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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<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>20/5/2014</em></strong>
- </div>
- </td>
- <td> <!-- New features -->
- <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
- <ul>
- </ul> <em>Other improvements</em>
- <ul>
- </ul>
- </td>
- <td><!-- issues resolved -->
- <ul>
- </ul>
- </td>
- </tr>
- <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>
<li>ClassCastException when generating EPS in headless
mode</li>
<li>Adjusting sequence-associated shading threshold only
- changes one row's threshold</li>
+ changes one row's threshold</li>
<li>Preferences and Feature settings panel panel
doesn't open</li>
- </ul>
+ <li>hide consensus histogram also hides conservation and
+ quality histograms</li>
+ </ul>
</td>
</tr>
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git://source.jalview.org / jalview.git / blobdiff