Release History

+ + +

Alignment doesn't appear to scroll vertically via trackpad and scrollwheel
Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment
Helix annotation has 'notches' when scrolled into view if columns are hidden

+ 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) +
+ 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 +

+ Rendering +

+ More robust colours and shader + model for alignments and groups +
+ Custom shading schemes created via groovy + scripts +

+ 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 +
+ Drag and drop load of AAIndex and NCBI + format sequence substitution matrices +

+ User Interface +

+ Experimental Features Checkbox in + Desktop's Tools menu to hide or show untested features in + the application. +
+ 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 + aligned positions were available to create a 3D structure + superposition. +

+ 3D Structure +

+ Hidden regions in alignment views are not + coloured in linked structure views +
+ Faster Chimera/Jalview communication by + file-based command exchange +
+ 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 +
+ Filter non-standard amino acids and + nucleotides when submitting to AACon and other MSA + Analysis services +
+ URLs for viewing database + cross-references provided by identifiers.org and the + EMBL-EBI's MIRIAM DB +

+ + Scripting +

+ 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) +

+ 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 +

+ Calculations +

+ Fixed incorrect value in BLOSUM 62 score + matrix - C->R should be '-3'
Old matrix restored + with this one-line groovy script:
jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3 +
Fixed + Jalview's treatment of gaps in PCA and substitution matrix + based Tree calculations.

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.
Jalview + now treats gaps in the same way as SeqSpace (ie it scores + them as 0).

Enter the following in the + Groovy console to restore pre-2.10.2 behaviour:
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true + // for 2.10.1 mode
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false + // to restore 2.10.2 mode

Note: + these settings will affect all subsequent tree and PCA + calculations (not recommended)

+ Fixed off-by-one bug that affected + scaling of branch lengths for trees computed using + Sequence Feature Similarity. +

+ PCA calculation could hang when + generating output report when working with highly + redundant alignments +

+ Sort by features includes features to + right of selected region when gaps present on right-hand + boundary +

+ User Interface +

+ Reopening Colour by annotation dialog + doesn't reselect a specific sequence's associated + annotation after it was used for colouring a view +
+ Current selection lost if popup menu + opened on a region of alignment without groups +
+ Popup menu not always shown for regions + of an alignment with overlapping groups +
+ Finder double counts if both a sequence's + name and description match +
+ Hiding column selection containing two + hidden regions results in incorrect hidden regions +
+ 'Apply to all groups' setting when + changing colour does not apply Conservation slider value + to all groups +
+ Percentage identity and conservation menu + items do not show a tick or allow shading to be disabled +
+ Conservation shading or PID threshold + lost when base colourscheme changed if slider not visible +
+ Sequence features shown in tooltip for + gaps before start of features +
+ Graduated feature colour threshold not + restored to UI when feature colour is edited +
+ Vertical scrollbar jumps one page-width at + a time when scrolling vertically in wrapped mode. +
+ Structure and alignment overview update + as graduate feature colour settings are modified via the + dialog box +
+ Overview window doesn't always update + when a group defined on the alignment is resized +
+ Mouseovers on left/right scale region in + wrapped view result in positional status updates +
+ 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 +

+ Web Services +

+ 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 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) +
+ Text colour threshold's 'Cancel' button + doesn't restore group-specific text colour thresholds +
+ Feature settings panel does not update as + new features are added to alignment +
+ Cancel in feature settings reverts + changes to feature colours via the Amend features dialog +
+ 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 + from alignment calculation workers after alignment has + been closed +
+ Typo in selection popup menu - Create + groups now 'Create Group' +
+ CMD/CTRL and G or Shift G for + Create/Undefine group doesn't always work +
+ Tree Viewer's Print Dialog doesn't get + shown again after pressing 'Cancel' +
+ Trackpad horizontal scroll gesture + adjusts start position in wrap mode +
+ Status bar doesn't show positions for + ambiguous amino acids +
+ cDNA Consensus annotation not shown in + CDS/Protein view after CDS sequences added for aligned + proteins +
+ 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 +
+ Features not rendered as transparent on + overview or linked structure view +
+ Colour group by conservation doesn't + work (since 2.8) +
+ Hitting Cancel after applying + user-defined colourscheme doesn't restore original + 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 +

+ Protein/CDS view scrolling not always in + phase after a sequence motif find operation +
+ Importing annotation file with rows + containing just upper and lower case letters are + interpreted as WUSS RNA secondary structure symbols +
+ Cannot load and display Newick trees + reliably from eggnog Ortholog database +
+ 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. +

+ + +

+ 2.10.1
29/11/2016 +

+ General +

+ Improved memory usage: sparse arrays used + for all consensus calculations +
+ Jmol updated to version 14.6.4 (released + 3rd Oct 2016) +
Updated Jalview's Certum code signing certificate + for 2016-2017

+ Application +

+ Sequence ID tool tip presents abridged + set of database cross-references, sorted alphabetically +
+ New replacement token for creating URLs just + from database cross references. Users with custom links + will receive a warning + dialog asking them to update their preferences. +
+ Cancel button and escape listener on + dialog warning user about disconnecting Jalview from a + Chimera session +
+ Jalview's Chimera control window closes if + the Chimera it is connected to is shut down +
+ New keystroke (B) and Select highlighted + columns menu item to mark columns containing highlighted + regions (e.g. from structure selections or results of a + Find operation) +
+ Command line option for batch-generation + of HTML pages rendering alignment data with the BioJS + MSAviewer +

+ General +

+ Columns with more than one modal residue + are not coloured or thresholded according to percent + identity (first observed in Jalview 2.8.2) +
+ Threonine incorrectly reported as not + hydrophobic +
+ Updates to documentation pages (above PID + threshold, amino acid properties) +
+ Lower case residues in sequences are not + reported as mapped to residues in a structure file in the + View Mapping report +
+ Identical features with non-numeric scores + could be added multiple times to a sequence +
+ Disulphide + bond features shown as two highlighted residues rather + than a range in linked structure views, and treated + correctly when selecting and computing trees from features +
+ Custom URL links for database + cross-references are matched to database name regardless + of case +

+ Application +

+ Custom URL links for specific database + names without regular expressions also offer links from + Sequence ID +
+ Removing a single configured link in the + URL links pane in Connections preferences doesn't actually + update Jalview configuration +
+ CTRL-Click on a selected region to open + the alignment area popup menu doesn't work on El-Capitan +
+ Jalview doesn't offer to associate mmCIF + files with similarly named sequences if dropped onto the + alignment +
+ Additional mappings are shown for PDB + entries where more chains exist in the PDB accession than + are reported in the SIFTS file +
+ Certain structures do not get mapped to + the structure view when displayed with Chimera +
+ No chains shown in the Chimera view + panel's View->Show Chains submenu +
+ Export as HTML with embedded SVG doesn't + work for wrapped alignment views +
+ Rename UI components for running JPred + predictions from 'JNet' to 'JPred' +
+ Export as PNG or SVG is + corrupted when annotation panel vertical scroll is not at + first annotation row +
+ Attempting to view structure for Hen + lysozyme results in a PDB Client error dialog box +
+ Structure View's mapping report switched + ranges for PDB and sequence for SIFTS +

+ +

+ 2.10.0b1
+ 25/10/2016 +

Application

3D Structure chooser opens with 'Cached structures' + view if structures already loaded
Progress bar reports models as they are loaded to + structure views

+ General +

Colour by conservation always enabled and no tick + shown in menu when BLOSUM or PID shading applied
FER1_ARATH and FER2_ARATH labels were switched in + example sequences/projects/trees

+ Application +

Jalview projects with views of local PDB structure + files saved on Windows cannot be opened on OSX
Multiple structure views can be opened and superposed + without timeout for structures with multiple models or + multiple sequences in alignment
Cannot import or associated local PDB files without a + PDB ID HEADER line
RMSD is not output in Jmol console when superposition + is performed
Drag and drop of URL from Browser fails for Linux and + OSX versions earlier than El Capitan
ENA client ignores invalid content from ENA server
Exceptions are not raised in console when ENA client + attempts to fetch non-existent IDs via Fetch DB Refs UI + option
Exceptions are not raised in console when a new view + is created on the alignment
OSX right-click fixed for group selections: CMD-click + to insert/remove gaps in groups and CTRL-click to open group + pop-up menu

+ Build and deployment +

URL link checker now copes with multi-line anchor + tags

+ New Known Issues +

Drag and drop from URL links in browsers do not work + on Windows

- 2.10.0
27/9/2016 + 2.10.0
06/10/2016

General

Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.
Alignment ruler shows positions relative to reference sequence
Position/residue shown in status bar when mousing over sequence associated annotation
Default RNA SS symbol to 'matching bracket' for manual entry
RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column
Feature settings popup menu options for showing or hiding columns containing a feature
Edit selected group by double clicking on group and sequence associated annotation labels
+ Updated Spanish translations. +
+ Jmol now primary parser + for importing structure data to Jalview. Enables mmCIF and + better PDB parsing. +
+ Alignment ruler shows positions relative to + reference sequence +
+ Position/residue shown in status bar when + mousing over sequence associated annotation +
+ Default RNA SS symbol to 'matching bracket' + for manual entry +
+ RNA Structure consensus indicates wc-only + '()', canonical '[]' and invalid '{}' base pair populations + for each column +
+ Feature settings popup menu options for + showing or hiding columns containing a feature +
+ Edit selected group by double clicking on + group and sequence associated annotation labels +
+ Sequence name added to annotation label in + select/hide columns by annotation and colour by annotation + dialogs +

Application

Updated download sites used for Rfam and Pfam sources to xfam.org
Disabled Rfam(Full) in the sequence fetcher
Show residue labels in Chimera when mousing over sequences in Jalview
Support for reverse-complement coding regions in ENA and EMBL
Upgrade to EMBL XML 1.2 for ENA record retrieval
Support for ENA CDS records with reverse complement operator
New 'execute Groovy script' option in an alignment window's Calculate menu
Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
Support for creating new alignment calculation workers from groovy scripts
Store/restore reference sequence in Jalview projects
Chain codes for a sequence's PDB associations are now saved/restored from project
Double click on an entry in Jalview's database chooser opens a sequence fetcher
Free-text search client for UniProt using the UniProt REST API
-nonews command line parameter to prevent the news reader opening

Applet

+ Automatically hide introns when opening a + gene/transcript view +
+ Uniprot Sequence fetcher Free Text Search + dialog +
+ UniProt - PDB protein + structure mappings with the EMBL-EBI PDBe SIFTS database +
+ Updated download sites used for Rfam and + Pfam sources to xfam.org +
+ Disabled Rfam(Full) in the sequence fetcher +
+ Show residue labels in Chimera when mousing + over sequences in Jalview +
+ Support for reverse-complement coding + regions in ENA and EMBL +
+ Upgrade to EMBL XML 1.2 + for record retrieval via ENA rest API +
+ Support for ENA CDS records with reverse + complement operator +
+ Update to groovy-2.4.6-indy - for faster + groovy script execution +
+ New 'execute Groovy script' option in an + alignment window's Calculate menu +
+ Allow groovy scripts that call + Jalview.getAlignFrames() to run in headless mode +
+ Support for creating new alignment + calculation workers from groovy scripts +
+ Store/restore reference sequence in + Jalview projects +
+ Chain codes for a sequence's PDB + associations are now saved/restored from project +
+ Database selection dialog always shown + before sequence fetcher is opened +
+ Double click on an entry in Jalview's + database chooser opens a sequence fetcher +
+ Free-text search client for UniProt using + the UniProt REST API +
+ -nonews command line parameter to prevent + the news reader opening +
+ Displayed columns for PDBe and Uniprot + querying stored in preferences +
+ Pagination for displaying PDBe and Uniprot + search results +
+ Tooltips shown on database chooser +
+ Reverse complement function in calculate + menu for nucleotide sequences +
+ Alignment sort by feature scores + and feature counts preserves alignment ordering (and + debugged for complex feature sets). +
+ Chimera 1.11.1 minimum requirement for + viewing structures with Jalview 2.10 +
+ Retrieve + genome, transcript CCDS and gene ids via the Ensembl and + Ensembl Genomes REST API +
+ Protein sequence variant annotation + computed for 'sequence_variant' annotation on CDS regions + (Ensembl) +
+ ENA CDS 'show cross references' for Uniprot + sequences +
+ Improved warning messages when DB + Ref Fetcher fails to match, or otherwise updates sequence + data from external database records. +
+ Revised Jalview Project format for + efficient recovery of sequence coding and alignment + annotation relationships. +

+ -- JAL--- +

+ -->

General

reinstate CTRL-click for opening pop-up menu on OSX
Export features in Jalview format (again) includes graduated colourschemes
More responsive when working with big alignments and lots of hidden columns
Hidden column markers not always rendered at right of alignment window
Tidied up links in help file table of contents
Feature based tree calculation not shown for DNA alignments
Hidden columns ignored during feature based tree calculation
Alignment view stops updating when show unconserved enabled for group on alignment
Cannot insert gaps into sequence when set as reference
Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation
Incorrect column numbers in ruler when hidden columns present
Colour by RNA Helices not enabled when user created annotation added to alignment
RNA Structure consensus only computed for '()' base pair annotation
Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus
Extend selection with columns containing feature not working
+ reinstate CTRL-click for opening pop-up + menu on OSX +
+ Export features in Jalview format (again) + includes graduated colourschemes +
+ More responsive when + working with big alignments and lots of hidden columns +
+ Hidden column markers not always rendered + at right of alignment window +
+ Tidied up links in help file table of + contents +
+ Feature based tree calculation not shown + for DNA alignments +
+ Hidden columns ignored during feature + based tree calculation +
+ Alignment view stops updating when show + unconserved enabled for group on alignment +
+ Cannot insert gaps into sequence when + set as reference +
+ Alignment column in status incorrectly + shown as "Sequence position" when mousing over + annotation +
+ Incorrect column numbers in ruler when + hidden columns present +
+ Colour by RNA Helices not enabled when + user created annotation added to alignment +
+ RNA Structure consensus only computed for + '()' base pair annotation +
+ Enabling 'Ignore Gaps' results + in zero scores for all base pairs in RNA Structure + Consensus +
+ Extend selection with columns containing + feature not working +
+ Pfam format writer puts extra space at + beginning of sequence +
+ Incomplete sequence extracted from pdb + entry 3a6s +
+ Cannot create groups on an alignment from + from a tree when t-coffee scores are shown +
+ Cannot import and view PDB + structures with chains containing negative resnums (4q4h) +
+ ArithmeticExceptions raised when parsing + some structures +
+ 'Empty' alignment blocks added + to Clustal, PIR and PileUp output +
+ Reordering sequence features that are + not visible causes alignment window to repaint +
+ Threshold sliders don't work in + graduated colour and colour by annotation row for e-value + scores associated with features and annotation rows +
+ amino acid physicochemical conservation + calculation should be case independent +
+ Remove annotation also updates hidden + columns +
+ FER1_ARATH and FER2_ARATH mislabelled in + example file (uniref50.fa, feredoxin.fa, unaligned.fa, + exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar) +
+ Null pointer exceptions and redraw + problems when reference sequence defined and 'show + non-conserved' enabled +
+ Quality and Conservation are now shown on + load even when Consensus calculation is disabled +
+ Remove right on penultimate column of + alignment does nothing +

Application

Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
URLs and links can imported by drag'n'drop on OSX webstart
InstallAnywhere distribution fails when launching Chimera
Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
Cannot save project when view has a reference sequence defined
Columns are suddenly selected in other alignments and views when revealing hidden columns
Hide columns not mirrored in complement view in a cDNA/Protein splitframe
Cannot save/restore representative sequence from project when only one sequence is represented
Disabled 'Best Uniprot Coverage' option in Structure Chooser
Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
+ URLs and links can't be imported by + drag'n'drop on OSX when launched via webstart (note - not + yet fixed for El Capitan) +
+ Corrupt preferences for SVG, EPS & HTML + output when running on non-gb/us i18n platforms +
+ Error thrown when exporting a view with + hidden sequences as flat-file alignment +
+ InstallAnywhere distribution fails when + launching Chimera +
+ Jalview very slow to launch via webstart + (also hotfix for 2.9.0b2) +
+ Cannot save project when view has a + reference sequence defined +
+ Columns are suddenly selected in other + alignments and views when revealing hidden columns +
+ Hide columns not mirrored in complement + view in a cDNA/Protein splitframe +
+ Cannot save/restore representative + sequence from project when only one sequence is + represented +
+ Disabled 'Best Uniprot Coverage' option + in Structure Chooser +
+ Modifying 'Ignore Gaps' on consensus or + structure consensus didn't refresh annotation panel +
+ View mapping in structure view shows + mappings between sequence and all chains in a PDB file +
+ PDB and Uniprot FTS + dialogs format columns correctly, don't display array + data, sort columns according to type +
+ Export complete shown after destination + file chooser is cancelled during an image export +
+ Error when querying PDB Service with + sequence name containing special characters +
+ Manual PDB structure querying should be + case insensitive +
+ Large tooltips with broken HTML + formatting don't wrap +
+ Figures exported from wrapped view are + truncated so L looks like I in consensus annotation +
+ Export features should only export the + currently displayed features for the current selection or + view +
+ Enable 'Get Cross-References' in menu + after fetching cross-references, and restoring from + project +
+ Mouseover of a copy of a sequence is not + followed in the structure viewer +
+ Titles for individual alignments in + splitframe not restored from project +
+ missing autocalculated annotation at + trailing end of protein alignment in transcript/product + splitview when pad-gaps not enabled by default +
+ amino acid physicochemical conservation + is case dependent +
+ RSS reader doesn't stay hidden after last + article has been read (reopened issue due to + internationalisation problems) +
+ Only offer PDB structures in structure + viewer based on sequence name, PDB and UniProt + cross-references +
+ No progress bar shown during export of + alignment as HTML +
+ Structures not always superimposed after + multiple structures are shown for one or more sequences. +
+ Reference sequence characters should not + be replaced with '.' when 'Show unconserved' format option + is enabled. +
+ Cannot specify chain code when entering + specific PDB id for sequence +
+ File->Export->.. as doesn't work when + 'Export hidden sequences' is enabled, but 'export hidden + columns' is disabled. +
+ Best Quality option in structure chooser + selects lowest rather than highest resolution structures + for each sequence +
+ Incorrect start and end reported for PDB + to sequence mapping in 'View Mappings' report +
+ Unable to read old Jalview projects that + contain non-XML data added after Jalvew wrote project. +
+ Newly created annotation row reorders + 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. +

Applet

Incorrect columns are selected when hidden columns present before start of sequence
+ Incorrect columns are selected when + hidden columns present before start of sequence +
+ Missing dependencies on applet pages + (JSON jars) +
+ Overview pixel size changes when + sequences are hidden in applet +
+ Updated instructions for applet + deployment on examples pages. +

@@ -165,13 +1748,19 @@

Updated Spanish translations of localized text for 2.9

Application -

Signed OSX InstallAnywhere installer
Support for per-sequence based annotations in BioJSON

Applet

Split frame example added to applet examples page

Build and Deployment

+ New ant target for running Jalview's test + suite +

@@ -559,10 +2148,10 @@

Deployment and Documentation +

+ General +

+ --> Deployment and Documentation

2G and 1G options in launchApp have no effect on memory allocation

Certum

Jalview SRS links replaced by UniProt and EBI-search -
Jalview SRS links replaced by UniProt and EBI-search
Output in Stockholm format
Allow import of data from gzipped files
Export/import group and sequence associated line @@ -1400,7 +2988,6 @@
- URL links generated from description line for regular-expression based URL links (applet and application) -
- Non-positional feature URL links are shown in link menu
- Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
- Group-associated consensus, sequence logos and conservation plots
- Symbol distributions for each column can be exported @@ -1444,7 +3031,8 @@ between different screens.
- New preference items for sequence ID tooltip and consensus annotation
- Client to submit sequences and IDs to Envision2 Workflows
- Client to submit sequences and IDs to Envision2 + Workflows
- Vamsas Capabilities
  - Improved VAMSAS synchronization (Jalview archive @@ -1852,7 +3440,6 @@
  - Cancel button for DAS Feature Fetching
  - PCA and PDB Viewers zoom via mouse roller
  - User-defined sub-tree colours and sub-tree selection -
  - 'New Window' button on the 'Output to Text box'
  @@ -1867,7 +3454,6 @@
- Fixed Remove Empty Columns Bug (empty columns at end of alignment)
- Slowed DAS Feature Fetching for increased robustness. -
- Made angle brackets in ASCII feature descriptions display correctly @@ -1879,7 +3465,6 @@
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box. -