<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
</div>
</td>
</tr>
- <tr>
- <td><div align="center">
- <strong><a name="Jalview.2.9">2.9</a><br /> <em>23/2/2015</em></strong>
- </div></td>
- <td><em>General</em>
- <ul>
- </ul> <em>Application</em>
- <ul>
- </ul>
- <em>Applet</em>
- <ul>
- </ul>
- </td>
+ <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>Link cDNA or Protein product sequences by loading
+ them onto Protein or cDNA alignments</li>
+ <li>Reconstruct linked cDNA alignment from aligned
+ protein sequences</li>
+ </ul>
+ </li>
+ <li>Jmol integration updated to Jmol v14.2.14</li>
+ <li>Import and export of Jalview alignment views as <a href="">BioJSON</a></li>
+ <li>New alignment annotation file statements for
+ reference sequences and marking hidden columns</li>
+ <li>Assign an alignment reference sequence to highlight
+ variation</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>
+ <li>Alignments can be sorted by number of RNA helices</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>
+ </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="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+
+ <li>Export scrollable SVG in HTML page</li>
+
+ <li>Interactive free text and structured queries with the
+ PDBe Search API for PDB data retrieval</li>
+ <li>PDBe Search API based discovery and selection of PDB structures to
+ view for a sequence set</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>
+ <li>(Nearly) Native 'Quaqua' dialogs for browsing file
+ system on OSX<br />LGPL libraries courtesy of <a
+ href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
+ </li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>New parameters to enable SplitFrame view (file2, scaleProteinAsCdna)</li>
+ <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 in v2.7 example file means
+ alignment appears unaligned when pad-gaps is not enabled</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 tooltips shown
+ on some platforms</li>
+ <li>Chimera viewer 'View | Show Chain' menu is not
+ populated</li>
+ <li>'New View' fails with a Null Pointer Exception in
+ console 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>Save as '.jar' option removed for saving Jalview
+ projects</li>
+ <li>Colour by Sequence colouring in Chimera more
+ responsive</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>
+ <li>Applet example pages appear different to the rest of
+ www.jalview.org</li>
+ </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>
+ <li>Cannot disable consensus calculation independently of
+ quality and conservation</li>
+ <li>Mouseover highlighting between cDNA and protein can
+ become sluggish with more than one splitframe shown</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>
+ </div>
+ </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>
+ <div align="center">
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ <ul><li>Reinstated the display of default example file on startup</li>
+ <li>All pairs shown in Jalview window when viewing result of pairwise alignment</li>
+ </ul>
+ </div>
</td>
</tr>
<tr>
<li>RNA pseudoknot annotation can be
imported/exported/displayed</li>
<li>'colour by annotation' 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
<li>Hide sequence doesn't hide associated annotation</li>
<li>User defined colours dialog box too big to fit on screen
and buttons not visible</li>
- <li>author list isn't updated if already written to jalview
+ <li>author list isn't updated if already written to Jalview
properties</li>
<li>Popup menu won't open after retrieving sequence from
database</li>
</li>
<li>
<!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
- out of memory errors are not raised when saving jalview project
+ out of memory errors are not raised when saving Jalview project
from alignment window file menu
</li>
<li>
<li>Newly created RNA secondary structure line doesn't have
'display all symbols' flag set</li>
<li>T-COFFEE alignment score shading scheme and other
- annotation shading not saved in jalview project</li>
+ annotation shading not saved in Jalview project</li>
<li>Local file cannot be loaded in freshly downloaded Jalview</li>
<li>Jalview icon not shown on dock in Mountain Lion/Webstart</li>
<li>Load file from desktop file browser fails</li>
</li>
<li>Not all working JABAWS services are shown in Jalview's
menu</li>
- <li>JAVAWS version of jalview fails to launch with 'invalid
+ <li>JAVAWS version of Jalview fails to launch with 'invalid
literal/length code'</li>
<li>Annotation/RNA Helix colourschemes cannot be applied to
alignment with groups (actually fixed in 2.8.0b1)</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>
+ <li>Groovy scripting for headless Jalview operation</li>
</ul> <em>Other improvements</em>
<ul>
<li>Upgrade desktop installer to InstallAnywhere 2013</li>
git://source.jalview.org / jalview.git / blobdiff