<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>General</em>
+ <em></em>
+ <ul>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
<ul>
+ </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">
+ <em>Calculations</em>
+ <ul>
+
+ <li>
+ <!-- JAL-1933 -->Occupancy annotation row shows number of
+ ungapped positions in each column of the alignment.
+ </li>
+ <li>
+ <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
+ a calculation dialog box
+ </li>
<li>
<!-- JAL-2379 -->Revised implementation of PCA for speed
and memory efficiency (~30x faster)
<!-- JAL-2403 -->Revised implementation of sequence
similarity scores as used by Tree, PCA, Shading Consensus
and other calculations
- <ul>
- <li>
- <!-- JAL-2416 -->Score matrices are stored as resource
- files within the Jalview codebase
- <li>
- <!-- JAL-2500 -->Trees computed on Sequence Feature
- Similarity may have different topology due to
- increased precision
- </li>
- </ul>
</li>
<li>
- <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
- a calculation dialog box
+ <!-- JAL-2416 -->Score matrices are stored as resource
+ files within the Jalview codebase
</li>
<li>
+ <!-- JAL-2500 -->Trees computed on Sequence Feature
+ Similarity may have different topology due to increased
+ precision
+ </li>
+ </ul>
+ <em>Rendering</em>
+ <ul>
+ <li>
<!-- JAL-2360,JAL-2371, -->More robust colours and shader
model for alignments and groups
</li>
<!-- JAL-384 -->Custom shading schemes created via groovy
scripts
</li>
- <li>
- <!-- JAL-2491 -->linked scrolling of CDS/Protein views
- via Overview or sequence motif search operations
- </li>
+ </ul>
+ <em>Overview</em>
+ <ul>
<li>
<!-- JAL-2526 -->Efficiency improvements for interacting
with alignment and overview windows
</li>
<li>
+ <!-- JAL-2514 -->Scrolling of wrapped alignment views via
+ overview
+ </li>
+ <li>
<!-- JAL-2388 -->Hidden columns and sequences can be
omitted in Overview
</li>
<li>
+ <!-- JAL-2611 -->Click-drag in visible area allows fine
+ adjustment of visible position
+ </li>
+ </ul>
+
+ <em>Data import/export</em>
+ <ul>
+ <li>
<!-- JAL-2535 -->Posterior probability annotation from
Stockholm files imported as sequence associated annotation
</li>
<li>
+ <!-- JAL-2507 -->More robust per-sequence positional
+ annotation input/output via stockholm flatfile
+ </li>
+ <li>
<!-- JAL-2533 -->Sequence names don't include file
extension when importing structure files without embedded
names or PDB accessions
</li>
<li>
- <!-- JAL-2547 -->Amend sequence features dialog box can be
- opened by double clicking gaps within sequence feature
- extent
+ <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
+ format sequence substitution matrices
</li>
+ </ul>
+ <em>User Interface</em>
+ <ul>
<li>
- <!-- JAL-2631 -->Graduated feature colour style example
- included in the example feature file
+ <!-- JAL-2447 --> Experimental Features Checkbox in
+ Desktop's Tools menu to hide or show untested features in
+ the application.
</li>
<li>
- <!-- JAL-1933 -->Occupancy annotation row shows number of
- ungapped positions in each column of the alignment.
+ <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
+ via Overview or sequence motif search operations
</li>
<li>
- <!-- JAL-2533 -->File extension pruned from Sequence ID
- for sequences derived from structure files without
- embedded database accession
+ <!-- JAL-2547 -->Amend sequence features dialog box can be
+ opened by double clicking gaps within sequence feature
+ extent
</li>
<li>
<!-- JAL-1476 -->Status bar message shown when not enough
aligned positions were available to create a 3D structure
superposition.
</li>
- <li>
- <!-- JAL-2507 -->More robust per-sequence positional
- annotation input/output via stockholm flatfile
- </li>
-
</ul>
- <em>Application</em>
+ <em>3D Structure</em>
<ul>
<li>
- <!-- JAL-2447 --> Experimental Features Checkbox in
- Desktop's Tools menu to hide or show untested features in
- the application.
- </li>
- <li>
- <!-- JAL-1476 -->Warning in alignment status bar when
- there are not enough columns to superimpose structures in
- Chimera
+ <!-- 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>
<li>
- <!-- JAL-2316, -->URLs for viewing database
- cross-references provided by identifiers.org and the
- EMBL-EBI's MIRIAM DB
- </li>
- <li>
- <!-- JAL-2549 -->Updated JABAWS client to v2.2
- </li>
- <li>
- <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
- format sequence substitution matrices
- </li>
- <li>
<!-- JAL-2375 -->Structure chooser automatically shows
Cached Structures rather than querying the PDBe if
structures are already available for sequences
the Jalview project rather than downloaded again when the
project is reopened.
</li>
-
- </ul>
- <em>Experimental features</em>
- <ul>
<li>
<!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
to transfer Chimera's structure attributes as Jalview
- features, and vice-versa.
+ features, and vice-versa (<strong>Experimental
+ Feature</strong>)
</li>
</ul>
- <em>Applet</em>
+ <em>Web Services</em>
<ul>
<li>
- <!-- -->
+ <!-- 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
</li>
</ul>
- <em>Test Suite</em>
+
+ <em>Scripting</em>
<ul>
<li>
- <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
+ <!-- JAL-2344 -->FileFormatI interface for describing and
+ identifying file formats (instead of String constants)
</li>
<li>
- <!-- JAL-2326 -->Prevent or clear modal dialogs raised
- during tests
+ <!-- JAL-2228 -->FeatureCounter script refactored for
+ efficiency when counting all displayed features (not
+ backwards compatible with 2.10.1)
+ </li>
+ </ul>
+ <em>Example files</em>
+ <ul>
+ <li>
+ <!-- JAL-2631 -->Graduated feature colour style example
+ included in the example feature file
+ </li>
+ </ul>
+ <em>Documentation</em>
+ <ul>
+ <li>
+ <!-- JAL-2339 -->Release notes reformatted for readability
+ with the built-in Java help viewer
+ </li>
+ <li>
+ <!-- JAL-1644 -->Find documentation updated with 'search
+ sequence description' option
</li>
+ </ul>
+ <em>Test Suite</em>
+ <ul>
<li>
<!-- JAL-2485, -->External service integration tests for
Uniprot REST Free Text Search Client
</li>
<li>
- <!-- --> <em>Scripting</em>
- <ul>
- <li>
- <!-- JAL-2344 -->FileFormatI interface for describing
- and identifying file formats (instead of String
- constants)
- </li>
- <li>
- <!-- JAL-2228 -->FeatureCounter script refactored for
- efficiency when counting all displayed features (not
- backwards compatible with 2.10.1)
- </li>
- <li></li>
-
-
- </ul>
+ <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
+ </li>
+ <li>
+ <!-- JAL-2326 -->Prevent or clear modal dialogs raised
+ during tests
+ </li>
</ul>
</div></td>
<td><div align="left">
- <em>General</em>
+ <em>Calculations</em>
<ul>
<li>
<!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
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>
+ <li><a name="2102scoremodelbugs"/>
<!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
- and substitution matrix based Tree calculations.<br />In
+ 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). 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
+ 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
Sequence Feature Similarity.
</li>
<li>
+ <!-- JAL-2377 -->PCA calculation could hang when
+ generating output report when working with highly
+ redundant alignments
+ </li>
+ <li>
+ <!-- JAL-2544 --> Sort by features includes features to
+ right of selected region when gaps present on right-hand
+ boundary
+ </li>
+ </ul>
+ <em>User Interface</em>
+ <ul>
+ <li>
<!-- JAL-2346 -->Reopening Colour by annotation dialog
doesn't reselect a specific sequence's associated
annotation after it was used for colouring a view
</li>
<li>
- <!-- JAL-2430 -->Hidden regions in alignment views are not
- coloured in linked structure views
- </li>
- <li>
<!-- JAL-2419 -->Current selection lost if popup menu
opened on a region of alignment without groups
</li>
hidden regions results in incorrect hidden regions
</li>
<li>
- <!-- JAL-2377 -->PCA calculation could hang when
- generating output report when working with highly
- redundant alignments
- </li>
- <li>
- <!-- JAL-2365 -->Cannot configure feature colours with
- lightGray or darkGray via features file
- </li>
- <li>
- <!-- JAL-2421 -->Overview window visible region moves
- erratically when hidden rows or columns are present
- </li>
- <li>
- <!-- JAL-2362 -->Per-residue colourschemes applied via the
- Structure Viewer's colour menu don't correspond to
- sequence colouring
- </li>
- <li>
- <!-- JAL-2405 -->Protein specific colours only offered in
- colour and group colour menu for protein alignments
- </li>
- <li>
<!-- JAL-2386 -->'Apply to all groups' setting when
changing colour does not apply Conservation slider value
to all groups
</li>
<li>
- <!-- JAL-2385 -->Colour threshold slider doesn't update to
- reflect currently selected view or group's shading
- thresholds
- </li>
- <li>
<!-- JAL-2373 -->Percentage identity and conservation menu
items do not show a tick or allow shading to be disabled
</li>
gaps before start of features
</li>
<li>
- <!-- JAL-2576 -->Very large alignments take a long time to
- load
- </li>
- <li>
<!-- JAL-2623 -->Graduated feature colour threshold not
restored to UI when feature colour is edited
</li>
<li>
- <!-- JAL-2624 -->Feature colour thresholds not respected
- when rendered on overview and structures when opacity at
- 100%
+ <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
+ a time when scrolling vertically in wrapped mode.
</li>
<li>
<!-- JAL-2630 -->Structure and alignment overview update
dialog box
</li>
<li>
- <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
- a time when scrolling vertically in wrapped mode.
- </li>
- <li>
<!-- JAL-2034 -->Overview window doesn't always update
when a group defined on the alignment is resized
</li>
<!-- JAL-2605 -->Mouseovers on left/right scale region in
wrapped view result in positional status updates
</li>
+
<li>
- <!-- JAL-2563 -->Status bar shows position for ambiguous
- amino acid and nucleotide symbols
+ <!-- JAL-2563 -->Status bar doesn't show position for
+ ambiguous amino acid and nucleotide symbols
</li>
<li>
<!-- JAL-2602 -->Copy consensus sequence failed if
alignment included gapped columns
</li>
<li>
- <!-- JAL-2589 -->User defined gap colour not shown in
- overview when features overlaid on alignment
- </li>
- <li>
<!-- JAL-2473 -->Minimum size set for Jalview windows so
widgets don't permanently disappear
</li>
T-Coffee column reliability scores)
</li>
<li>
- <!-- JAL-2589 -->Gap colours in user-defined colourschemes
- are not shown
- </li>
- <li>
<!-- JAL-2594 -->Exception thrown if trying to create a
sequence feature on gaps only
</li>
<li>
- <!-- JAL-2544 --> Sort by features includes features to
- right of selected region when gaps present on right-hand
- boundary
- </li>
- <li>
<!-- JAL-2504 -->Features created with 'New feature'
button from a Find inherit previously defined feature type
rather than the Find query string
exporting tree calculated in Jalview
</li>
<li>
- <!-- JAL-2507 -->Per-sequence RNA secondary structures
- added after a sequence was imported are not written to
- Stockholm File
- </li>
- <li>
- <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
- when importing RNA secondary structure via Stockholm
- </li>
- <li>
- <!-- JAL-2509 -->Secondary structure arrows for [] and {}
- not shown in correct direction for simple pseudoknots
- </li>
- <li>
<!-- JAL-2437 -->Hiding sequences at bottom of alignment
and then revealing them reorders sequences on the
alignment
Linux
</li>
<li>
- <!-- JAL -->
+ <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
+ only excluded gaps in current sequence and ignored
+ selection.
</li>
+ </ul>
+ <em>Rendering</em>
+ <ul>
<li>
- <!-- JAL -->
+ <!-- JAL-2421 -->Overview window visible region moves
+ erratically when hidden rows or columns are present
</li>
<li>
- <!-- JAL -->
+ <!-- JAL-2362 -->Per-residue colourschemes applied via the
+ Structure Viewer's colour menu don't correspond to
+ sequence colouring
</li>
- </ul>
- <strong>Documentation</strong>
- <ul>
<li>
- <!-- JAL-2339 -->Release notes reformatted for readibility
- with the built-in Java help viewer
+ <!-- JAL-2405 -->Protein specific colours only offered in
+ colour and group colour menu for protein alignments
</li>
<li>
- <!-- JAL-1644 -->Find documentation updated with 'search
- sequence description' option
+ <!-- JAL-2385 -->Colour threshold slider doesn't update to
+ reflect currently selected view or group's shading
+ thresholds
+ </li>
+ <li>
+ <!-- JAL-2624 -->Feature colour thresholds not respected
+ when rendered on overview and structures when opacity at
+ 100%
+ </li>
+ <li>
+ <!-- JAL-2589 -->User defined gap colour not shown in
+ overview when features overlaid on alignment
</li>
</ul>
- <em>Application</em>
+ <em>Data import/export</em>
<ul>
<li>
- <!-- JAL-2225 -->Sequence Database chooser doesn't show
- available databases panel on Linux
+ <!-- JAL-2576 -->Very large alignments take a long time to
+ load
+ </li>
+ <li>
+ <!-- JAL-2507 -->Per-sequence RNA secondary structures
+ added after a sequence was imported are not written to
+ Stockholm File
+ </li>
+ <li>
+ <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
+ when importing RNA secondary structure via Stockholm
+ </li>
+ <li>
+ <!-- JAL-2509 -->Secondary structure arrows for [] and {}
+ not shown in correct direction for simple pseudoknots
+ </li>
+ <li>
+ <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
+ with lightGray or darkGray via features file (but can
+ specify lightgray)
+ </li>
+ <li>
+ <!-- JAL-2383 -->Above PID colour threshold not recovered
+ when alignment view imported from project
</li>
<li>
+ <!-- JAL-2520,JAL-2465 -->No mappings generated between
+ structure and sequences extracted from structure files
+ imported via URL and viewed in Jmol
+ </li>
+ <li>
+ <!-- JAL-2520 -->Structures loaded via URL are saved in
+ Jalview Projects rather than fetched via URL again when
+ the project is loaded and the structure viewed
+ </li>
+ </ul>
+ <em>Web Services</em>
+ <ul>
+ <li>
<!-- JAL-2519 -->EnsemblGenomes example failing after
release of Ensembl v.88
</li>
<li>
+ <!-- JAL-2366 -->Proxy server address and port always
+ appear enabled in Preferences->Connections
+ </li>
+ <li>
+ <!-- JAL-2461 -->DAS registry not found exceptions
+ removed from console output
+ </li>
+ <li>
+ <!-- JAL-2582 -->Cannot retrieve protein products from
+ Ensembl by Peptide ID
+ </li>
+ <li>
+ <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
+ created from SIFTs, and spurious 'Couldn't open structure
+ in Chimera' errors raised after April 2017 update (problem
+ due to 'null' string rather than empty string used for
+ residues with no corresponding PDB mapping).
+ </li>
+ </ul>
+ <em>Application UI</em>
+ <ul>
+ <li>
<!-- JAL-2361 -->User Defined Colours not added to Colour
menu
</li>
selection menu changes colours of alignment views
</li>
<li>
- <!-- JAL-2366 -->Proxy server address and port always
- appear enabled in Preferences->Connections
- </li>
- <li>
<!-- JAL-2426 -->Spurious exceptions in console raised
from alignment calculation workers after alignment has
been closed
shown again after pressing 'Cancel'
</li>
<li>
- <!-- JAL-2461 -->DAS registry not found exceptions
- removed from console output
- </li>
- <li>
- <!-- JAL-2383 -->Above PID colour threshold not recovered
- when alignment view imported from project
- </li>
- <li>
- <!-- JAL-2520,JAL-2465 -->No mappings generated between
- structure and sequences extracted from structure files
- imported via URL and viewed in Jmol
- </li>
- <li>
- <!-- JAL-2520 -->Structures loaded via URL are saved in
- Jalview Projects rather than fetched via URL again when
- the project is loaded and the structure viewed
- </li>
- <li>
<!-- JAL-1256 -->Trackpad horizontal scroll gesture
adjusts start position in wrap mode
</li>
ambiguous amino acids
</li>
<li>
- <!-- JAL-2291 -->Hide insertions in PopUp menu excludes
- gaps in selection, current sequence and only within
- selected columns
- </li>
- <li>
- <!-- JAL-2582 -->Cannot retrieve protein products from
- Ensembl by Peptide ID
- </li>
- <li>
<!-- JAL-2431 -->cDNA Consensus annotation not shown in
CDS/Protein view after CDS sequences added for aligned
proteins
</li>
<li>
- <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
- created from SIFTs, and spurious 'Couldn't open structure
- in Chimera' errors raised after April 2017 update (problem
- due to 'null' string rather than empty string used for
- residues with no corresponding PDB mapping).
+ <!-- JAL-2592 -->User defined colourschemes called 'User
+ Defined' don't appear in Colours menu
</li>
-
-
</ul>
<em>Applet</em>
<ul>
<li>
- <!-- JAL- -->
- </li>
- <li>
<!-- JAL-2468 -->Switching between Nucleotide and Protein
score models doesn't always result in an updated PCA plot
</li>
colourscheme
</li>
</ul>
+ <em>Test Suite</em>
+ <ul>
+ <li>
+ <!-- JAL-2314 -->Unit test failure:
+ jalview.ws.jabaws.RNAStructExportImport setup fails
+ </li>
+ <li>
+ <!-- JAL-2307 -->Unit test failure:
+ jalview.ws.sifts.SiftsClientTest due to compatibility
+ problems with deep array comparison equality asserts in
+ successive versions of TestNG
+ </li>
+ <li>
+ <!-- JAL-2479 -->Relocated StructureChooserTest and
+ ParameterUtilsTest Unit tests to Network suite
+ </li>
+ </ul>
<em>New Known Issues</em>
<ul>
<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
- containing features of type Highlight' when 'B" is pressed
+ containing features of type Highlight' when 'B' is pressed
to mark columns containing highlighted regions.
</li>
- </ul>
- <em>Test Suite</em>
- <ul>
- <li>
- <!-- JAL-2314 -->Unit test failure:
- jalview.ws.jabaws.RNAStructExportImport setup fails
- </li>
- <li>
- <!-- JAL-2307 -->Unit test failure:
- jalview.ws.sifts.SiftsClientTest due to compatibility
- problems with deep array comparison equality asserts in
- successive versions of TestNG
- </li>
<li>
- <!-- JAL-2479 -->Relocated StructureChooserTest and
- ParameterUtilsTest Unit tests to Network suite
+ <!-- JAL-2321 -->Dropping a PDB file onto a sequence
+ 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