<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Release History</title>
<div align="center"><em><strong>Issues Resolved</strong></em></div>
</td>
</tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
+ </div></td>
+ <td>
+ <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+ <em>General</em>
+ <ul>
+ <li>Internationalisation of user interface (usually called
+ i18n support) and translation for Spanish locale</li>
+ <li>Define/Undefine group on current selection with
+ Ctrl-G/Shift Ctrl-G</li>
+ <li>Improved group creation/removal options in
+ alignment/sequence Popup menu</li>
+ <li>Sensible precision for symbol distribution percentages
+ shown in logo tooltip.</li>
+ <li>Annotation panel height set according to amount of
+ annotation when alignment first opened</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>Interactive consensus RNA secondary structure prediction
+ VIENNA RNAAliFold JABA 2.1 service</li>
+ <li>Select columns containing particular features from Feature
+ Settings dialog</li>
+ <li>View all 'representative' PDB structures for selected
+ sequences</li>
+ <li>Update Jalview project format:
+ <ul>
+ <li>New file extension for Jalview projects '.jvp'</li>
+ <li>Preserve sequence and annotation dataset (to store
+ secondary structure annotation,etc)</li>
+ <li>Per group and alignment annotation and RNA helix
+ colouring</li>
+ </ul>
+ </li>
+ <li>New similarity measures for PCA and Tree calculation
+ (PAM250)</li>
+ <li>Experimental support for retrieval and viewing of flanking
+ regions for an alignment</li>
+ </ul>
+ </td>
+ <td>
+ <!-- issues resolved --> <em>Application</em>
+ <ul>
+ <li>logo keeps spinning and status remains at queued or
+ running after job is cancelled</li>
+ <li>cannot export features from alignments imported from
+ Jalview/VAMSAS projects</li>
+ <li>Buggy slider for web service parameters that take float
+ values</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>
+ <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>Occasional NPE thrown when calculating large trees</li>
+ <li>Cannot reorder or slide sequences after dragging an
+ alignment onto desktop</li>
+ <li>Colour by annotation dialog throws NPE after using
+ 'extract scores' function</li>
+ <li>Loading/cut'n'pasting an empty file leads to a grey
+ alignment window</li>
+ <li>Disorder thresholds rendered incorrectly after performing
+ IUPred disorder prediction</li>
+ <li>Multiple group annotated consensus rows shown when
+ changing 'normalise logo' display setting</li>
+ <li>Find shows blank dialog after 'finished searching' if
+ nothing matches query</li>
+ <li>Null Pointer Exceptions raised when sorting by feature
+ with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
+ </li>
+ <li>Errors in Jmol console when structures in alignment don't
+ overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
+ </li>
+ <li>Not all working JABAWS services are shown in Jalview's
+ menu</li>
+ <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>RNA Helices and T-Coffee Scores available as default colourscheme</li>
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Remove group option is shown even when selection is not a
+ group</li>
+ <li>Apply to all groups ticked but colourscheme changes don't
+ affect groups</li>
+ <li>Documented RNA Helices and T-Coffee Scores as valid colourscheme name</li>
+ <li>Annotation labels drawn on sequence IDs when Annotation panel is not displayed</li>
+ <li>Increased font size for dropdown menus on OSX and embedded windows</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Consensus sequence for alignments/groups with a single
+ sequence were not calculated</li>
+ <li>annotation files that contain only groups imported as
+ annotation and junk sequences</li>
+ <li>Fasta files with sequences containing '*' incorrectly
+ recognised as PFAM or BLC</li>
+ <li>conservation/PID slider apply all groups option doesn't
+ affect background (2.8.0b1)
+ <li></li>
+ <li>redundancy highlighting is erratic at 0% and 100%</li>
+ <li>Remove gapped columns fails for sequences with ragged
+ trailing gaps</li>
+ <li>AMSA annotation row with leading spaces is not registered
+ correctly on import</li>
+ <li>Jalview crashes when selecting PCA analysis for certain
+ alignments</li>
+ <li>Opening the colour by annotation dialog for an existing
+ annotation based 'use original colours' colourscheme loses
+ original colours setting</li>
+ </ul>
+ </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 '' 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't
+ discover PDB xRefs</li>
+ <li>Exception encountered while trying to retrieve
+ features with DAS</li>
+ <li>Lowest value in annotation row isn'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>'Right click to add annotations' 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 'combine' statements in annotation file</li>
+ <li>Pressing return several times causes Number Format
+ exceptions in keyboard mode</li>
+ <li>Multi-harmony (SHMMR) method doesn'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't understood</li>
+ <li>ClassCastException when generating EPS in headless
+ mode</li>
+ <li>Adjusting sequence-associated shading threshold only
+ changes one row's threshold</li>
+ <li>Preferences and Feature settings panel panel
+ doesn't open</li>
+ <li>hide consensus histogram also hides conservation and
+ quality histograms</li>
+ </ul>
+ </td>
+ </tr>
<tr>
<td><div align="center">
<strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
</div></td>
<td><em>Application</em>
- <li>Support for JABAWS 2.0 Services (AACon alignment
+ <ul><li>Support for JABAWS 2.0 Services (AACon alignment
conservation, protein disorder and Clustal Omega)</li>
<li>JABAWS server status indicator in Web Services preferences
</li>
git://source.jalview.org / jalview.git / blobdiff