<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>8/8/2017</em></strong>
+ <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
+ <em>TBA</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2588 -->Show gaps in overview window by colouring
+ in grey (sequences used to be coloured grey, and gaps were
+ white)
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2603 -->Overview window throws NPE if show boxes
+ format setting is unticked
+ </li>
+ <li>
+ <!-- JAL-2610 -->Groups are coloured wrongly in overview
+ if group has show boxes format setting unticked
+ </li>
+ </ul>
+ </div></td>
+
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
</div>
</td>
<td><div align="left">
with alignment and overview windows
</li>
<li>
- <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
- via Overview or sequence motif search operations
- </li>
- <li>
<!-- JAL-2514 -->Scrolling of wrapped alignment views via
overview
</li>
the application.
</li>
<li>
+ <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
+ via Overview or sequence motif search operations
+ </li>
+ <li>
<!-- JAL-2547 -->Amend sequence features dialog box can be
opened by double clicking gaps within sequence feature
extent
<em>3D Structure</em>
<ul>
<li>
+ <!-- JAL-2430 -->Hidden regions in alignment views are not
+ coloured in linked structure views
+ </li>
+ <li>
<!-- JAL-1596 -->Faster Chimera/Jalview communication by
file-based command exchange
</li>
<!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
to transfer Chimera's structure attributes as Jalview
features, and vice-versa (<strong>Experimental
- Feauture</strong>)
+ Feature</strong>)
</li>
</ul>
<em>Web Services</em>
<!-- JAL-2549 -->Updated JABAWS client to v2.2
</li>
<li>
+ <!-- JAL-2335 -->Filter non-standard amino acids and
+ nucleotides when submitting to AACon and other MSA
+ Analysis services
+ </li>
+ <li>
<!-- JAL-2316, -->URLs for viewing database
cross-references provided by identifiers.org and the
EMBL-EBI's MIRIAM DB
<em>Documentation</em>
<ul>
<li>
- <!-- JAL-2339 -->Release notes reformatted for readibility
+ <!-- JAL-2339 -->Release notes reformatted for readability
with the built-in Java help viewer
</li>
<li>
matrix - C->R should be '-3'<br />Old matrix restored
with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
</li>
- <li>
- <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
- and substitution matrix based Tree calculations.<br />In
- earlier versions of Jalview, gaps matching gaps were
- penalised, and gaps matching non-gaps penalised even more.
- In the PCA calculation, gaps were actually treated as
- non-gaps - so different costs were applied, which meant
- Jalview's PCAs were different to those produced by
- SeqSpace.<br />Jalview now treats gaps in the same way as
- SeqSpace (ie it scores them as 0). To restore pre-2.10.2
- behaviour<br />
- jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
- 2.10.1 mode<br />
- jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
- restore 2.10.2 mode
- </li>
+ <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
+ Jalview's treatment of gaps in PCA and substitution matrix
+ based Tree calculations.<br /> <br />In earlier versions
+ of Jalview, gaps matching gaps were penalised, and gaps
+ matching non-gaps penalised even more. In the PCA
+ calculation, gaps were actually treated as non-gaps - so
+ different costs were applied, which meant Jalview's PCAs
+ were different to those produced by SeqSpace.<br />Jalview
+ now treats gaps in the same way as SeqSpace (ie it scores
+ them as 0). <br /> <br />Enter the following in the
+ Groovy console to restore pre-2.10.2 behaviour:<br />
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+ // for 2.10.1 mode <br />
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
+ // to restore 2.10.2 mode <br /> <br /> <em>Note:
+ these settings will affect all subsequent tree and PCA
+ calculations (not recommended)</em></li>
<li>
<!-- JAL-2424 -->Fixed off-by-one bug that affected
scaling of branch lengths for trees computed using
<em>Rendering</em>
<ul>
<li>
- <!-- JAL-2430 -->Hidden regions in alignment views are not
- coloured in linked structure views
- </li>
- <li>
<!-- JAL-2421 -->Overview window visible region moves
erratically when hidden rows or columns are present
</li>
<li>
<!-- JAL-2550 -->Importing annotation file with rows
containing just upper and lower case letters are
- interpreted as WUSS rna secondary structure symbols
+ interpreted as WUSS RNA secondary structure symbols
</li>
<li>
- <!-- JAL-2590 -->Cannot load Newick trees from eggnog
- ortholog database
+ <!-- JAL-2590 -->Cannot load and display Newick trees
+ reliably from eggnog Ortholog database
</li>
<li>
<!-- JAL-2468 -->Status bar shows 'Marked x columns
doesn't always add secondary structure annotation.
</li>
</ul>
- </div><tr>
+ </div>
+ <tr>
<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
git://source.jalview.org / jalview.git / blobdiff