translation</li>
+		<li>Improved Headless-mode operation for DAS annotation
+			retrieval, groovy script execution and alignment figure generation</li>
+    <li>annotation label tooltip text needs to be wrapped</li>
+	</ul>
 </body>
 </html>