From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 8 Sep 2015 12:33:34 +0000 (+0100)
Subject: Merge branch 'develop' into release/2_9_documentation
X-Git-Tag: Release_2_10_0~457^2~14
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=514a7c485f6e779c68478aa1f020bf96778bf87d;hp=a0ff6ae6bd847a2740052c5be6a610ac9a36f836;p=jalview.git

Merge branch 'develop' into release/2_9_documentation
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 19fa285..07d05ea 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -42,43 +42,233 @@
 				</div>
 			</td>
 		</tr>
-		<tr>
-			<td><div align="center">
-					<strong><a name="Jalview.2.9">2.9</a><br /> <em>1/9/2015</em></strong>
-				</div></td>
-			<td><em>General</em>
-				<ul>
-				</ul> <em>Application</em>
-				<ul>
-				</ul>
-        <em>Applet</em>
-				<ul>
-				</ul>
-		  </td>
-			<td>
-				<em>General</em>
-				<ul>
-					<li>Make selection for columns now works on marked columns
-						rather than columns in rubber-band selection region.</li>
-				</ul>
-				<!--  issues resolved -->
-				<em>Application</em>
-				<ul>
-				</ul>
-				<!--  <em>Applet</em>
-				<ul>
-				</ul> <em>General</em>
-				<ul> 
-				</ul>--> <em>Deployment and Documentation</em>
-				<ul>
-				</ul> <em>Application Known issues</em>
-				<ul>
-				</ul> <em>Applet Known Issues</em>
-				<ul>
-				</ul>
-			</td>
-		</tr>
-		<tr>
+    <tr>
+      <td><div align="center">
+          <strong><a name="Jalview.2.9">2.9</a><br /> <em>9/9/2015</em></strong>
+        </div></td>
+      <td><em>General</em>
+        <ul>
+          <li>Linked visualisation and analysis of DNA and Protein
+            alignments:<ul>
+          <li>Translated cDNA alignments shown as split protein and
+            DNA alignment views</li>
+          <li>Codon consensus annotation for linked protein and
+            cDNA alignment views</li>
+          <li>Add cDNA or Protein product sequences to Protein or
+            cDNA alignments</li>
+          <li>Reconstruct linked cDNA alignment from aligned
+            protein sequences</i>
+            </ul></li>
+
+          <li>Update Jmol to v14.2n</li>
+
+          <li>BioJSON data exchange</li>
+
+          <li>New alignment annotation file statements for
+            reference sequences and marking hidden columns</li>
+
+          <li>Alignments can be sorted by number of RNA helices</li>
+            
+          <li>Assign a reference sequence to highlight
+            variation and consensus analysis</li>
+
+          <li>Select or hide columns according to alignment
+            annotation</li>
+          <li>Find option for locating sequences by
+            description</li>
+
+          <li>Conserved physicochemical properties shown in amino
+            acid conservation row</li>
+
+        </ul> <em>Application</em>
+        <ul>
+          <li>Optional embedding of BioJSON data when exporting
+            alignment figures to HTML</li>
+          <li>New Export Settings dialog to control hidden region export in flat file
+            generation</li>
+          <li>New cDNA/Protein analysis capabilities<ul>
+          <li>Get Cross-References should open a Split Frame view
+            with cDNA/Protein</li>
+          <li>Detect when nucleotide sequences and protein
+            sequences are placed in the same alignment</li>
+          <li>Split cDNA/Protein views are saved in Jalview
+            projects</li>
+          <li>support '*' in amino acid sequences to indicate stop
+            codon</li>
+            </ul></li>
+
+          <li>Use REST API to talk to Chimera</li>
+          <li>Selected regions in Chimera are highlighted in linked Jalview windows</li>
+
+          <li>Calculate UPGMA and NJ trees using sequence feature
+            similarity</li>
+
+          <li>VARNA RNA viewer updated to v3.93</li>
+          <li>VARNA views are saved in Jalview
+            Projects</li>
+          <li>Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA</li>
+
+          <li>changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'</li>
+          <li>change "View protein structure" menu option to "3D
+            Structure ..."</li>
+
+          <li>Make groups for selection uses marked columns as well
+            as the active selected region</li>
+
+          <li>allow different similarity matrix calculations for
+            tree building and PCA</li>
+
+          <li>Export alignment views for display with the <a
+            href="">BioJS MSAViewer</a></li>
+          <li>Scrollable SVG for HTML export</li>
+
+          <li>Novel data discovery and retrieval mechanism using
+            PDBe Search API</li>
+          <li>Smarter technique for selecting PDB structures to
+            view in Jalview</li>
+
+          <li>JPred4 employed for protein secondary structure
+            predictions</li>
+          <li>Hide Insertions menu option to hide unaligned columns
+            for one or a group of sequences</li>
+          <li>Automatically hide insertions in alignments imported from the JPred4 web server</li>
+        </ul> <em>Applet</em>
+        <ul>
+          <li>Parameter to enable SplitFrame view</li>? check other
+          parameters in applet ?
+          <li>New example demonstrating linked viewing of cDNA and
+            Protein alignments</li>
+          <li>New layout for applet example pages</li>
+        </ul>
+        <em>Development and deployment</em>
+        <li>Java 1.7 minimum requirement for Jalview 2.9</li>
+        <li>Include installation type and git revision in build
+          properties and console log output</li>
+        <li>Github project and web URL for storing BioJsMSA
+          Templates</li>
+        <li>Jalview's unit tests now managed with TestNG</li></td>
+      <td><em>General</em>
+        <ul>
+        </ul> <!--  issues resolved --> <em>Application</em>
+        <ul>
+          <li>Escape should close any open find dialogs</li>
+          <li>typo in select-by-features status report</li>
+          <li>Consensus RNA secondary secondary structure
+            predictions are not highlighted in amber</li>
+          <li>missing gap character means v2.7 example file appears
+            unaligned REVIEW</li>
+          <li>First switch to RNA Helices colouring doesn't colour
+            associated structure views</li>
+          <li>ID width preference option is greyed out when auto
+            width checkbox not enabled</li>
+          <li>Stopped a warning dialog from being shown when
+            creating user defined colours</li>
+          <li>'View Mapping' in structure viewer shows sequence
+            mappings for just that viewer's sequences</li>
+          <li>Workaround for superposing PDB files containing
+            multiple models in Chimera</li>
+          <li>Report sequence position in status bar when hovering
+            over Jmol structure</li>
+          <li>Cannot output gaps as '.' symbols with Selection ->
+            output to text box</li>
+          <li>Flat file exports of alignments with hidden columns
+            have incorrect sequence start/end</li>
+          <li>'Aligning' a second chain to a Chimera structure from
+            Jalview fails</li>
+          <li>Colour schemes applied to structure viewers don't
+            work for nucleotide</li>
+          <li>Loading/cut'n'pasting an empty or invalid file leads
+            to a grey/invisible alignment window</li>
+          <li>Exported Jpred annotation from a sequence region
+            imports to different position</li>
+          <li>Space at beginning of sequence feature mouseover
+            tooltip on some platforms</li>
+          <li>Chimera viewer 'View | Show Chain' menu is not
+            populated</li>
+          <li>'New View' fails with a Null Pointer Exception if
+            Chimera has been opened</li>
+          <li>Mouseover to Chimera not working</li>
+          <li>Miscellaneous ENA XML feature qualifiers not
+            retrieved</li>
+          <li>NPE in annotation renderer after 'Extract Scores'</li>
+          <li>If two structures in one Chimera window, mouseover of
+            either sequence shows on first structure</li>
+          <li>'Show annotations' options should not make
+            non-positional annotations visible</li>
+          <li>subsequence secondary structure annotation not shown
+            in right place after 'view flanking regions'</li>
+          <li>File Save As type unset when current file format is
+            unknown</li>
+          <li>Native 'Quaqua' dialogs for saving and loading files
+            on OSX</li>
+          <li>Save as '.jar' option removed for saving Jalview
+            projects</li>
+          <li>Colour by Sequence colouring in Chimera more
+            responsive</li>
+          <li>Can disable consensus calculation independently of
+            quality and conservation</li>
+          <li>Cannot 'add reference annotation' for a sequence in
+            several views on same alignment</li>
+          <li>Cannot show linked products for EMBL / ENA records</li>
+          <li>Jalview's tooltip wraps long texts containing no
+            spaces</li>
+        </ul> <em>Applet</em>
+        <li>Jmol to JalviewLite mouseover/link not working</li>
+        <li>JalviewLite can't import sequences with ID descriptions
+          containing angle brackets</li>
+        <ul>
+        </ul> <em>General</em>
+        <ul>
+          <li>Cannot export and reimport RNA secondary structure
+            via jalview annotation file</li>
+          <li>Random helix colour palette for colour by annotation
+            with RNA secondary structure</li>
+          <li>Mouseover to cDNA from STOP residue in protein
+            translation doesn't work.</li>
+          <li>hints when using the select by annotation dialog box</li>
+          <li>Jmol alignment incorrect if PDB file has alternate CA
+            positions</li>
+          <li>FontChooser message dialog appears to hang after
+            choosing 1pt font</li>
+          <li>Peptide secondary structure incorrectly imported from
+            annotation file when annotation display text includes 'e' or
+            'h'</li>
+          <li>Cannot set colour of new feature type whilst creating
+            new feature</li>
+          <li>cDNA translation alignment should not be sequence
+            order dependent</li>
+          <li>'Show unconserved' doesn't work for lower case
+            sequences</li>
+          <li>Nucleotide ambiguity codes involving R not recognised</li>
+        </ul> <em>Deployment and Documentation</em>
+        <ul>
+
+        </ul> <em>Application Known issues</em>
+        <ul>
+          <li>Incomplete sequence extracted from PDB entry 3a6s</li>
+          <li>Misleading message appears after trying to delete
+            solid column.</li>
+          <li>Jalview icon not shown in dock after InstallAnywhere
+            version launches</li>
+          <li>Fetching EMBL reference for an RNA sequence results
+            fails with a sequence mismatch</li>
+          <li>Corrupted or unreadable alignment display when
+            scrolling alignment to right</li>
+          <li>ArrayIndexOutOfBoundsException thrown when remove
+            empty columns called on alignment with ragged gapped ends</li>
+          <li>auto calculated alignment annotation rows do not get
+            placed above or below non-autocalculated rows</li>
+          <li>Jalview dekstop becomes sluggish at full screen in
+            ultra-high resolution</li>
+        </ul> <em>Applet Known Issues</em>
+        <ul>
+          <li>Core PDB parsing code requires Jmol</li>
+          <li>Sequence canvas panel goes white when alignment
+            window is being resized
+          <li>
+        </ul></td>
+    </tr>
+    <tr>
 			<td width="60" nowrap>
 				<div align="center">
 					<strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br /> <em>15/12/2014</em></strong>
@@ -108,7 +298,9 @@
 					<li>RNA pseudoknot annotation can be
 						imported/exported/displayed</li>
 					<li>&#39;colour by annotation&#39; can colour by RNA and
-						protein secondary structure</li>
+					  protein secondary structure</li>
+				<li>Warn user if 'Find' regular expression is invalid (<em>mentioned post-hoc with 2.9 release</em>)</li>
+
 				</ul> <em>Application</em>
 				<ul>
 					<li>Extract and display secondary structure for sequences with