<div align="center"><em><strong>Issues Resolved</strong></em></div>
</td>
</tr>
- <tr>
+ <tr>
<td><div align="center">
- <strong><a name="Jalview.2.8.1">2.8.1</a><br />
- <em>20/5/2014</em></strong>
+ <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>3/6/2014</em></strong>
</div></td>
<td>
<!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
<ul>
- <li>Internationalisation of user interface (usually called i18n support) and
- translation for Spanish locale</li>
+ <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>Improved group creation/removal options in
+ alignment/sequence Popup menu</li>
+
</ul> <em>Application</em>
- <ul>
+ <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>
- 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>
+ <li>Update Jalview project format:
+ <ul>
+ <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> <em>Applet</em>
- <ul>
+ <ul>
</ul> <em>Other improvements</em>
- <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>
+ <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>
</td>
<td>
<!-- issues resolved --> <em>Application</em>
- <ul>
+ <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
+ <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>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>??? unresolved ??? Jalview icon not shown on dock in
- Mountain Lion/Webstart</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
+ <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>
+ IUPred disorder prediction</li>
<li>Multiple group annotated consensus rows shown when
changing 'normalise logo' display setting</li>
- <li>Annotation/RNA Helix colourschemes cannot be applied to alignment
- with groups (2.8.0b1)</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>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>
- <li>Remove group option shown in applet when selection is not a group</li>
+ <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>
+ <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
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
+ <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>
+ <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>
+ <tr>
<td><div align="center">
<strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
</div>
git://source.jalview.org / jalview.git / blobdiff