<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* 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/>.
---!>
+-->
<head>
<title>Release History</title>
</head>
</td>
</tr>
<tr>
+ <td>
+ <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
+ <em>14/6/2010</em></div>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li>Alignment prettyprinter doesn't cope with long sequence IDs
+ </li>
+ <li>clustalx colourscheme colours Ds preferentially when both
+ D+E are present in over 50% of the column</li>
+ <li>nucleic acid structures retrieved from PDB do not import
+ correctly</li>
+ <li>More columns get selected than were clicked on when a number
+ of columns are hidden</li>
+ <li>annotation label popup menu not providing correct
+ add/hide/show options when rows are hidden or none are present</li>
+ <li>Stockholm format shown in list of readable formats.</li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>annotation panel disappears when annotation is
+ hidden/removed</li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>Alignment view not redrawn properly when new alignment
+ opened where annotation panel is visible but no annotations are
+ present on alignment</li>
+ <li>pasted region containing hidden columns is incorrectly
+ displayed in new alignment window</li>
+ <li>Jalview slow to complete operations when stdout is flooded
+ (fix is to close the Jalview console)</li>
+ <li>CSV output of consensus only includes the percentage of all
+ symbols if sequence logo display is enabled</li>
+ <li>typo in AlignmentFrame->View->Hide->all but
+ selected Rregions menu item.</li>
+ <li>inconsistent group submenu and Format submenu entry 'Un' or
+ 'Non'conserved</li>
+ <li>Sequence feature settings are being shared by multiple
+ distinct alignments</li>
+ <li>group annotation not recreated when tree partition is
+ changed</li>
+ <li>double click on group annotation to select sequences does
+ not propagate to associated trees</li>
+ <li>Mac OSX specific issues:
+ <ul>
+ <li>exception raised when mouse clicked on desktop window
+ background</li>
+ <li>Desktop menu placed on menu bar and application name set
+ correctly</li>
+ <li>sequence feature settings not wide enough for the save
+ feature colourscheme button</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
<td>
- <div align="center"><strong>2.5</strong><br>
+ <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
<em>30/4/2010</em></div>
</td>
<td>
<li>Optional automatic sort of associated alignment view when a
new tree is opened.</li>
<li>Jalview Java Console</li>
+ <li>Better placement of desktop window when moving between different screens.</li>
<li>New preference items for sequence ID tooltip and consensus
annotation</li>
<li>Client to submit sequences and IDs to <a
<li>PDB files without embedded PDB IDs given a friendly name</li>
<li>Find incrementally searches ID string matches as well as
subsequence matches, and correctly reports total number of both.</li>
- <li>Applet:
- <ul>
- <li></li>
- </ul>
- </li>
<li>Application:
<ul>
<li>Better handling of exceptions during sequence retrieval</li>
<li>Dasobert generated non-positional feature URL link text
- excludes the start_end suffix (application)</li>
+ excludes the start_end suffix</li>
+ <li>DAS feature and source retrieval buttons disabled when fetch
+ or registry operations in progress.</li>
<li>PDB files retrieved from URLs are cached properly</li>
<li>Sequence description lines properly shared via VAMSAS</li>
<li>Sequence fetcher fetches multiple records for all data
<li>Reduced time taken when opening file browser for first time.</li>
<li>isAligned check prior to calculating tree, PCA or submitting
an MSA to JNet now excludes hidden sequences.</li>
+ <li>User defined group colours properly recovered from Jalview projects.</li>
</ul>
</li>
</ul>
git://source.jalview.org / jalview.git / blobdiff