X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=dac2c0b0c949d651bd7c3dbb780a7911693f35c0;hb=a0f5e2532e4114b22cb0203636e90d5ed3ba2d86;hp=307b04ae4f921a0de1a31acffaa1704c18c3c883;hpb=c695b1c1ec45b75551c3c03587b62259139eb715;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 307b04a..dac2c0b 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -70,13 +70,386 @@ li:before {
- 2.10.2
8/8/2017 + 2.10.3b1
23/1/2018
+ + +
+ + + + + +
+ 2.10.3
17/11/2017 +
+ +
+ +
    +
  • + Faster and more efficient management and + rendering of sequence features +
    • +
  • + More reliable Ensembl fetching with HTTP + 429 rate limit request hander +
    • +
  • + Structure views don't get updated unless + their colours have changed +
    • +
  • + All linked sequences are highlighted for + a structure mousover (Jmol) or selection (Chimera) +
    • +
  • + 'Cancel' button in progress bar for + JABAWS AACon, RNAAliFold and Disorder prediction jobs +
    • +
  • + Stop codons are excluded in CDS/Protein + view from Ensembl locus cross-references +
    • +
  • + Start/End limits are shown in Pairwise + Alignment report +
    • +
  • + Sequence fetcher's Free text 'autosearch' + feature can be disabled +
    • +
  • + Retrieve IDs tab added for UniProt and + PDB easier retrieval of sequences for lists of IDs +
    • +
  • + Short names for sequences retrieved from + Uniprot +
    • +
+ Scripting +
    +
  • Groovy interpreter updated to 2.4.12
    • +
  • Example groovy script for generating a matrix of + percent identity scores for current alignment.
    • +
+ Testing and Deployment +
    +
  • + Test to catch memory leaks in Jalview UI +
    • +
+
+
General
  • + Pressing tab after updating the colour + threshold text field doesn't trigger an update to the + alignment view +
    • +
  • + Race condition when parsing sequence ID + strings in parallel +
    • +
  • + Overview windows are also closed when + alignment window is closed +
    • +
  • + Export of features doesn't always respect + group visibility +
    • +
  • + Jumping from column 1 to column 100,000 + takes a long time in Cursor mode +
    • +
+ Desktop +
    +
  • + Structures with whitespace chainCode + cannot be viewed in Chimera +
    • +
  • + Protein annotation panel too high in + CDS/Protein view +
    • +
  • + Can't edit the query after the server + error warning icon is shown in Uniprot and PDB Free Text + Search Dialogs +
    • +
  • + Slow EnsemblGenome ID lookup +
    • +
  • + Revised Ensembl REST API CDNA query +
    • +
  • + Hidden column marker in last column not + rendered when switching back from Wrapped to normal view +
    • +
  • + Annotation display corrupted when + scrolling right in unwapped alignment view +
    • +
  • + Existing features on subsequence + incorrectly relocated when full sequence retrieved from + database +
    • +
  • + Last reported memory still shown when + Desktop->Show Memory is unticked (OSX only) +
    • +
  • + Amend Features dialog doesn't allow + features of same type and group to be selected for + amending +
    • +
  • + Jalview becomes sluggish in wide + alignments when hidden columns are present +
    • +
  • + Jalview freezes when loading and + displaying several structures +
    • +
  • + Black outlines left after resizing or + moving a window +
    • +
  • + Unable to minimise windows + within the Jalview desktop on OSX +
    • +
  • + Mouse wheel doesn't scroll vertically + when in wrapped alignment mode +
    • +
  • + Scale mark not shown when close to right + hand end of alignment +
    • +
  • + Pairwise alignment of selected regions of + each selected sequence do not have correct start/end + positions +
    • +
  • + Alignment ruler height set incorrectly + after canceling the Alignment Window's Font dialog +
    • +
  • + Show cross-references not enabled after + restoring project until a new view is created +
    • +
  • + Warning popup about use of SEQUENCE_ID in + URL links appears when only default EMBL-EBI link is + configured (since 2.10.2b2) +
    • +
  • + Overview redraws whole window when box + position is adjusted +
    • +
  • + Structure viewer doesn't map all chains + in a multi-chain structure when viewing alignment + involving more than one chain (since 2.10) +
    • +
  • + Double residue highlights in cursor mode + if new selection moves alignment window +
    • +
  • + Alignment vanishes when using + arrow key in cursor mode to pass hidden column marker +
    • +
  • + Ensembl Genomes example ID changed to one + that produces correctly annotated transcripts and products +
    • +
  • + Toggling a feature group after first time + doesn't update associated structure view +
    • +
+ Applet
+
    +
  • + Concurrent modification exception when + closing alignment panel +
    • +
+ BioJSON
+
    +
  • + BioJSON export does not preserve + non-positional features +
    • +
+ New Known Issues +
    +
  • + Delete/Cut selection doesn't relocate + sequence features correctly (for many previous versions of + Jalview) +
    • +
  • + Cursor mode unexpectedly scrolls when + using cursor in wrapped panel other than top +
    • +
  • + Select columns containing feature ignores + graduated colour threshold +
    • +
  • + Edit sequence operation doesn't + always preserve numbering and sequence features +
    • +
+ Known Java 9 Issues +
    +
  • + Groovy Console very slow to open and is + not responsive when entering characters (Webstart, Java + 9.01, OSX 10.10) +
    • +
+
+ + + +
+ 2.10.2b2
+ 2/10/2017 +
+ +
+ New features in Jalview Desktop +
    +
  • + Uniprot Sequence Fetcher now uses web API at uniprot.org +
    • +
  • HTTPS used for all connections to ebi.ac.uk +
    • +
+
+
+
+ + + +
+ 2.10.2b1
+ 7/9/2017 +
+ +
+ +
    +
  • + Show gaps in overview window by colouring + in grey (sequences used to be coloured grey, and gaps were + white) +
    • +
  • + Overview tab in Jalview Desktop + Preferences +
    • +
  • + Overview updates immediately on increase + in size and progress bar shown as higher resolution + overview is recalculated +
    • + +
+
+
+ +
    +
  • + Overview window redraws every hidden + column region row by row +
    • +
  • + duplicate protein sequences shown after + retrieving Ensembl crossrefs for sequences from Uniprot +
    • +
  • + Overview window throws NPE if show boxes + format setting is unticked +
    • +
  • + Groups are coloured wrongly in overview + if group has show boxes format setting unticked +
    • +
  • + Redraw problems when + autoscrolling whilst dragging current selection group to + include sequences and columns not currently displayed +
    • +
  • + Not all chains are mapped when multimeric + assemblies are imported via CIF file +
    • +
  • + Gap colour in custom colourscheme is not + displayed when threshold or conservation colouring is also + enabled. +
    • +
  • + JABAWS 2.2 services report wrong JABAWS + server version +
    • +
  • + Jalview continues to scroll after + dragging a selected region off the visible region of the + alignment +
    • +
  • + Cannot apply annotation based + colourscheme to all groups in a view +
    • +
  • + IDs don't line up with sequences + initially after font size change using the Font chooser or + middle-mouse zoom +
    • +
+
+ + + +
+ 2.10.2
17/8/2017 +
+ +
+ Calculations +
    + +
  • + Occupancy annotation row shows number of + ungapped positions in each column of the alignment. +
    • +
  • + Tree/PCA calculation menu items merged to + a calculation dialog box +
    • +
  • Revised implementation of PCA for speed and memory efficiency (~30x faster)
    • @@ -84,21 +457,19 @@ li:before { Revised implementation of sequence similarity scores as used by Tree, PCA, Shading Consensus and other calculations -
      -
    • - Score matrices are stored as resource - files within the Jalview codebase -
    • - Trees computed on Sequence Feature - Similarity may have different topology due to - increased precision -
      • -
  • - Tree/PCA calculation menu items merged to - a calculation dialog box + Score matrices are stored as resource + files within the Jalview codebase +
    • +
  • + Trees computed on Sequence Feature + Similarity may have different topology due to increased + precision
    • +
+ Rendering +
  • More robust colours and shader model for alignments and groups @@ -107,39 +478,62 @@ li:before { Custom shading schemes created via groovy scripts
    • -
  • - linked scrolling of CDS/Protein views - via Overview or sequence motif search operations -
    • +
+ Overview +
  • Efficiency improvements for interacting with alignment and overview windows
  • + Scrolling of wrapped alignment views via + overview +
    • +
  • Hidden columns and sequences can be omitted in Overview
  • + Click-drag in visible area allows fine + adjustment of visible position +
    • +
+ + Data import/export +
    +
  • Posterior probability annotation from Stockholm files imported as sequence associated annotation
  • + More robust per-sequence positional + annotation input/output via stockholm flatfile +
    • +
  • Sequence names don't include file extension when importing structure files without embedded names or PDB accessions
  • - Amend sequence features dialog box can be - opened by double clicking gaps within sequence feature - extent + Drag and drop load of AAIndex and NCBI + format sequence substitution matrices
    • +
+ User Interface +
  • - Graduated feature colour style example - included in the example feature file + Experimental Features Checkbox in + Desktop's Tools menu to hide or show untested features in + the application.
  • - Occupancy annotation row shows number of - ungapped positions in each column of the alignment. + Linked scrolling of CDS/Protein views + via Overview or sequence motif search operations +
    • +
  • + Amend sequence features dialog box can be + opened by double clicking gaps within sequence feature + extent
  • Status bar message shown when not enough @@ -147,111 +541,144 @@ li:before { superposition.
- Application + 3D Structure
  • - Experimental Features Checkbox in - Desktop's Tools menu to hide or show untested features in - the application. -
    • -
  • - Warning in alignment status bar when - there are not enough columns to superimpose structures in - Chimera + Hidden regions in alignment views are not + coloured in linked structure views
  • Faster Chimera/Jalview communication by file-based command exchange
  • - URLs for viewing database - cross-references provided by identifiers.org and the - EMBL-EBI's MIRIAM DB + Structure chooser automatically shows + Cached Structures rather than querying the PDBe if + structures are already available for sequences +
    • +
  • + Structures imported via URL are cached in + the Jalview project rather than downloaded again when the + project is reopened.
  • + New entries in the Chimera menu + to transfer Chimera's structure attributes as Jalview + features, and vice-versa (Experimental + Feature) +
    • +
+ Web Services +
    +
  • Updated JABAWS client to v2.2
  • - Drag and drop load of AAIndex and NCBI - format sequence substitution matrices + Filter non-standard amino acids and + nucleotides when submitting to AACon and other MSA + Analysis services
  • - Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences + URLs for viewing database + cross-references provided by identifiers.org and the + EMBL-EBI's MIRIAM DB
- Experimental features + + Scripting
  • - New entries in the Chimera menu - to transfer Chimera's structure attributes as Jalview - features, and vice-versa. + FileFormatI interface for describing and + identifying file formats (instead of String constants) +
    • +
  • + FeatureCounter script refactored for + efficiency when counting all displayed features (not + backwards compatible with 2.10.1)
- Applet + Example files
  • - + Graduated feature colour style example + included in the example feature file +
    • +
+ Documentation +
    +
  • + Release notes reformatted for readability + with the built-in Java help viewer +
    • +
  • + Find documentation updated with 'search + sequence description' option
Test Suite
  • + External service integration tests for + Uniprot REST Free Text Search Client +
    • +
  • Added PrivilegedAccessor to test suite
  • Prevent or clear modal dialogs raised during tests
    • -
  • - Scripting -
      -
    • - FileFormatI interface for describing - and identifying file formats (instead of String - constants) -
      • -
    • - -
      • - - -
- General + Calculations + User Interface +
  • Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view
  • - Hidden regions in alignment views are not - coloured in linked structure views -
    • -
  • Current selection lost if popup menu opened on a region of alignment without groups
    • @@ -268,38 +695,11 @@ li:before { hidden regions results in incorrect hidden regions
  • - PCA calculation could hang when - generating output report when working with highly - redundant alignments -
    • -
  • - Cannot configure feature colours with - lightGray or darkGray via features file -
    • -
  • - Overview window visible region moves - erratically when hidden rows or columns are present -
    • -
  • - Per-residue colourschemes applied via the - Structure Viewer's colour menu don't correspond to - sequence colouring -
    • -
  • - Protein specific colours only offered in - colour and group colour menu for protein alignments -
    • -
  • 'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups
  • - Colour threshold slider doesn't update to - reflect currently selected view or group's shading - thresholds -
    • -
  • Percentage identity and conservation menu items do not show a tick or allow shading to be disabled
    • @@ -312,17 +712,12 @@ li:before { gaps before start of features
  • - Very large alignments take a long time to - load -
    • -
  • Graduated feature colour threshold not restored to UI when feature colour is edited
  • - Feature colour thresholds not respected - when rendered on overview and structures when opacity at - 100% + Vertical scrollbar jumps one page-width at + a time when scrolling vertically in wrapped mode.
  • Structure and alignment overview update @@ -330,10 +725,6 @@ li:before { dialog box
  • - Vertical scrollbar jumps one page-width at - a time when scrolling vertically in wrapped mode. -
    • -
  • Overview window doesn't always update when a group defined on the alignment is resized
    • @@ -341,41 +732,159 @@ li:before { Mouseovers on left/right scale region in wrapped view result in positional status updates +
  • - Status bar shows position for ambiguous - amino acid and nucleotide symbols + Status bar doesn't show position for + ambiguous amino acid and nucleotide symbols
  • Copy consensus sequence failed if alignment included gapped columns
  • + Minimum size set for Jalview windows so + widgets don't permanently disappear +
    • +
  • + Cannot select or filter quantitative + annotation that are shown only as column labels (e.g. + T-Coffee column reliability scores) +
    • +
  • + Exception thrown if trying to create a + sequence feature on gaps only +
    • +
  • + Features created with 'New feature' + button from a Find inherit previously defined feature type + rather than the Find query string +
    • +
  • + incorrect title in output window when + exporting tree calculated in Jalview +
    • +
  • + Hiding sequences at bottom of alignment + and then revealing them reorders sequences on the + alignment +
    • +
  • + Group panel in sequence feature settings + doesn't update to reflect available set of groups after + interactively adding or modifying features +
    • +
  • + Sequence Database chooser unusable on + Linux +
    • +
  • + Hide insertions in PopUp->Selection menu + only excluded gaps in current sequence and ignored + selection. +
    • +
+ Rendering +
    +
  • + Overview window visible region moves + erratically when hidden rows or columns are present +
    • +
  • + Per-residue colourschemes applied via the + Structure Viewer's colour menu don't correspond to + sequence colouring +
    • +
  • + Protein specific colours only offered in + colour and group colour menu for protein alignments +
    • +
  • + Colour threshold slider doesn't update to + reflect currently selected view or group's shading + thresholds +
    • +
  • + Feature colour thresholds not respected + when rendered on overview and structures when opacity at + 100% +
    • +
  • User defined gap colour not shown in overview when features overlaid on alignment
    • +
+ Data import/export +
    +
  • + Very large alignments take a long time to + load +
  • - + Per-sequence RNA secondary structures + added after a sequence was imported are not written to + Stockholm File
  • - + WUSS notation for simple pseudoknots lost + when importing RNA secondary structure via Stockholm
  • - + Secondary structure arrows for [] and {} + not shown in correct direction for simple pseudoknots
  • - + Cannot configure feature colours + with lightGray or darkGray via features file (but can + specify lightgray) +
    • +
  • + Above PID colour threshold not recovered + when alignment view imported from project +
    • +
  • + No mappings generated between + structure and sequences extracted from structure files + imported via URL and viewed in Jmol +
    • +
  • + Structures loaded via URL are saved in + Jalview Projects rather than fetched via URL again when + the project is loaded and the structure viewed
- Documentation + Web Services
  • - Release notes reformatted for readibility - with the built-in Java help viewer + EnsemblGenomes example failing after + release of Ensembl v.88 +
    • +
  • + Proxy server address and port always + appear enabled in Preferences->Connections +
    • +
  • + DAS registry not found exceptions + removed from console output +
    • +
  • + Cannot retrieve protein products from + Ensembl by Peptide ID +
    • +
  • + 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).
- Application + Application UI
  • + User Defined Colours not added to Colour + menu +
    • +
  • Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added) @@ -389,12 +898,17 @@ li:before { new features are added to alignment
  • - Structure viewer's View -> Colour By view - selection menu changes colours of alignment views + Cancel in feature settings reverts + changes to feature colours via the Amend features dialog
  • - Proxy server address and port always - appear enabled in Preferences->Connections + Null pointer exception when attempting to + edit graduated feature colour via amend features dialog + box +
    • +
  • + Structure viewer's View -> Colour By view + selection menu changes colours of alignment views
  • Spurious exceptions in console raised @@ -414,24 +928,6 @@ li:before { shown again after pressing 'Cancel'
  • - DAS registry not found exceptions - removed from console output -
    • -
  • - Above PID colour threshold not recovered - when alignment view imported from project -
    • -
  • - No mappings generated between structure - and sequences extracted from structure files imported via - URL -
    • -
  • - Structures loaded via URL are saved in - Jalview Projects rather than fetched via URL again when - the project is loaded and the structure viewed -
    • -
  • Trackpad horizontal scroll gesture adjusts start position in wrap mode
    • @@ -440,31 +936,18 @@ li:before { ambiguous amino acids
  • - Hide insertions in PopUp menu excludes - gaps in selection, current sequence and only within - selected columns -
    • -
  • - Cannot retrieve protein products from - Ensembl by Peptide ID -
    • -
  • cDNA Consensus annotation not shown in CDS/Protein view after CDS sequences added for aligned proteins
  • - cDNA Consensus not shown + User defined colourschemes called 'User + Defined' don't appear in Colours menu
    • - -
Applet
  • - -
    • -
  • Switching between Nucleotide and Protein score models doesn't always result in an updated PCA plot
    • @@ -482,6 +965,23 @@ li:before { colourscheme
+ Test Suite +
    +
  • + Unit test failure: + jalview.ws.jabaws.RNAStructExportImport setup fails +
    • +
  • + Unit test failure: + jalview.ws.sifts.SiftsClientTest due to compatibility + problems with deep array comparison equality asserts in + successive versions of TestNG +
    • +
  • + Relocated StructureChooserTest and + ParameterUtilsTest Unit tests to Network suite +
    • +
New Known Issues
  • @@ -491,21 +991,20 @@ li:before {
  • 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
  • - Cannot load Newick trees from eggnog - ortholog database + Cannot load and display Newick trees + reliably from eggnog Ortholog database
    • -
- Test Suite -
  • - Unit test failure: - jalview.ws.jabaws.RNAStructExportImport setup fails + Status bar shows 'Marked x columns + containing features of type Highlight' when 'B' is pressed + to mark columns containing highlighted regions.
  • - + Dropping a PDB file onto a sequence + doesn't always add secondary structure annotation.
@@ -1186,6 +1685,10 @@ li:before { after clicking on it to create new annotation for a column. +
  • + Null Pointer Exception raised when + pressing Add on an orphaned cut'n'paste window. +