<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>15/8/2017</em></strong>
+ <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <ul><li>Updated Certum Codesigning Certificate
+ (Valid till 30th November 2018)</li></ul></div></td>
+ <td><div align="left">
+ <em>Desktop</em><ul>
+ <ul>
+ <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
+ <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
+ <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
+ <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
+ <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
+ <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
+ <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2446 -->Faster and more efficient management and
+ rendering of sequence features
+ </li>
+ <li>
+ <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
+ 429 rate limit request hander
+ </li>
+ <li>
+ <!-- JAL-2773 -->Structure views don't get updated unless
+ their colours have changed
+ </li>
+ <li>
+ <!-- JAL-2495 -->All linked sequences are highlighted for
+ a structure mousover (Jmol) or selection (Chimera)
+ </li>
+ <li>
+ <!-- JAL-2790 -->'Cancel' button in progress bar for
+ JABAWS AACon, RNAAliFold and Disorder prediction jobs
+ </li>
+ <li>
+ <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
+ view from Ensembl locus cross-references
+ </li>
+ <li>
+ <!-- JAL-2685 -->Start/End limits are shown in Pairwise
+ Alignment report
+ </li>
+ <li>
+ <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
+ feature can be disabled
+ </li>
+ <li>
+ <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
+ PDB easier retrieval of sequences for lists of IDs
+ </li>
+ <li>
+ <!-- JAL-2758 -->Short names for sequences retrieved from
+ Uniprot
+ </li>
+ </ul>
+ <em>Scripting</em>
+ <ul>
+ <li>Groovy interpreter updated to 2.4.12</li>
+ <li>Example groovy script for generating a matrix of
+ percent identity scores for current alignment.</li>
+ </ul>
+ <em>Testing and Deployment</em>
+ <ul>
+ <li>
+ <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em>General</em>
+ <ul>
+ <li>
+ <!-- JAL-2643 -->Pressing tab after updating the colour
+ threshold text field doesn't trigger an update to the
+ alignment view
+ </li>
+ <li>
+ <!-- JAL-2682 -->Race condition when parsing sequence ID
+ strings in parallel
+ </li>
+ <li>
+ <!-- JAL-2608 -->Overview windows are also closed when
+ alignment window is closed
+ </li>
+ <li>
+ <!-- JAL-2548 -->Export of features doesn't always respect
+ group visibility
+ </li>
+ <li>
+ <!-- JAL-2831 -->Jumping from column 1 to column 100,000
+ takes a long time in Cursor mode
+ </li>
+ </ul>
+ <em>Desktop</em>
+ <ul>
+ <li>
+ <!-- JAL-2777 -->Structures with whitespace chainCode
+ cannot be viewed in Chimera
+ </li>
+ <li>
+ <!-- JAL-2728 -->Protein annotation panel too high in
+ CDS/Protein view
+ </li>
+ <li>
+ <!-- JAL-2757 -->Can't edit the query after the server
+ error warning icon is shown in Uniprot and PDB Free Text
+ Search Dialogs
+ </li>
+ <li>
+ <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
+ </li>
+ <li>
+ <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
+ </li>
+ <li>
+ <!-- JAL-2739 -->Hidden column marker in last column not
+ rendered when switching back from Wrapped to normal view
+ </li>
+ <li>
+ <!-- JAL-2768 -->Annotation display corrupted when
+ scrolling right in unwapped alignment view
+ </li>
+ <li>
+ <!-- JAL-2542 -->Existing features on subsequence
+ incorrectly relocated when full sequence retrieved from
+ database
+ </li>
+ <li>
+ <!-- JAL-2733 -->Last reported memory still shown when
+ Desktop->Show Memory is unticked (OSX only)
+ </li>
+ <li>
+ <!-- JAL-2658 -->Amend Features dialog doesn't allow
+ features of same type and group to be selected for
+ amending
+ </li>
+ <li>
+ <!-- JAL-2524 -->Jalview becomes sluggish in wide
+ alignments when hidden columns are present
+ </li>
+ <li>
+ <!-- JAL-2392 -->Jalview freezes when loading and
+ displaying several structures
+ </li>
+ <li>
+ <!-- JAL-2732 -->Black outlines left after resizing or
+ moving a window
+ </li>
+ <li>
+ <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
+ within the Jalview desktop on OSX
+ </li>
+ <li>
+ <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
+ when in wrapped alignment mode
+ </li>
+ <li>
+ <!-- JAL-2636 -->Scale mark not shown when close to right
+ hand end of alignment
+ </li>
+ <li>
+ <!-- JAL-2684 -->Pairwise alignment of selected regions of
+ each selected sequence do not have correct start/end
+ positions
+ </li>
+ <li>
+ <!-- JAL-2793 -->Alignment ruler height set incorrectly
+ after canceling the Alignment Window's Font dialog
+ </li>
+ <li>
+ <!-- JAL-2036 -->Show cross-references not enabled after
+ restoring project until a new view is created
+ </li>
+ <li>
+ <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
+ URL links appears when only default EMBL-EBI link is
+ configured (since 2.10.2b2)
+ </li>
+ <li>
+ <!-- JAL-2775 -->Overview redraws whole window when box
+ position is adjusted
+ </li>
+ <li>
+ <!-- JAL-2225 -->Structure viewer doesn't map all chains
+ in a multi-chain structure when viewing alignment
+ involving more than one chain (since 2.10)
+ </li>
+ <li>
+ <!-- JAL-2811 -->Double residue highlights in cursor mode
+ if new selection moves alignment window
+ </li>
+ <li>
+ <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
+ arrow key in cursor mode to pass hidden column marker
+ </li>
+ <li>
+ <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
+ that produces correctly annotated transcripts and products
+ </li>
+ <li>
+ <!-- JAL-2776 -->Toggling a feature group after first time
+ doesn't update associated structure view
+ </li>
+ </ul>
+ <em>Applet</em><br />
+ <ul>
+ <li>
+ <!-- JAL-2687 -->Concurrent modification exception when
+ closing alignment panel
+ </li>
+ </ul>
+ <em>BioJSON</em><br />
+ <ul>
+ <li>
+ <!-- JAL-2546 -->BioJSON export does not preserve
+ non-positional features
+ </li>
+ </ul>
+ <em>New Known Issues</em>
+ <ul>
+ <li>
+ <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
+ sequence features correctly (for many previous versions of
+ Jalview)
+ </li>
+ <li>
+ <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
+ using cursor in wrapped panel other than top
+ </li>
+ <li>
+ <!-- JAL-2791 -->Select columns containing feature ignores
+ graduated colour threshold
+ </li>
+ <li>
+ <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
+ always preserve numbering and sequence features
+ </li>
+ </ul>
+ <em>Known Java 9 Issues</em>
+ <ul>
+ <li>
+ <!-- JAL-2902 -->Groovy Console very slow to open and is
+ not responsive when entering characters (Webstart, Java
+ 9.01, OSX 10.10)
+ </li>
+ </ul>
+ </div></td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
+ <em>2/10/2017</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em>New features in Jalview Desktop</em>
+ <ul>
+ <li>
+ <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
+ </li>
+ <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ </div></td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
+ <em>7/9/2017</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>
+ <li>
+ <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
+ Preferences
+ </li>
+ <li>
+ <!-- JAL-2587 -->Overview updates immediately on increase
+ in size and progress bar shown as higher resolution
+ overview is recalculated
+ </li>
+
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2664 -->Overview window redraws every hidden
+ column region row by row
+ </li>
+ <li>
+ <!-- JAL-2681 -->duplicate protein sequences shown after
+ retrieving Ensembl crossrefs for sequences from Uniprot
+ </li>
+ <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>
+ <li>
+ <!-- JAL-2672,JAL-2665 -->Redraw problems when
+ autoscrolling whilst dragging current selection group to
+ include sequences and columns not currently displayed
+ </li>
+ <li>
+ <!-- JAL-2691 -->Not all chains are mapped when multimeric
+ assemblies are imported via CIF file
+ </li>
+ <li>
+ <!-- JAL-2704 -->Gap colour in custom colourscheme is not
+ displayed when threshold or conservation colouring is also
+ enabled.
+ </li>
+ <li>
+ <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
+ server version
+ </li>
+ <li>
+ <!-- JAL-2673 -->Jalview continues to scroll after
+ dragging a selected region off the visible region of the
+ alignment
+ </li>
+ <li>
+ <!-- JAL-2724 -->Cannot apply annotation based
+ colourscheme to all groups in a view
+ </li>
+ <li>
+ <!-- JAL-2511 -->IDs don't line up with sequences
+ initially after font size change using the Font chooser or
+ middle-mouse zoom
+ </li>
+ </ul>
+ </div></td>
+ </tr>
+ <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>
after clicking on it to create new annotation for a
column.
</li>
+ <li>
+ <!-- JAL-1980 -->Null Pointer Exception raised when
+ pressing Add on an orphaned cut'n'paste window.
+ </li>
<!-- may exclude, this is an external service stability issue JAL-1941
-- > RNA 3D structure not added via DSSR service</li> -->
</ul>
git://source.jalview.org / jalview.git / blobdiff