Release History

Release	New Features	Issues Resolved
2.11 14/05/2019 (final due date !)	Annotate nucleotide alignments from VCF data files Optional automatic backups when saving Jalview project or alignment files Principal Components Analysis and Viewer state is saved in Jalview Project The 'Change parameters' option has also been removed from the PCA viewer New 'Colour by Sequence ID' (subgroup) option Alternative genetic code tables supported for 'Translate as cDNA' Finder panel remembers last position in each view More efficient creation of selections and multiple groups when working with large alignments Speedier import of annotation rows when parsing stockholm files Update of Ensembl Rest Client to API v10.0 Sequence features can be filtered and shaded according to any associated attributes (e.g. variant attributes from VCF file, or key-value pairs imported from column 9 of GFF file) Show synonymous codon variants on peptide sequences Popup report of a selected sequence feature's details More efficient sequence feature render algorithm (Z-sort/transparency and filter aware) Alignment Overview now by default shows only visible region of alignment (this can be changed in user preferences) File Chooser stays open after Cancel overwrite Better popup menu behaviour when all sequences are hidden Status bar shows bounds when dragging a selection region, and gap count when inserting or deleting gaps Status bar updates over sequence and annotation labels Show annotation tooltips and popup menus in wrapped mode Can select columns by dragging left/right in annotations Improved tooltips in Feature Settings dialog Help button on Uniprot and PDB search panels Cursor changes over draggable box in Overview panel Overview panel default changed to not show hidden regions Consistent ordering of links in sequence id popup menu Sequence Details report opens positioned to top of report Scale panel popup menu allows Hide selected columns adjacent to a hidden column marker Can use shift + arrow keys to rotate PCA image incrementally PCA depth cueing with graduated colours Deprecations DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop Release Processes Atlassian Bamboo continuous integration server for unattended Test Suite execution Memory test suite to detect leaks in common operations IntervalStoreJ (new updatable NCList implementation) used for Sequence Feature collections Castor library for XML marshalling and unmarshalling has been replaced by JAXB for Jalview projects and XML based data retrieval clients	Timeouts when retrieving data from Ensembl 'View [Structure] Mappings' and structure superposition in Jmol fail on Windows Text misaligned in EPS or SVG image export with monospaced font Warning of 'Duplicate entry' when saving Jalview project involving multiple views Overview for complementary view in a linked CDS/Protein alignment is not updated when Hide Columns by Annotation dialog hides columns Selection highlighting in the complement of a CDS/Protein alignment stops working after making a selection in one view, then making another selection in the other view Annotations tooltip changes beyond visible columns Table Columns could be re-ordered in Feature Settings and Jalview Preferences panels Jalview hangs when closing windows or the overview updates with large alignments Tree and PCA calculation fails for selected region if columns were selected by dragging right-to-left and the mouse moved to the left of the first column Error message for trying to load in invalid URLs doesn't tell users the invalid URL Nonpositional features lose feature group on export as Jalview features file Blank extra columns drawn or printed when columns are hidden Regular expression error for '(' in Select Columns by Annotation description Scroll doesn't stop on mouse up after dragging out of Scale or Annotation Panel Column selection incorrect after scrolling out of scale panel Left/right drag in annotation can scroll alignment down Error if mouse moved before clicking Reveal in scale panel Column display is out by one after Page Down, Page Up in wrapped mode Finder doesn't skip hidden regions Finder searches in minimised alignments 'Apply Colour to All Groups' not always selected on opening an alignment 'Colour by Annotation' not marked selected in Colour menu Per-group Clustal colour scheme changes when different groups in the alignment are selected Internationalised colour scheme names not shown correctly in menu Colour by Annotation can go black at min/max threshold limit Value input for graduated feature colour threshold gets 'unrounded' PCA image export doesn't respect background colour PCA points don't dim when rotated about y axis PCA Print dialog continues after Cancel Cancel in Tree Font dialog resets alignment, not Tree font Associate Tree with All Views not restored from project file Scrolling of split frame is sluggish if Overview shown in complementary view stop_gained variants not shown correctly on peptide sequence Help page can be opened twice Editing Start and End should be updated when sequence data at beginning or end of alignment added/removed via 'Edit' sequence Delete/Cut selection doesn't relocate sequence features correctly when start of sequence is removed (Known defect since 2.10) New Known Defects Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project Alignment panel height can be too small after 'New View' Display is incorrect after removing gapped columns within hidden columns
2.10.5 10/09/2018	Default memory for Jalview webstart and InstallAnywhere increased to 1G. Hidden sequence markers and representative sequence bolding included when exporting alignment as EPS, SVG, PNG or HTML. Display is configured via the Format menu, or for command-line use via a jalview properties file. Ensembl client updated to Version 7 REST API and sequence data now imported as JSON. Change in recommended way of starting Jalview via a Java command line: add jars in lib directory to CLASSPATH, rather than via the deprecated java.ext.dirs property. Development Support added to execute test suite instrumented with Open Clover	Poorly scaled bar in quality annotation row shown in Feredoxin Structure alignment view of example alignment. Annotation obscures sequences if lots of annotation displayed. Group conservation/consensus not shown for newly created group when 'Apply to all groups' selected Corrupted display when switching to wrapped mode when sequence panel's vertical scrollbar is visible. Alignment is black in exported EPS file when sequences are selected in exported view. Groups with different coloured borders aren't rendered with correct colour. Jalview could hang when importing certain types of knotted RNA secondary structure. Sequence highlight and selection in trimmed VARNA 2D structure is incorrect for sequences that do not start at 1. '.' inserted into RNA secondary structure annotation when columns are inserted into an alignment, and when exporting as Stockholm flatfile. Jalview annotation rows containing upper and lower-case 'E' and 'H' do not automatically get treated as RNA secondary structure. .jvp should be used as default extension (not .jar) when saving a jalview project file. Mac Users: closing a window correctly transfers focus to previous window on OSX Java 10 Issues Resolved OSX - Can't save new files via the File or export menus by typing in a name into the Save dialog box. Jalview now uses patched version of the VAqua5 'look and feel' which has improved compatibility with the latest version of OSX.
2.10.4b1 7/06/2018	Use HGVS nomenclature for variant annotation retrieved from Uniprot Windows File Shortcuts can be dragged onto the Jalview Desktop	Cannot import features with multiple variant elements (blocks import of some Uniprot records) Clustal files with sequence positions in right-hand column parsed correctly Wrap view - export to SVG - IDs shown but not alignment area in exported graphic F2/Keyboard mode edits work when Overview window has input focus Annotation panel set too high when annotation added to view (Windows) Jalview Desktop is slow to start up when network connectivity is poor Drag URL from chrome, firefox, IE to Jalview desktop on Windows doesn't open file Dragging the currently open URL and links from a page viewed in Firefox or Chrome on Windows is now fully supported. If you are using Edge, only links in the page can be dragged, and with Internet Explorer, only the currently open URL in the browser can be dropped onto Jalview.
2.10.4 10/05/2018	New Structure Chooser control for disabling automatic superposition of multiple structures and open structures in existing views Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them. Jalview uses HTTPS for Uniprot, Xfam and Ensembl services Improved performance for large alignments and lots of hidden columns Improved performance when rendering lots of features (particularly when transparency is disabled)	Structure and Overview aren't updated when Colour By Annotation threshold slider is adjusted Slow redraw when Overview panel shown overlapping alignment panel Overview doesn't show end of unpadded sequence as gaps Cross-reference handling improved: CDS not handled correctly if transcript has no UTR Secondary structure and temperature factor annotation not added to sequence when local PDB file associated with it by drag'n'drop or structure chooser Answering 'No' to PDB Autoassociate dialog doesn't import PDB files dropped on an alignment Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+. Tooltip shouldn't be displayed for empty columns in annotation row Preferences panel's ID Width control is not honored in batch mode Linked sequence highlighting doesn't work for structures added to existing Jmol view 'View Mappings' includes duplicate entries after importing project with multiple views Viewing or annotating Uniprot protein sequences via SIFTS from associated PDB entries with negative residue numbers or missing residues fails Exception when shading sequence with negative Temperature Factor values from annotated PDB files (e.g. as generated by CONSURF) Uniprot 'sequence variant' features tooltip doesn't include a text description of mutation Invert displayed features very slow when structure and/or overview windows are also shown Selecting columns from highlighted regions very slow for alignments with large numbers of sequences Copy Consensus fails for group consensus with 'StringIndexOutOfBounds' VAqua(4) provided as fallback Look and Feel for OSX platforms running Java 10 Adding a structure to existing structure view appears to do nothing because the view is hidden behind the alignment view Applet Copy consensus sequence option in applet should copy the group consensus when popup is opened on it Batch Mode Fixed ID width preference is not respected New Known Defects Exceptions occasionally raised when editing a large alignment and overview is displayed 'Overview updating' progress bar is shown repeatedly after a series of edits even when the overview is no longer reflecting updates 'SIFTS Mapping Error' when viewing structures for protein subsequence (if 'Trim Retrieved Sequences' enabled) or Ensembl isoforms (Workaround in 2.10.4 is to fail back to N&W mapping)
2.10.3b1 24/1/2018	Updated Certum Codesigning Certificate (Valid till 30th November 2018)	Desktop Only one structure is loaded when several sequences and structures are selected for viewing/superposing 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 Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns User preference for disabling inclusion of sequence limits when exporting as flat file has no effect Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes
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 SIFTS 'Not_Observed' residues mapped to non-existant coordindate data
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 06/10/2016	General 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 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.	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 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 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 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.
2.9.0b2 16/10/2015	General Time stamps for signed Jalview application and applet jars	Application Duplicate group consensus and conservation rows shown when tree is partitioned Erratic behaviour when tree partitions made with multiple cDNA/Protein split views
2.9.0b1 8/10/2015	General 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	General Mapping of cDNA to protein in split frames incorrect when sequence start > 1 Broken images in filter column by annotation dialog documentation Feature colours not parsed from features file Exceptions and incomplete link URLs recovered when loading a features file containing HTML tags in feature description Application Annotations corrupted after BioJS export and reimport Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences' Incorrect warning about deleting all data when deleting selected columns Patch to build system for shipping properly signed JNLP templates for webstart launch EMBL-PDBe fetcher/viewer dialogs do not offer unreleased structures for download or viewing Tab/space/return keystroke operation of EMBL-PDBe fetcher/viewer dialogs works correctly Disabled 'minimise' button on Jalview windows running on OSX to workaround redraw hang bug Split cDNA/Protein view position and geometry not recovered from jalview project Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view Restoring of Clustal, RNA Helices and T-Coffee color schemes from BioJSON Applet Reorder sequences mirrored in cDNA/Protein split frame Applet with Jmol examples not loading correctly
2.9 10/9/2015	General Linked visualisation and analysis of DNA and Protein alignments: Translated cDNA alignments shown as split protein and DNA alignment views Codon consensus annotation for linked protein and cDNA alignment views Link cDNA or Protein product sequences by loading them onto Protein or cDNA alignments Reconstruct linked cDNA alignment from aligned protein sequences Jmol integration updated to Jmol v14.2.14 Import and export of Jalview alignment views as BioJSON New alignment annotation file statements for reference sequences and marking hidden columns Reference sequence based alignment shading to highlight variation Select or hide columns according to alignment annotation Find option for locating sequences by description Conserved physicochemical properties shown in amino acid conservation row Alignments can be sorted by number of RNA helices Application New cDNA/Protein analysis capabilities Get Cross-References should open a Split Frame view with cDNA/Protein Detect when nucleotide sequences and protein sequences are placed in the same alignment Split cDNA/Protein views are saved in Jalview projects Use REST API to talk to Chimera Selected regions in Chimera are highlighted in linked Jalview windows VARNA RNA viewer updated to v3.93 VARNA views are saved in Jalview Projects Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA Make groups for selection uses marked columns as well as the active selected region Calculate UPGMA and NJ trees using sequence feature similarity New Export options New Export Settings dialog to control hidden region export in flat file generation Export alignment views for display with the BioJS MSAViewer Export scrollable SVG in HTML page Optional embedding of BioJSON data when exporting alignment figures to HTML 3D structure retrieval and display Free text and structured queries with the PDBe Search API PDBe Search API based discovery and selection of PDB structures for a sequence set JPred4 employed for protein secondary structure predictions Hide Insertions menu option to hide unaligned columns for one or a group of sequences Automatically hide insertions in alignments imported from the JPred4 web server (Nearly) Native 'Quaqua' dialogs for browsing file system on OSX LGPL libraries courtesy of http://www.randelshofer.ch/quaqua/ changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure' change "View protein structure" menu option to "3D Structure ..." Applet New layout for applet example pages New parameters to enable SplitFrame view (file2,enableSplitFrame, scaleProteinAsCdna) New example demonstrating linked viewing of cDNA and Protein alignments Development and deployment Java 1.7 minimum requirement for Jalview 2.9 Include installation type and git revision in build properties and console log output Jalview Github organisation, and new github site for storing BioJsMSA Templates Jalview's unit tests now managed with TestNG	Application Escape should close any open find dialogs Typo in select-by-features status report Consensus RNA secondary secondary structure predictions are not highlighted in amber Missing gap character in v2.7 example file means alignment appears unaligned when pad-gaps is not enabled First switch to RNA Helices colouring doesn't colour associated structure views ID width preference option is greyed out when auto width checkbox not enabled Stopped a warning dialog from being shown when creating user defined colours 'View Mapping' in structure viewer shows sequence mappings for just that viewer's sequences Workaround for superposing PDB files containing multiple models in Chimera Report sequence position in status bar when hovering over Jmol structure Cannot output gaps as '.' symbols with Selection -> output to text box Flat file exports of alignments with hidden columns have incorrect sequence start/end 'Aligning' a second chain to a Chimera structure from Jalview fails Colour schemes applied to structure viewers don't work for nucleotide Loading/cut'n'pasting an empty or invalid file leads to a grey/invisible alignment window Exported Jpred annotation from a sequence region imports to different position Space at beginning of sequence feature tooltips shown on some platforms Chimera viewer 'View \| Show Chain' menu is not populated 'New View' fails with a Null Pointer Exception in console if Chimera has been opened Mouseover to Chimera not working Miscellaneous ENA XML feature qualifiers not retrieved NPE in annotation renderer after 'Extract Scores' If two structures in one Chimera window, mouseover of either sequence shows on first structure 'Show annotations' options should not make non-positional annotations visible Subsequence secondary structure annotation not shown in right place after 'view flanking regions' File Save As type unset when current file format is unknown Save as '.jar' option removed for saving Jalview projects Colour by Sequence colouring in Chimera more responsive Cannot 'add reference annotation' for a sequence in several views on same alignment Cannot show linked products for EMBL / ENA records Jalview's tooltip wraps long texts containing no spaces Applet Jmol to JalviewLite mouseover/link not working JalviewLite can't import sequences with ID descriptions containing angle brackets General Cannot export and reimport RNA secondary structure via jalview annotation file Random helix colour palette for colour by annotation with RNA secondary structure Mouseover to cDNA from STOP residue in protein translation doesn't work. hints when using the select by annotation dialog box Jmol alignment incorrect if PDB file has alternate CA positions FontChooser message dialog appears to hang after choosing 1pt font Peptide secondary structure incorrectly imported from annotation file when annotation display text includes 'e' or 'h' Cannot set colour of new feature type whilst creating new feature cDNA translation alignment should not be sequence order dependent 'Show unconserved' doesn't work for lower case sequences Nucleotide ambiguity codes involving R not recognised Deployment and Documentation Applet example pages appear different to the rest of www.jalview.org Application Known issues Incomplete sequence extracted from PDB entry 3a6s Misleading message appears after trying to delete solid column. Jalview icon not shown in dock after InstallAnywhere version launches Fetching EMBL reference for an RNA sequence results fails with a sequence mismatch Corrupted or unreadable alignment display when scrolling alignment to right ArrayIndexOutOfBoundsException thrown when remove empty columns called on alignment with ragged gapped ends auto calculated alignment annotation rows do not get placed above or below non-autocalculated rows Jalview dekstop becomes sluggish at full screen in ultra-high resolution Cannot disable consensus calculation independently of quality and conservation Mouseover highlighting between cDNA and protein can become sluggish with more than one splitframe shown Applet Known Issues Core PDB parsing code requires Jmol Sequence canvas panel goes white when alignment window is being resized
2.8.2 3/12/2014	General Updated Java code signing certificate donated by Certum.PL. Features and annotation preserved when performing pairwise alignment RNA pseudoknot annotation can be imported/exported/displayed 'colour by annotation' can colour by RNA and protein secondary structure Warn user if 'Find' regular expression is invalid (mentioned post-hoc with 2.9 release) Application Extract and display secondary structure for sequences with 3D structures Support for parsing RNAML Annotations menu for layout sort sequence annotation rows by alignment place sequence annotation above/below alignment annotation Output in Stockholm format Internationalisation: improved Spanish (es) translation Structure viewer preferences tab Disorder and Secondary Structure annotation tracks shared between alignments UCSF Chimera launch and linked highlighting from Jalview Show/hide all sequence associated annotation rows for all or current selection disorder and secondary structure predictions available as dataset annotation Per-sequence rna helices colouring Sequence database accessions imported when fetching alignments from Rfam update VARNA version to 3.91 New groovy scripts for exporting aligned positions, conservation values, and calculating sum of pairs scores. Command line argument to set default JABAWS server include installation type in build properties and console log output Updated Jalview project format to preserve dataset annotation	Application Distinguish alignment and sequence associated RNA structure in structure->view->VARNA Raise dialog box if user deletes all sequences in an alignment Pressing F1 results in documentation opening twice Sequence feature tooltip is wrapped Double click on sequence associated annotation selects only first column Redundancy removal doesn't result in unlinked leaves shown in tree Undos after several redundancy removals don't undo properly Hide sequence doesn't hide associated annotation User defined colours dialog box too big to fit on screen and buttons not visible author list isn't updated if already written to Jalview properties Popup menu won't open after retrieving sequence from database File open window for associate PDB doesn't open Left-then-right click on a sequence id opens a browser search window Cannot open sequence feature shading/sort popup menu in feature settings dialog better tooltip placement for some areas of Jalview desktop Allow addition of JABAWS Server which doesn't pass validation Web services parameters dialog box is too large to fit on screen Muscle nucleotide alignment preset obscured by tooltip JABAWS preset submenus don't contain newly defined user preset MSA web services warns user if they were launched with invalid input Jalview cannot contact DAS Registy when running on Java 8 'Superpose with' submenu not shown when new view created Deployment and Documentation 2G and 1G options in launchApp have no effect on memory allocation launchApp service doesn't automatically open www.jalview.org/examples/exampleFile.jar if no file is given InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is available Application Known issues corrupted or unreadable alignment display when scrolling alignment to right retrieval fails but progress bar continues for DAS retrieval with large number of ID flatfile output of visible region has incorrect sequence start/end rna structure consensus doesn't update when secondary structure tracks are rearranged invalid rna structure positional highlighting does not highlight position of invalid base pairs out of memory errors are not raised when saving Jalview project from alignment window file menu Switching to RNA Helices colouring doesn't propagate to structures colour by RNA Helices not enabled when user created annotation added to alignment Jalview icon not shown on dock in Mountain Lion/Webstart Applet Known Issues JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies Jalview and Jmol example not compatible with IE9 Sort by annotation score doesn't reverse order when selected
2.8.1 4/6/2014	General Internationalisation of user interface (usually called i18n support) and translation for Spanish locale Define/Undefine group on current selection with Ctrl-G/Shift Ctrl-G Improved group creation/removal options in alignment/sequence Popup menu Sensible precision for symbol distribution percentages shown in logo tooltip. Annotation panel height set according to amount of annotation when alignment first opened Application Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service Select columns containing particular features from Feature Settings dialog View all 'representative' PDB structures for selected sequences Update Jalview project format: New file extension for Jalview projects '.jvp' Preserve sequence and annotation dataset (to store secondary structure annotation,etc) Per group and alignment annotation and RNA helix colouring New similarity measures for PCA and Tree calculation (PAM250) Experimental support for retrieval and viewing of flanking regions for an alignment	Application logo keeps spinning and status remains at queued or running after job is cancelled cannot export features from alignments imported from Jalview/VAMSAS projects Buggy slider for web service parameters that take float values Newly created RNA secondary structure line doesn't have 'display all symbols' flag set T-COFFEE alignment score shading scheme and other annotation shading not saved in Jalview project Local file cannot be loaded in freshly downloaded Jalview Jalview icon not shown on dock in Mountain Lion/Webstart Load file from desktop file browser fails Occasional NPE thrown when calculating large trees Cannot reorder or slide sequences after dragging an alignment onto desktop Colour by annotation dialog throws NPE after using 'extract scores' function Loading/cut'n'pasting an empty file leads to a grey alignment window Disorder thresholds rendered incorrectly after performing IUPred disorder prediction Multiple group annotated consensus rows shown when changing 'normalise logo' display setting Find shows blank dialog after 'finished searching' if nothing matches query Null Pointer Exceptions raised when sorting by feature with lots of groups Errors in Jmol console when structures in alignment don't overlap Not all working JABAWS services are shown in Jalview's menu JAVAWS version of Jalview fails to launch with 'invalid literal/length code' Annotation/RNA Helix colourschemes cannot be applied to alignment with groups (actually fixed in 2.8.0b1) RNA Helices and T-Coffee Scores available as default colourscheme Applet Remove group option is shown even when selection is not a group Apply to all groups ticked but colourscheme changes don't affect groups Documented RNA Helices and T-Coffee Scores as valid colourscheme name Annotation labels drawn on sequence IDs when Annotation panel is not displayed Increased font size for dropdown menus on OSX and embedded windows Other Consensus sequence for alignments/groups with a single sequence were not calculated annotation files that contain only groups imported as annotation and junk sequences Fasta files with sequences containing '*' incorrectly recognised as PFAM or BLC conservation/PID slider apply all groups option doesn't affect background (2.8.0b1) redundancy highlighting is erratic at 0% and 100% Remove gapped columns fails for sequences with ragged trailing gaps AMSA annotation row with leading spaces is not registered correctly on import Jalview crashes when selecting PCA analysis for certain alignments Opening the colour by annotation dialog for an existing annotation based 'use original colours' colourscheme loses original colours setting
2.8.0b1 30/1/2014	Trusted certificates for JalviewLite applet and Jalview Desktop application Certificate was donated by Certum to the Jalview open source project). 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 graph thresholds Nucleotide substitution matrix that supports RNA and ambiguity codes Allow disorder predictions to be made on the current selection (or visible selection) in the same way that JPred works Groovy scripting for headless Jalview operation Other improvements Upgrade desktop installer to InstallAnywhere 2013 COMBINE statement uses current SEQUENCE_REF and GROUP_REF scope to group annotation rows Support '' style escaping of quotes in Newick files Group options for JABAWS service by command line name Empty tooltip shown for JABA service options with a link but no description Select primary source when selecting authority in database fetcher GUI Add .mfa to FASTA file extensions recognised by Jalview Annotation label tooltip text wrap	Slow scrolling when lots of annotation rows are displayed Lots of NPE (and slowness) after creating RNA secondary structure annotation line Sequence database accessions not imported when fetching alignments from Rfam Incorrect SHMR submission for sequences with identical IDs View all structures does not always superpose structures Option widgets in service parameters not updated to reflect user or preset settings Null pointer exceptions for some services without presets or adjustable parameters Discover PDB IDs entry in structure menu doesn't discover PDB xRefs Exception encountered while trying to retrieve features with DAS Lowest value in annotation row isn't coloured when colour by annotation (per sequence) is coloured Keyboard mode P jumps to start of gapped region when residue follows a gap Jalview appears to hang importing an alignment with Wrap as default or after enabling Wrap 'Right click to add annotations' message shown in wrap mode when no annotations present Disorder predictions fail with NPE if no automatic annotation already exists on alignment oninit javascript function should be called after initialisation completes Remove redundancy after disorder prediction corrupts alignment window display Example annotation file in documentation is invalid Grouped line graph annotation rows are not exported to annotation file Multi-harmony analysis cannot be run when only two groups created Cannot create multiple groups of line graphs with several 'combine' statements in annotation file Pressing return several times causes Number Format exceptions in keyboard mode Multi-harmony (SHMMR) method doesn't submit correct partitions for input data Translation from DNA to Amino Acids fails Jalview fail to load newick tree with quoted label --headless flag isn't understood ClassCastException when generating EPS in headless mode Adjusting sequence-associated shading threshold only changes one row's threshold Preferences and Feature settings panel panel doesn't open hide consensus histogram also hides conservation and quality histograms
2.8 12/11/2012	Application Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega) JABAWS server status indicator in Web Services preferences VARNA (http://varna.lri.fr) viewer for RNA structures in Jalview alignment window Updated Jalview build and deploy framework for OSX mountain lion, windows 7, and 8 Nucleotide substitution matrix for PCA that supports RNA and ambiguity codes Improved sequence database retrieval GUI Support fetching and database reference look up against multiple DAS sources (Fetch all from in 'fetch db refs') Jalview project improvements Store and retrieve the 'belowAlignment' flag for annotation calcId attribute to group annotation rows on the alignment Store AACon calculation settings for a view in Jalview project horizontal scrolling gesture support Visual progress indicator when PCA calculation is running Simpler JABA web services menus visual indication that web service results are still being retrieved from server Serialise the dialogs that are shown when Jalview starts up for first time Jalview user agent string for interacting with HTTP services DAS 1.6 and DAS 2.0 source support using new JDAS client library Examples directory and Groovy library included in InstallAnywhere distribution Applet RNA alignment and secondary structure annotation visualization applet example General Normalise option for consensus sequence logo Reset button in PCA window to return dimensions to defaults Allow seqspace or Jalview variant of alignment PCA calculation PCA with either nucleic acid and protein substitution matrices Allow windows containing HTML reports to be exported in HTML Interactive display and editing of RNA secondary structure contacts RNA Helix Alignment Colouring RNA base pair logo consensus Parse sequence associated secondary structure information in Stockholm files HTML Export database accessions and annotation information presented in tooltip for sequences Import secondary structure from LOCARNA clustalw style RNA alignment files import and visualise T-COFFEE quality scores for an alignment 'colour by annotation' per sequence option to shade each sequence according to its associated alignment annotation New Jalview Logo Documentation and Development documentation for score matrices used in Jalview New Website!	Application PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch REST service Stop windows being moved outside desktop on OSX Filetype associations not installed for webstart launch Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete revise SHMR RSBS definition to ensure alignment is uploaded via ali_file parameter Jalview 2.7 is incompatible with Jmol-12.2.2 View all structures superposed fails with exception Jnet job queues forever if a very short sequence is submitted for prediction Cut and paste menu not opened when mouse clicked on desktop window Putting fractional value into integer text box in alignment parameter dialog causes Jalview to hang Structure view highlighting doesn't work on windows 7 View all structures fails with exception shown in structure view Characters in filename associated with PDBEntry not escaped in a platform independent way Jalview desktop fails to launch with exception when using proxy Tree calculation reports 'you must have 2 or more sequences selected' when selection is empty Jalview desktop fails to launch with jar signature failure when java web start temporary file caching is disabled DAS Sequence retrieval with range qualification results in sequence xref which includes range qualification Errors during processing of command line arguments cause progress bar (JAL-898) to be removed Replace comma for semi-colon option not disabled for DAS sources in sequence fetcher Cannot close news reader when JABAWS server warning dialog is shown Option widgets not updated to reflect user settings Edited sequence not submitted to web service Jalview 2.7 Webstart does not launch on mountain lion InstallAnywhere installer doesn't unpack and run on OSX Mountain Lion Annotation panel not given a scroll bar when sequences with alignment annotation are pasted into the alignment Sequence associated annotation rows not associated when loaded from Jalview project Browser launch fails with NPE on java 1.7 JABAWS alignment marked as finished when job was cancelled or job failed due to invalid input NPE with v2.7 example when clicking on Tree associated with all views Exceptions when copy/paste sequences with grouped annotation rows to new window Applet Sequence features are momentarily displayed before they are hidden using hidefeaturegroups applet parameter loading features via javascript API automatically enables feature display scrollToColumnIn javascript API method doesn't work General Redundancy removal fails for rna alignment PCA calculation fails when sequence has been selected and then deselected PCA window shows grey box when first opened on OSX Letters coloured pink in sequence logo when alignment coloured with clustalx Choosing fonts without letter symbols defined causes exceptions and redraw errors Initial PCA plot view is not same as manually reconfigured view Grouped annotation graph label has incorrect line colour Grouped annotation graph label display is corrupted for lots of labels
2.7 27/09/2011	Application Jalview Desktop News Reader Tweaked default layout of web services menu View/alignment association menu to enable user to easily specify which alignment a multi-structure view takes its colours/correspondences from Allow properties file location to be specified as URL Extend Jalview project to preserve associations between many alignment views and a single Jmol display Store annotation row height in Jalview project file Annotation row column label formatting attributes stored in project file Annotation row order for auto-calculated annotation rows preserved in Jalview project file Visual progress indication when Jalview state is saved using Desktop window menu Visual indication that command line arguments are still being processed Groovy script execution from URL Colour by annotation default min and max colours in preferences Automatically associate PDB files dragged onto an alignment with sequences that have high similarity and matching IDs Update JGoogleAnalytics to latest release (0.3) 'view structures' option to open many structures in same window Sort associated views menu option for tree panel Group all JABA and non-JABA services for a particular analysis function in its own submenu Applet Userdefined and autogenerated annotation rows for groups Adjustment of alignment annotation pane height Annotation scrollbar for annotation panel Drag to reorder annotation rows in annotation panel 'automaticScrolling' parameter Allow sequences with partial ID string matches to be annotated from GFF/Jalview features files Sequence logo annotation row in applet Absolute paths relative to host server in applet parameters are treated as such New in the JalviewLite javascript API: JalviewLite.js javascript library Javascript callbacks for Applet initialisation Sequence/alignment mouse-overs and selections scrollTo row and column alignment scrolling functions Select sequence/alignment regions from javascript javascript structure viewer harness to pass messages between Jmol and Jalview when running as distinct applets sortBy method Set of applet and application examples shipped with documentation New example to demonstrate JalviewLite and Jmol javascript message exchange General Enable Jmol displays to be associated with multiple multiple alignments Option to automatically sort alignment with new tree User configurable link to enable redirects to a www.Jalview.org mirror Jmol colours option for Jmol displays Configurable newline string when writing alignment and other flat files Allow alignment annotation description lines to contain html tags Documentation and Development Add groovy test harness for bulk load testing to examples Groovy script to load and align a set of sequences using a web service before displaying the result in the Jalview desktop Restructured javascript and applet api documentation Ant target to publish example html files with applet archive Netbeans project for building Jalview from source ant task to create online javadoc for Jalview source	Application User defined colourscheme throws exception when current built in colourscheme is saved as new scheme AlignFrame->Save in application pops up save dialog for valid filename/format Cannot view associated structure for UniProt sequence PDB file association breaks for UniProt sequence P37173 Associate PDB from file dialog does not tell you which sequence is to be associated with the file Find All raises null pointer exception when query only matches sequence IDs Pre 2.6 Jalview project cannot be loaded into v2.6 Jalview project with Jmol views created with Jalview 2.4 cannot be loaded Filetype associations not installed for webstart launch Two or more chains in a single PDB file associated with sequences in different alignments do not get coloured by their associated sequence Visibility status of autocalculated annotation row not preserved when project is loaded Annotation row height and visibility attributes not stored in Jalview project Tree bootstraps are not preserved when saved as a Jalview project Envision2 workflow tooltips are corrupted Enabling show group conservation also enables colour by conservation Duplicate group associated conservation or consensus created on new view Annotation scrollbar not displayed after 'show all hidden annotation rows' option selected Alignment quality not updated after alignment annotation row is hidden then shown Preserve colouring of structures coloured by sequences in pre Jalview 2.7 projects Web service job parameter dialog is not laid out properly Web services menu not refreshed after 'reset services' button is pressed in preferences Annotation off by one in Jalview v2_3 example project Structures imported from file and saved in project get name like jalview_pdb1234.txt when reloaded Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete Applet Alignment height set incorrectly when lots of annotation rows are displayed Relative URLs in feature HTML text not resolved to codebase View follows highlighting does not work for positions in sequences <= shown as = in tooltip Export features raises exception when no features exist Separator string used for serialising lists of IDs for javascript api is modified when separator string provided as parameter Null pointer exception when selecting tree leaves for alignment with no existing selection Relative URLs for datasources assumed to be relative to applet's codebase Status bar not updated after finished searching and search wraps around to first result StructureSelectionManager instance shared between several Jalview applets causes race conditions and memory leaks Hover tooltip and mouseover of position on structure not sent from Jmol in applet Certain sequences of javascript method calls to applet API fatally hang browser General View follows structure mouseover scrolls beyond position with wrapped view and hidden regions Find sequence position moves to wrong residue with/without hidden columns Sequence length given in alignment properties window is off by 1 InvalidNumberFormat exceptions thrown when trying to import PDB like structure files Positional search results are only highlighted between user-supplied sequence start/end bounds End attribute of sequence is not validated Find dialog only finds first sequence containing a given sequence position Sequence numbering not preserved in MSF alignment output Jalview PDB file reader does not extract sequence from nucleotide chains correctly Structure colours not updated when tree partition changed in alignment Sequence associated secondary structure not correctly parsed in interleaved stockholm Colour by annotation dialog does not restore current state Hiding (nearly) all sequences doesn't work properly Sequences containing lowercase letters are not properly associated with their pdb files Documentation and Development schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright tool
2.6.1 15/11/2010	Application New warning dialog when the Jalview Desktop cannot contact web services JABA service parameters for a preset are shown in service job window JABA Service menu entries reworded	Modeller PIR IO broken - cannot correctly import a pir file emitted by Jalview Existing feature settings transferred to new alignment view created from cut'n'paste Improved test for mixed amino/nucleotide chains when parsing PDB files Consensus and conservation annotation rows occasionally become blank for all new windows Exception raised when right clicking above sequences in wrapped view mode Application multiple multiply aligned structure views cause cpu usage to hit 100% and computer to hang Web Service parameter layout breaks for long user parameter names Jaba service discovery hangs desktop if Jaba server is down
2.6 26/9/2010	Application Support for Java bioinformatics analysis web services (JABAWS) Web Services preference tab Analysis parameters dialog box and user defined preferences Improved speed and layout of Envision2 service menu Superpose structures using associated sequence alignment Export coordinates and projection as CSV from PCA viewer Applet enable javascript: execution by the applet via the link out mechanism Other Updated the Jmol Jalview interface to work with Jmol series 12 The Jalview Desktop and JalviewLite applet now require Java 1.5 Allow Jalview feature colour specification for GFF sequence annotation files New 'colour by label' keword in Jalview feature file type colour specification New Jalview Desktop Groovy API method that allows a script to check if it being run in an interactive session or in a batch operation from the Jalview command line	clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column Application typo in AlignmentFrame->View->Hide->all but selected Regions menu item sequence fetcher replaces ',' for ';' when the ',' is part of a valid accession ID fatal OOM if object retrieved by sequence fetcher runs out of memory unhandled Out of Memory Error when viewing pca analysis results InstallAnywhere builds fail to launch on OS X java 10.5 update 4 (due to apple Java 1.6 update) Installanywhere Jalview silently fails to launch Applet Jalview.getFeatureGroups() raises an ArrayIndexOutOfBoundsException if no feature groups are defined.
2.5.1 14/6/2010		Alignment prettyprinter doesn't cope with long sequence IDs clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column nucleic acid structures retrieved from PDB do not import correctly More columns get selected than were clicked on when a number of columns are hidden annotation label popup menu not providing correct add/hide/show options when rows are hidden or none are present Stockholm format shown in list of readable formats, and parser copes better with alignments from RFAM. CSV output of consensus only includes the percentage of all symbols if sequence logo display is enabled Applet annotation panel disappears when annotation is hidden/removed Application Alignment view not redrawn properly when new alignment opened where annotation panel is visible but no annotations are present on alignment pasted region containing hidden columns is incorrectly displayed in new alignment window Jalview slow to complete operations when stdout is flooded (fix is to close the Jalview console) typo in AlignmentFrame->View->Hide->all but selected Rregions menu item. inconsistent group submenu and Format submenu entry 'Un' or 'Non'conserved Sequence feature settings are being shared by multiple distinct alignments group annotation not recreated when tree partition is changed double click on group annotation to select sequences does not propagate to associated trees Mac OSX specific issues: exception raised when mouse clicked on desktop window background Desktop menu placed on menu bar and application name set correctly sequence feature settings not wide enough for the save feature colourscheme button
2.5 30/4/2010	New Capabilities 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 Linked viewing of nucleic acid sequences and structures Automatic Scrolling option in View menu to display the currently highlighted region of an alignment. Order an alignment by sequence length, or using the average score or total feature count for each sequence. Shading features by score or associated description Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection). New hide/show options including Shift+Control+H to hide everything but the currently selected region. Application Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources Local DAS Sequence sources can be added via the command line or via the Add local source dialog box. DAS Dbref and DbxRef feature types are parsed as database references and protein_name is parsed as description line (BioSapiens terms). 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 and visualized as sequence logos Optionally scale multi-character column labels to fit within each column of annotation row Optional automatic sort of associated alignment view when a new tree is opened. Jalview Java Console Better placement of desktop window when moving between different screens. New preference items for sequence ID tooltip and consensus annotation Client to submit sequences and IDs to Envision2 Workflows Vamsas Capabilities Improved VAMSAS synchronization (Jalview archive used to preserve views, structures, and tree display settings) Import of vamsas documents from disk or URL via command line Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!) Updated API to VAMSAS version 0.2 Applet Middle button resizes annotation row height New Parameters sortByTree (true/false) - automatically sort the associated alignment view by the tree when a new tree is opened. showTreeBootstraps (true/false) - show or hide branch bootstraps (default is to show them if available) showTreeDistances (true/false) - show or hide branch lengths (default is to show them if available) showUnlinkedTreeNodes (true/false) - indicate if unassociated nodes should be highlighted in the tree view heightScale and widthScale (1.0 or more) - increase the height or width of a cell in the alignment grid relative to the current font size. Non-positional features displayed in sequence ID tooltip Other Features format: graduated colour definitions and specification of feature scores Alignment Annotations format: new keywords for group associated annotation (GROUP_REF) and annotation row display properties (ROW_PROPERTIES) XML formats extended to support graduated feature colourschemes, group associated annotation, and profile visualization settings.	Source field in GFF files parsed as feature source rather than description Non-positional features are now included in sequence feature and gff files (controlled via non-positional feature visibility in tooltip). URL links generated for all feature links (bugfix) Added URL embedding instructions to features file documentation. Codons containing ambiguous nucleotides translated as 'X' in peptide product Match case switch in find dialog box works for both sequence ID and sequence string and query strings do not have to be in upper case to match case-insensitively. AMSA files only contain first column of multi-character column annotation labels Jalview Annotation File generation/parsing consistent with documentation (e.g. Stockholm annotation can be exported and re-imported) PDB files without embedded PDB IDs given a friendly name Find incrementally searches ID string matches as well as subsequence matches, and correctly reports total number of both. Application: Better handling of exceptions during sequence retrieval Dasobert generated non-positional feature URL link text excludes the start_end suffix DAS feature and source retrieval buttons disabled when fetch or registry operations in progress. PDB files retrieved from URLs are cached properly Sequence description lines properly shared via VAMSAS Sequence fetcher fetches multiple records for all data sources Ensured that command line das feature retrieval completes before alignment figures are generated. Reduced time taken when opening file browser for first time. isAligned check prior to calculating tree, PCA or submitting an MSA to JNet now excludes hidden sequences. User defined group colours properly recovered from Jalview projects.
2.4.0.b2 28/10/2009	Experimental support for google analytics usage tracking. Jalview privacy settings (user preferences and docs).	Race condition in applet preventing startup in jre1.6.0u12+. Exception when feature created from selection beyond length of sequence. Allow synthetic PDB files to be imported gracefully Sequence associated annotation rows associate with all sequences with a given id Find function matches case-insensitively for sequence ID string searches Non-standard characters do not cause pairwise alignment to fail with exception Application Issues Sequences are now validated against EMBL database Sequence fetcher fetches multiple records for all data sources InstallAnywhere Issues Dock icon works for Mac OS X java (Mac 1.6 update issue with installAnywhere mechanism) Command line launching of JARs from InstallAnywhere version (java class versioning error fixed)
2.4 27/8/2008	User Interface Linked highlighting of codon and amino acid from translation and protein products Linked highlighting of structure associated with residue mapping to codon position Sequence Fetcher provides example accession numbers and 'clear' button MemoryMonitor added as an option under Desktop's Tools menu Extract score function to parse whitespace separated numeric data in description line Column labels in alignment annotation can be centred. Tooltip for sequence associated annotation give name of sequence Web Services and URL fetching JPred3 web service Prototype sequence search client (no public services available yet) Fetch either seed alignment or full alignment from PFAM URL Links created for matching database cross references as well as sequence ID URL Links can be created using regular-expressions Sequence Database Connectivity Retrieval of cross-referenced sequences from other databases Generalised database reference retrieval and validation to all fetchable databases Fetch sequences from DAS sources supporting the sequence command Import and Export export annotation rows as CSV for spreadsheet import Jalview projects record alignment dataset associations, EMBL products, and cDNA sequence mappings Sequence Group colour can be specified in Annotation File Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme VAMSAS Client capabilities (Experimental) treenode binding for VAMSAS tree exchange local editing and update of sequences in VAMSAS alignments (experimental) Create new or select existing session to join load and save of vamsas documents Application command line -tree parameter to open trees (introduced for passing from applet) -fetchfrom command line argument to specify nicknames of DAS servers to query for alignment features -dasserver command line argument to add new servers that are also automatically queried for features -groovy command line argument executes a given groovy script after all input data has been loaded and parsed Applet-Application data exchange Trees passed as applet parameters can be passed to application (when using "View in full application") Applet Parameters feature group display control parameter debug parameter showbutton parameter Applet API methods newView public method Window (current view) specific get/set public methods Feature display control methods get list of currently selected sequences New Jalview distribution features InstallAnywhere Installer upgraded to IA 2008 VP1 RELEASE file gives build properties for the latest Jalview release. Java 1.1 Applet build made easier and donotobfuscate property controls execution of obfuscator Build target for generating source distribution Debug flag for javacc .jalview_properties file is documented (slightly) in jalview.bin.Cache Continuous Build Integration for stable and development version of Application, Applet and source distribution	selected region output includes visible annotations (for certain formats) edit label/displaychar contains existing label/char for editing update PDBEntries when DBRefEntries change (vamsas) shorter peptide product names from EMBL records Newick string generator makes compact representations bootstrap values parsed correctly for tree files with comments pathological filechooser bug avoided by not allowing filenames containing a ':' Fixed exception when parsing GFF files containing global sequence features Alignment datasets are finalized only when number of references from alignment sequences goes to zero Close of tree branch colour box without colour selection causes cascading exceptions occasional negative imgwidth exceptions better reporting of non-fatal warnings to user when file parsing fails. Save works when Jalview project is default format Save as dialog opened if current alignment format is not a valid output format UniProt canonical names introduced for both das and vamsas Histidine should be midblue (not pink!) in Zappo error messages passed up and output when data read fails edit undo recovers previous dataset sequence when sequence is edited allow PDB files without pdb ID HEADER lines (like those generated by MODELLER) to be read in properly allow reading of JPred concise files as a normal filetype Stockholm annotation parsing and alignment properties import fixed for PFAM records Structure view windows have correct name in Desktop window list annotation consisting of sequence associated scores can be read and written correctly to annotation file Aligned cDNA translation to aligned peptide works correctly Fixed display of hidden sequence markers and non-italic font for representatives in Applet Applet Menus are always embedded in applet window on Macs. Newly shown features appear at top of stack (in Applet) Annotations added via parameter not drawn properly due to null pointer exceptions Secondary structure lines are drawn starting from first column of alignment UniProt XML import updated for new schema release in July 2008 Sequence feature to sequence ID match for Features file is case-insensitive Sequence features read from Features file appended to all sequences with matching IDs PDB structure coloured correctly for associated views containing a sub-sequence PDB files can be retrieved by applet from Jar files feature and annotation file applet parameters referring to different directories are retrieved correctly Fixed application hang whilst waiting for splash-screen version check to complete Applet properly URLencodes input parameter values when passing them to the launchApp service display name and local features preserved in results retrieved from web service Visual delay indication for sequence retrieval and sequence fetcher initialisation updated Application to use DAS 1.53e version of dasobert DAS client Re-instated Full AMSA support and .amsa file association Fixed parsing of JNet Concise annotation sans sequences
2.3 9/5/07	Jmol 11.0.2 integration PDB views stored in Jalview XML files Slide sequences Edit sequence in place EMBL CDS features DAS Feature mapping Feature ordering Alignment Properties Annotation Scores Sort by scores Feature/annotation editing in applet	Headless state operation in 2.2.1 Incorrect and unstable DNA pairwise alignment Cut and paste of sequences with annotation Feature group display state in XML Feature ordering in XML blc file iteration selection using filename # suffix Stockholm alignment properties Stockhom alignment secondary structure annotation 2.2.1 applet had no feature transparency Number pad keys can be used in cursor mode Structure Viewer mirror image resolved
2.2.1 12/2/07	Non standard characters can be read and displayed Annotations/Features can be imported/exported to the applet via textbox Applet allows editing of sequence/annotation/group name & description Preference setting to display sequence name in italics Annotation file format extended to allow Sequence_groups to be defined Default opening of alignment overview panel can be specified in preferences PDB residue numbering annotation added to associated sequences	Applet crash under certain Linux OS with Java 1.6 installed Annotation file export / import bugs fixed PNG / EPS image output bugs fixed
2.2 27/11/06	Multiple views on alignment Sequence feature editing "Reload" alignment "Save" to current filename Background dependent text colour Right align sequence ids User-defined lower case residue colours Format Menu Select Menu Menu item accelerator keys Control-V pastes to current alignment 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'	New memory efficient Undo/Redo System Optimised symbol lookups and conservation/consensus calculations Region Conservation/Consensus recalculated after edits 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 Re-instated Zoom function for PCA Sequence descriptions conserved in web service analysis results UniProt ID discoverer uses any word separated by ∣ WsDbFetch query/result association resolved Tree leaf to sequence mapping improved Smooth fonts switch moved to FontChooser dialog box.
2.1.1 12/9/06	Copy consensus sequence to clipboard	Image output - rightmost residues are rendered if sequence id panel has been resized Image output - all offscreen group boundaries are rendered Annotation files with sequence references - all elements in file are relative to sequence position Mac Applet users can use Alt key for group editing
2.1 22/8/06	MAFFT Multiple Alignment in default Web Service list DAS Feature fetching Hide sequences and columns Export Annotations and Features GFF file reading / writing Associate structures with sequences from local PDB files Add sequences to exisiting alignment Recently opened files / URL lists Applet can launch the full application Applet has transparency for features (Java 1.2 required) Applet has user defined colours parameter Applet can load sequences from parameter "sequencex"	Redundancy Panel reinstalled in the Applet Monospaced font - EPS / rescaling bug fixed Annotation files with sequence references bug fixed
2.08.1 2/5/06	Change case of selected region from Popup menu Choose to match case when searching Middle mouse button and mouse movement can compress / expand the visible width and height of the alignment	Annotation Panel displays complete JNet results
2.08b 18/4/06		Java 1.5 bug - InternalMessageDialog fix for threads Righthand label on wrapped alignments shows correct value
2.08 10/4/06	Editing can be locked to the selection area Keyboard editing Create sequence features from searches Precalculated annotations can be loaded onto alignments Features file allows grouping of features Annotation Colouring scheme added Smooth fonts off by default - Faster rendering Choose to toggle Autocalculate Consensus On/Off	Drag & Drop fixed on Linux Jalview Archive file faster to load/save, sequence descriptions saved.
2.07 12/12/05	PDB Structure Viewer enhanced Sequence Feature retrieval and display enhanced Choose to output sequence start-end after sequence name for file output Sequence Fetcher WSDBFetch@EBI Applet can read feature files, PDB files and can be used for HTML form input	HTML output writes groups and features Group editing is Control and mouse click File IO bugs
2.06 28/9/05	View annotations in wrapped mode More options for PCA viewer	GUI bugs resolved Runs with -nodisplay from command line
2.05b 15/9/05	Choose EPS export as lineart or text Jar files are executable Can read in Uracil - maps to unknown residue	Known OutOfMemory errors give warning message Overview window calculated more efficiently Several GUI bugs resolved
2.05 30/8/05	Edit and annotate in "Wrapped" view	Several GUI bugs resolved
2.04 24/8/05	Hold down mouse wheel & scroll to change font size	Improved JPred client reliability Improved loading of Jalview files
2.03 18/8/05	Set Proxy server name and port in preferences Multiple URL links from sequence ids User Defined Colours can have a scheme name and added to Colour Menu Choose to ignore gaps in consensus calculation Unix users can set default web browser Runs without GUI for batch processing Dynamically generated Web Service Menus	InstallAnywhere download for Sparc Solaris
2.02 18/7/05		Copy & Paste order of sequences maintains alignment order.
2.01 12/7/05	Use delete key for deleting selection. Use Mouse wheel to scroll sequences. Help file updated to describe how to add alignment annotations. Version and build date written to build properties file. InstallAnywhere installation will check for updates at launch of Jalview.	Delete gaps bug fixed. FileChooser sorts columns. Can remove groups one by one. Filechooser icons installed. Finder ignores return character when searching. Return key will initiate a search.
2.0 20/6/05	New codebase

Release

New Features

Issues Resolved

2.11
14/05/2019 (final due date !)

Annotate nucleotide alignments from VCF data files
Optional automatic backups when saving Jalview project or alignment files
Principal Components Analysis and Viewer state is saved in Jalview Project
The 'Change parameters' option has also been removed from the PCA viewer
New 'Colour by Sequence ID' (subgroup) option
Alternative genetic code tables supported for 'Translate as cDNA'
Finder panel remembers last position in each view
More efficient creation of selections and multiple groups when working with large alignments
Speedier import of annotation rows when parsing stockholm files
Update of Ensembl Rest Client to API v10.0
Sequence features can be filtered and shaded according to any associated attributes (e.g. variant attributes from VCF file, or key-value pairs imported from column 9 of GFF file)
Show synonymous codon variants on peptide sequences
Popup report of a selected sequence feature's details
More efficient sequence feature render algorithm (Z-sort/transparency and filter aware)
Alignment Overview now by default shows only visible region of alignment (this can be changed in user preferences)
File Chooser stays open after Cancel overwrite
Better popup menu behaviour when all sequences are hidden
Status bar shows bounds when dragging a selection region, and gap count when inserting or deleting gaps
Status bar updates over sequence and annotation labels
Show annotation tooltips and popup menus in wrapped mode
Can select columns by dragging left/right in annotations
Improved tooltips in Feature Settings dialog
Help button on Uniprot and PDB search panels
Cursor changes over draggable box in Overview panel
Overview panel default changed to not show hidden regions
Consistent ordering of links in sequence id popup menu
Sequence Details report opens positioned to top of report
Scale panel popup menu allows Hide selected columns adjacent to a hidden column marker
Can use shift + arrow keys to rotate PCA image incrementally
PCA depth cueing with graduated colours

Deprecations

DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop

Release Processes

Atlassian Bamboo continuous integration server for unattended Test Suite execution
Memory test suite to detect leaks in common operations
IntervalStoreJ (new updatable NCList implementation) used for Sequence Feature collections
Castor library for XML marshalling and unmarshalling has been replaced by JAXB for Jalview projects and XML based data retrieval clients

Timeouts when retrieving data from Ensembl
'View [Structure] Mappings' and structure superposition in Jmol fail on Windows
Text misaligned in EPS or SVG image export with monospaced font
Warning of 'Duplicate entry' when saving Jalview project involving multiple views
Overview for complementary view in a linked CDS/Protein alignment is not updated when Hide Columns by Annotation dialog hides columns
Selection highlighting in the complement of a CDS/Protein alignment stops working after making a selection in one view, then making another selection in the other view
Annotations tooltip changes beyond visible columns
Table Columns could be re-ordered in Feature Settings and Jalview Preferences panels
Jalview hangs when closing windows or the overview updates with large alignments
Tree and PCA calculation fails for selected region if columns were selected by dragging right-to-left and the mouse moved to the left of the first column
Error message for trying to load in invalid URLs doesn't tell users the invalid URL
Nonpositional features lose feature group on export as Jalview features file
Blank extra columns drawn or printed when columns are hidden
Regular expression error for '(' in Select Columns by Annotation description
Scroll doesn't stop on mouse up after dragging out of Scale or Annotation Panel
Column selection incorrect after scrolling out of scale panel
Left/right drag in annotation can scroll alignment down
Error if mouse moved before clicking Reveal in scale panel
Column display is out by one after Page Down, Page Up in wrapped mode
Finder doesn't skip hidden regions
Finder searches in minimised alignments
'Apply Colour to All Groups' not always selected on opening an alignment
'Colour by Annotation' not marked selected in Colour menu
Per-group Clustal colour scheme changes when different groups in the alignment are selected
Internationalised colour scheme names not shown correctly in menu
Colour by Annotation can go black at min/max threshold limit
Value input for graduated feature colour threshold gets 'unrounded'
PCA image export doesn't respect background colour
PCA points don't dim when rotated about y axis
PCA Print dialog continues after Cancel
Cancel in Tree Font dialog resets alignment, not Tree font
Associate Tree with All Views not restored from project file
Scrolling of split frame is sluggish if Overview shown in complementary view
stop_gained variants not shown correctly on peptide sequence
Help page can be opened twice

Editing

Start and End should be updated when sequence data at beginning or end of alignment added/removed via 'Edit' sequence
Delete/Cut selection doesn't relocate sequence features correctly when start of sequence is removed (Known defect since 2.10)

New Known Defects

Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
Alignment panel height can be too small after 'New View'
Display is incorrect after removing gapped columns within hidden columns

2.10.5
10/09/2018

Default memory for Jalview webstart and InstallAnywhere increased to 1G.
Hidden sequence markers and representative sequence bolding included when exporting alignment as EPS, SVG, PNG or HTML. Display is configured via the Format menu, or for command-line use via a jalview properties file.
Ensembl client updated to Version 7 REST API and sequence data now imported as JSON.
Change in recommended way of starting Jalview via a Java command line: add jars in lib directory to CLASSPATH, rather than via the deprecated java.ext.dirs property.

Development

Support added to execute test suite instrumented with Open Clover

Poorly scaled bar in quality annotation row shown in Feredoxin Structure alignment view of example alignment.
Annotation obscures sequences if lots of annotation displayed.
Group conservation/consensus not shown for newly created group when 'Apply to all groups' selected
Corrupted display when switching to wrapped mode when sequence panel's vertical scrollbar is visible.
Alignment is black in exported EPS file when sequences are selected in exported view.
Groups with different coloured borders aren't rendered with correct colour.
Jalview could hang when importing certain types of knotted RNA secondary structure.
Sequence highlight and selection in trimmed VARNA 2D structure is incorrect for sequences that do not start at 1.
'.' inserted into RNA secondary structure annotation when columns are inserted into an alignment, and when exporting as Stockholm flatfile.
Jalview annotation rows containing upper and lower-case 'E' and 'H' do not automatically get treated as RNA secondary structure.
.jvp should be used as default extension (not .jar) when saving a jalview project file.
Mac Users: closing a window correctly transfers focus to previous window on OSX

Java 10 Issues Resolved

OSX - Can't save new files via the File or export menus by typing in a name into the Save dialog box.
Jalview now uses patched version of the VAqua5 'look and feel' which has improved compatibility with the latest version of OSX.

2.10.4b1
7/06/2018

Use HGVS nomenclature for variant annotation retrieved from Uniprot
Windows File Shortcuts can be dragged onto the Jalview Desktop

Cannot import features with multiple variant elements (blocks import of some Uniprot records)
Clustal files with sequence positions in right-hand column parsed correctly
Wrap view - export to SVG - IDs shown but not alignment area in exported graphic
F2/Keyboard mode edits work when Overview window has input focus
Annotation panel set too high when annotation added to view (Windows)
Jalview Desktop is slow to start up when network connectivity is poor
Drag URL from chrome, firefox, IE to Jalview desktop on Windows doesn't open file
Dragging the currently open URL and links from a page viewed in Firefox or Chrome on Windows is now fully supported. If you are using Edge, only links in the page can be dragged, and with Internet Explorer, only the currently open URL in the browser can be dropped onto Jalview.

2.10.4
10/05/2018

New Structure Chooser control for disabling automatic superposition of multiple structures and open structures in existing views
Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.
Jalview uses HTTPS for Uniprot, Xfam and Ensembl services
Improved performance for large alignments and lots of hidden columns
Improved performance when rendering lots of features (particularly when transparency is disabled)

Structure and Overview aren't updated when Colour By Annotation threshold slider is adjusted
Slow redraw when Overview panel shown overlapping alignment panel
Overview doesn't show end of unpadded sequence as gaps
Cross-reference handling improved: CDS not handled correctly if transcript has no UTR
Secondary structure and temperature factor annotation not added to sequence when local PDB file associated with it by drag'n'drop or structure chooser
Answering 'No' to PDB Autoassociate dialog doesn't import PDB files dropped on an alignment
Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views
Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+.
Tooltip shouldn't be displayed for empty columns in annotation row
Preferences panel's ID Width control is not honored in batch mode
Linked sequence highlighting doesn't work for structures added to existing Jmol view
'View Mappings' includes duplicate entries after importing project with multiple views
Viewing or annotating Uniprot protein sequences via SIFTS from associated PDB entries with negative residue numbers or missing residues fails
Exception when shading sequence with negative Temperature Factor values from annotated PDB files (e.g. as generated by CONSURF)
Uniprot 'sequence variant' features tooltip doesn't include a text description of mutation
Invert displayed features very slow when structure and/or overview windows are also shown
Selecting columns from highlighted regions very slow for alignments with large numbers of sequences
Copy Consensus fails for group consensus with 'StringIndexOutOfBounds'
VAqua(4) provided as fallback Look and Feel for OSX platforms running Java 10
Adding a structure to existing structure view appears to do nothing because the view is hidden behind the alignment view

Applet

Copy consensus sequence option in applet should copy the group consensus when popup is opened on it

Batch Mode

Fixed ID width preference is not respected

New Known Defects

Exceptions occasionally raised when editing a large alignment and overview is displayed
'Overview updating' progress bar is shown repeatedly after a series of edits even when the overview is no longer reflecting updates
'SIFTS Mapping Error' when viewing structures for protein subsequence (if 'Trim Retrieved Sequences' enabled) or Ensembl isoforms (Workaround in 2.10.4 is to fail back to N&W mapping)

2.10.3b1
24/1/2018

Updated Certum Codesigning Certificate (Valid till 30th November 2018)

Desktop

Only one structure is loaded when several sequences and structures are selected for viewing/superposing
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
Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns
User preference for disabling inclusion of sequence limits when exporting as flat file has no effect
Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes

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
06/10/2016

General

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

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.

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
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

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
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.

2.9.0b2
16/10/2015

General

Time stamps for signed Jalview application and applet jars

Application

Duplicate group consensus and conservation rows shown when tree is partitioned
Erratic behaviour when tree partitions made with multiple cDNA/Protein split views

2.9.0b1
8/10/2015

General

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

General

Mapping of cDNA to protein in split frames incorrect when sequence start > 1
Broken images in filter column by annotation dialog documentation
Feature colours not parsed from features file
Exceptions and incomplete link URLs recovered when loading a features file containing HTML tags in feature description

Application

Annotations corrupted after BioJS export and reimport
Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'
Incorrect warning about deleting all data when deleting selected columns
Patch to build system for shipping properly signed JNLP templates for webstart launch
EMBL-PDBe fetcher/viewer dialogs do not offer unreleased structures for download or viewing
Tab/space/return keystroke operation of EMBL-PDBe fetcher/viewer dialogs works correctly
Disabled 'minimise' button on Jalview windows running on OSX to workaround redraw hang bug
Split cDNA/Protein view position and geometry not recovered from jalview project
Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view
Restoring of Clustal, RNA Helices and T-Coffee color schemes from BioJSON

Applet

Reorder sequences mirrored in cDNA/Protein split frame
Applet with Jmol examples not loading correctly

2.9
10/9/2015

General

Linked visualisation and analysis of DNA and Protein alignments:
- Translated cDNA alignments shown as split protein and DNA alignment views
- Codon consensus annotation for linked protein and cDNA alignment views
- Link cDNA or Protein product sequences by loading them onto Protein or cDNA alignments
- Reconstruct linked cDNA alignment from aligned protein sequences
Jmol integration updated to Jmol v14.2.14
Import and export of Jalview alignment views as BioJSON
New alignment annotation file statements for reference sequences and marking hidden columns
Reference sequence based alignment shading to highlight variation
Select or hide columns according to alignment annotation
Find option for locating sequences by description
Conserved physicochemical properties shown in amino acid conservation row
Alignments can be sorted by number of RNA helices

Application

New cDNA/Protein analysis capabilities
- Get Cross-References should open a Split Frame view with cDNA/Protein
- Detect when nucleotide sequences and protein sequences are placed in the same alignment
- Split cDNA/Protein views are saved in Jalview projects
Use REST API to talk to Chimera
Selected regions in Chimera are highlighted in linked Jalview windows
VARNA RNA viewer updated to v3.93
VARNA views are saved in Jalview Projects
Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA
Make groups for selection uses marked columns as well as the active selected region
Calculate UPGMA and NJ trees using sequence feature similarity
New Export options
- New Export Settings dialog to control hidden region export in flat file generation
- Export alignment views for display with the BioJS MSAViewer
- Export scrollable SVG in HTML page
- Optional embedding of BioJSON data when exporting alignment figures to HTML
- 3D structure retrieval and display
  - Free text and structured queries with the PDBe Search API
  - PDBe Search API based discovery and selection of PDB structures for a sequence set
- JPred4 employed for protein secondary structure predictions
- Hide Insertions menu option to hide unaligned columns for one or a group of sequences
- Automatically hide insertions in alignments imported from the JPred4 web server
- (Nearly) Native 'Quaqua' dialogs for browsing file system on OSX
  LGPL libraries courtesy of http://www.randelshofer.ch/quaqua/
- changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'
- change "View protein structure" menu option to "3D Structure ..."
Applet
- New layout for applet example pages
- New parameters to enable SplitFrame view (file2,enableSplitFrame, scaleProteinAsCdna)
- New example demonstrating linked viewing of cDNA and Protein alignments
Development and deployment
- Java 1.7 minimum requirement for Jalview 2.9
- Include installation type and git revision in build properties and console log output
- Jalview Github organisation, and new github site for storing BioJsMSA Templates
- Jalview's unit tests now managed with TestNG

Application

Escape should close any open find dialogs
Typo in select-by-features status report
Consensus RNA secondary secondary structure predictions are not highlighted in amber
Missing gap character in v2.7 example file means alignment appears unaligned when pad-gaps is not enabled
First switch to RNA Helices colouring doesn't colour associated structure views
ID width preference option is greyed out when auto width checkbox not enabled
Stopped a warning dialog from being shown when creating user defined colours
'View Mapping' in structure viewer shows sequence mappings for just that viewer's sequences
Workaround for superposing PDB files containing multiple models in Chimera
Report sequence position in status bar when hovering over Jmol structure
Cannot output gaps as '.' symbols with Selection -> output to text box
Flat file exports of alignments with hidden columns have incorrect sequence start/end
'Aligning' a second chain to a Chimera structure from Jalview fails
Colour schemes applied to structure viewers don't work for nucleotide
Loading/cut'n'pasting an empty or invalid file leads to a grey/invisible alignment window
Exported Jpred annotation from a sequence region imports to different position
Space at beginning of sequence feature tooltips shown on some platforms
Chimera viewer 'View | Show Chain' menu is not populated
'New View' fails with a Null Pointer Exception in console if Chimera has been opened
Mouseover to Chimera not working
Miscellaneous ENA XML feature qualifiers not retrieved
NPE in annotation renderer after 'Extract Scores'
If two structures in one Chimera window, mouseover of either sequence shows on first structure
'Show annotations' options should not make non-positional annotations visible
Subsequence secondary structure annotation not shown in right place after 'view flanking regions'
File Save As type unset when current file format is unknown
Save as '.jar' option removed for saving Jalview projects
Colour by Sequence colouring in Chimera more responsive
Cannot 'add reference annotation' for a sequence in several views on same alignment
Cannot show linked products for EMBL / ENA records
Jalview's tooltip wraps long texts containing no spaces

Applet

Jmol to JalviewLite mouseover/link not working
JalviewLite can't import sequences with ID descriptions containing angle brackets

General

Cannot export and reimport RNA secondary structure via jalview annotation file
Random helix colour palette for colour by annotation with RNA secondary structure
Mouseover to cDNA from STOP residue in protein translation doesn't work.
hints when using the select by annotation dialog box
Jmol alignment incorrect if PDB file has alternate CA positions
FontChooser message dialog appears to hang after choosing 1pt font
Peptide secondary structure incorrectly imported from annotation file when annotation display text includes 'e' or 'h'
Cannot set colour of new feature type whilst creating new feature
cDNA translation alignment should not be sequence order dependent
'Show unconserved' doesn't work for lower case sequences
Nucleotide ambiguity codes involving R not recognised

Deployment and Documentation

Applet example pages appear different to the rest of www.jalview.org

Application Known issues

Incomplete sequence extracted from PDB entry 3a6s
Misleading message appears after trying to delete solid column.
Jalview icon not shown in dock after InstallAnywhere version launches
Fetching EMBL reference for an RNA sequence results fails with a sequence mismatch
Corrupted or unreadable alignment display when scrolling alignment to right
ArrayIndexOutOfBoundsException thrown when remove empty columns called on alignment with ragged gapped ends
auto calculated alignment annotation rows do not get placed above or below non-autocalculated rows
Jalview dekstop becomes sluggish at full screen in ultra-high resolution
Cannot disable consensus calculation independently of quality and conservation
Mouseover highlighting between cDNA and protein can become sluggish with more than one splitframe shown

Applet Known Issues

Core PDB parsing code requires Jmol
Sequence canvas panel goes white when alignment window is being resized

2.8.2
3/12/2014

General

Updated Java code signing certificate donated by Certum.PL.
Features and annotation preserved when performing pairwise alignment
RNA pseudoknot annotation can be imported/exported/displayed
'colour by annotation' can colour by RNA and protein secondary structure
Warn user if 'Find' regular expression is invalid (mentioned post-hoc with 2.9 release)

Application

Extract and display secondary structure for sequences with 3D structures
Support for parsing RNAML
Annotations menu for layout
- sort sequence annotation rows by alignment
- place sequence annotation above/below alignment annotation
Output in Stockholm format
Internationalisation: improved Spanish (es) translation
Structure viewer preferences tab
Disorder and Secondary Structure annotation tracks shared between alignments
UCSF Chimera launch and linked highlighting from Jalview
Show/hide all sequence associated annotation rows for all or current selection
disorder and secondary structure predictions available as dataset annotation
Per-sequence rna helices colouring
Sequence database accessions imported when fetching alignments from Rfam
update VARNA version to 3.91
New groovy scripts for exporting aligned positions, conservation values, and calculating sum of pairs scores.
Command line argument to set default JABAWS server
include installation type in build properties and console log output
Updated Jalview project format to preserve dataset annotation

Application

Distinguish alignment and sequence associated RNA structure in structure->view->VARNA
Raise dialog box if user deletes all sequences in an alignment
Pressing F1 results in documentation opening twice
Sequence feature tooltip is wrapped
Double click on sequence associated annotation selects only first column
Redundancy removal doesn't result in unlinked leaves shown in tree
Undos after several redundancy removals don't undo properly
Hide sequence doesn't hide associated annotation
User defined colours dialog box too big to fit on screen and buttons not visible
author list isn't updated if already written to Jalview properties
Popup menu won't open after retrieving sequence from database
File open window for associate PDB doesn't open
Left-then-right click on a sequence id opens a browser search window
Cannot open sequence feature shading/sort popup menu in feature settings dialog
better tooltip placement for some areas of Jalview desktop
Allow addition of JABAWS Server which doesn't pass validation
Web services parameters dialog box is too large to fit on screen
Muscle nucleotide alignment preset obscured by tooltip
JABAWS preset submenus don't contain newly defined user preset
MSA web services warns user if they were launched with invalid input
Jalview cannot contact DAS Registy when running on Java 8
'Superpose with' submenu not shown when new view created

Deployment and Documentation

2G and 1G options in launchApp have no effect on memory allocation
launchApp service doesn't automatically open www.jalview.org/examples/exampleFile.jar if no file is given
InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is available

Application Known issues

corrupted or unreadable alignment display when scrolling alignment to right
retrieval fails but progress bar continues for DAS retrieval with large number of ID
flatfile output of visible region has incorrect sequence start/end
rna structure consensus doesn't update when secondary structure tracks are rearranged
invalid rna structure positional highlighting does not highlight position of invalid base pairs
out of memory errors are not raised when saving Jalview project from alignment window file menu
Switching to RNA Helices colouring doesn't propagate to structures
colour by RNA Helices not enabled when user created annotation added to alignment
Jalview icon not shown on dock in Mountain Lion/Webstart

Applet Known Issues

JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
Jalview and Jmol example not compatible with IE9
Sort by annotation score doesn't reverse order when selected

2.8.1
4/6/2014

General

Internationalisation of user interface (usually called i18n support) and translation for Spanish locale
Define/Undefine group on current selection with Ctrl-G/Shift Ctrl-G
Improved group creation/removal options in alignment/sequence Popup menu
Sensible precision for symbol distribution percentages shown in logo tooltip.
Annotation panel height set according to amount of annotation when alignment first opened

Application

Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service
Select columns containing particular features from Feature Settings dialog
View all 'representative' PDB structures for selected sequences
Update Jalview project format:
- New file extension for Jalview projects '.jvp'
- Preserve sequence and annotation dataset (to store secondary structure annotation,etc)
- Per group and alignment annotation and RNA helix colouring
New similarity measures for PCA and Tree calculation (PAM250)
Experimental support for retrieval and viewing of flanking regions for an alignment

Application

logo keeps spinning and status remains at queued or running after job is cancelled
cannot export features from alignments imported from Jalview/VAMSAS projects
Buggy slider for web service parameters that take float values
Newly created RNA secondary structure line doesn't have 'display all symbols' flag set
T-COFFEE alignment score shading scheme and other annotation shading not saved in Jalview project
Local file cannot be loaded in freshly downloaded Jalview
Jalview icon not shown on dock in Mountain Lion/Webstart
Load file from desktop file browser fails
Occasional NPE thrown when calculating large trees
Cannot reorder or slide sequences after dragging an alignment onto desktop
Colour by annotation dialog throws NPE after using 'extract scores' function
Loading/cut'n'pasting an empty file leads to a grey alignment window
Disorder thresholds rendered incorrectly after performing IUPred disorder prediction
Multiple group annotated consensus rows shown when changing 'normalise logo' display setting
Find shows blank dialog after 'finished searching' if nothing matches query
Null Pointer Exceptions raised when sorting by feature with lots of groups
Errors in Jmol console when structures in alignment don't overlap
Not all working JABAWS services are shown in Jalview's menu
JAVAWS version of Jalview fails to launch with 'invalid literal/length code'
Annotation/RNA Helix colourschemes cannot be applied to alignment with groups (actually fixed in 2.8.0b1)
RNA Helices and T-Coffee Scores available as default colourscheme

Applet

Remove group option is shown even when selection is not a group
Apply to all groups ticked but colourscheme changes don't affect groups
Documented RNA Helices and T-Coffee Scores as valid colourscheme name
Annotation labels drawn on sequence IDs when Annotation panel is not displayed
Increased font size for dropdown menus on OSX and embedded windows

Other

Consensus sequence for alignments/groups with a single sequence were not calculated
annotation files that contain only groups imported as annotation and junk sequences
Fasta files with sequences containing '*' incorrectly recognised as PFAM or BLC
conservation/PID slider apply all groups option doesn't affect background (2.8.0b1)
redundancy highlighting is erratic at 0% and 100%
Remove gapped columns fails for sequences with ragged trailing gaps
AMSA annotation row with leading spaces is not registered correctly on import
Jalview crashes when selecting PCA analysis for certain alignments
Opening the colour by annotation dialog for an existing annotation based 'use original colours' colourscheme loses original colours setting

2.8.0b1
30/1/2014

Trusted certificates for JalviewLite applet and Jalview Desktop application
Certificate was donated by Certum to the Jalview open source project).
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 graph thresholds
Nucleotide substitution matrix that supports RNA and ambiguity codes
Allow disorder predictions to be made on the current selection (or visible selection) in the same way that JPred works
Groovy scripting for headless Jalview operation

Other improvements

Upgrade desktop installer to InstallAnywhere 2013
COMBINE statement uses current SEQUENCE_REF and GROUP_REF scope to group annotation rows
Support '' style escaping of quotes in Newick files
Group options for JABAWS service by command line name
Empty tooltip shown for JABA service options with a link but no description
Select primary source when selecting authority in database fetcher GUI
Add .mfa to FASTA file extensions recognised by Jalview
Annotation label tooltip text wrap

Slow scrolling when lots of annotation rows are displayed
Lots of NPE (and slowness) after creating RNA secondary structure annotation line
Sequence database accessions not imported when fetching alignments from Rfam
Incorrect SHMR submission for sequences with identical IDs
View all structures does not always superpose structures
Option widgets in service parameters not updated to reflect user or preset settings
Null pointer exceptions for some services without presets or adjustable parameters
Discover PDB IDs entry in structure menu doesn't discover PDB xRefs
Exception encountered while trying to retrieve features with DAS
Lowest value in annotation row isn't coloured when colour by annotation (per sequence) is coloured
Keyboard mode P jumps to start of gapped region when residue follows a gap
Jalview appears to hang importing an alignment with Wrap as default or after enabling Wrap
'Right click to add annotations' message shown in wrap mode when no annotations present
Disorder predictions fail with NPE if no automatic annotation already exists on alignment
oninit javascript function should be called after initialisation completes
Remove redundancy after disorder prediction corrupts alignment window display
Example annotation file in documentation is invalid
Grouped line graph annotation rows are not exported to annotation file
Multi-harmony analysis cannot be run when only two groups created
Cannot create multiple groups of line graphs with several 'combine' statements in annotation file
Pressing return several times causes Number Format exceptions in keyboard mode
Multi-harmony (SHMMR) method doesn't submit correct partitions for input data
Translation from DNA to Amino Acids fails
Jalview fail to load newick tree with quoted label
--headless flag isn't understood
ClassCastException when generating EPS in headless mode
Adjusting sequence-associated shading threshold only changes one row's threshold
Preferences and Feature settings panel panel doesn't open
hide consensus histogram also hides conservation and quality histograms

2.8
12/11/2012

Application

Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega)
JABAWS server status indicator in Web Services preferences
VARNA (http://varna.lri.fr) viewer for RNA structures in Jalview alignment window
Updated Jalview build and deploy framework for OSX mountain lion, windows 7, and 8
Nucleotide substitution matrix for PCA that supports RNA and ambiguity codes
Improved sequence database retrieval GUI
Support fetching and database reference look up against multiple DAS sources (Fetch all from in 'fetch db refs')
Jalview project improvements
- Store and retrieve the 'belowAlignment' flag for annotation
- calcId attribute to group annotation rows on the alignment
- Store AACon calculation settings for a view in Jalview project
horizontal scrolling gesture support
Visual progress indicator when PCA calculation is running
Simpler JABA web services menus
visual indication that web service results are still being retrieved from server
Serialise the dialogs that are shown when Jalview starts up for first time
Jalview user agent string for interacting with HTTP services
DAS 1.6 and DAS 2.0 source support using new JDAS client library
Examples directory and Groovy library included in InstallAnywhere distribution

Applet

RNA alignment and secondary structure annotation visualization applet example

General

Normalise option for consensus sequence logo
Reset button in PCA window to return dimensions to defaults
Allow seqspace or Jalview variant of alignment PCA calculation
PCA with either nucleic acid and protein substitution matrices
Allow windows containing HTML reports to be exported in HTML
Interactive display and editing of RNA secondary structure contacts
RNA Helix Alignment Colouring
RNA base pair logo consensus
Parse sequence associated secondary structure information in Stockholm files
HTML Export database accessions and annotation information presented in tooltip for sequences
Import secondary structure from LOCARNA clustalw style RNA alignment files
import and visualise T-COFFEE quality scores for an alignment
'colour by annotation' per sequence option to shade each sequence according to its associated alignment annotation
New Jalview Logo

Documentation and Development

documentation for score matrices used in Jalview
New Website!

Application

PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch REST service
Stop windows being moved outside desktop on OSX
Filetype associations not installed for webstart launch
Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete
revise SHMR RSBS definition to ensure alignment is uploaded via ali_file parameter
Jalview 2.7 is incompatible with Jmol-12.2.2
View all structures superposed fails with exception
Jnet job queues forever if a very short sequence is submitted for prediction
Cut and paste menu not opened when mouse clicked on desktop window
Putting fractional value into integer text box in alignment parameter dialog causes Jalview to hang
Structure view highlighting doesn't work on windows 7
View all structures fails with exception shown in structure view
Characters in filename associated with PDBEntry not escaped in a platform independent way
Jalview desktop fails to launch with exception when using proxy
Tree calculation reports 'you must have 2 or more sequences selected' when selection is empty
Jalview desktop fails to launch with jar signature failure when java web start temporary file caching is disabled
DAS Sequence retrieval with range qualification results in sequence xref which includes range qualification
Errors during processing of command line arguments cause progress bar (JAL-898) to be removed
Replace comma for semi-colon option not disabled for DAS sources in sequence fetcher
Cannot close news reader when JABAWS server warning dialog is shown
Option widgets not updated to reflect user settings
Edited sequence not submitted to web service
Jalview 2.7 Webstart does not launch on mountain lion
InstallAnywhere installer doesn't unpack and run on OSX Mountain Lion
Annotation panel not given a scroll bar when sequences with alignment annotation are pasted into the alignment
Sequence associated annotation rows not associated when loaded from Jalview project
Browser launch fails with NPE on java 1.7
JABAWS alignment marked as finished when job was cancelled or job failed due to invalid input
NPE with v2.7 example when clicking on Tree associated with all views
Exceptions when copy/paste sequences with grouped annotation rows to new window

Applet

Sequence features are momentarily displayed before they are hidden using hidefeaturegroups applet parameter
loading features via javascript API automatically enables feature display
scrollToColumnIn javascript API method doesn't work

General

Redundancy removal fails for rna alignment
PCA calculation fails when sequence has been selected and then deselected
PCA window shows grey box when first opened on OSX
Letters coloured pink in sequence logo when alignment coloured with clustalx
Choosing fonts without letter symbols defined causes exceptions and redraw errors
Initial PCA plot view is not same as manually reconfigured view
Grouped annotation graph label has incorrect line colour
Grouped annotation graph label display is corrupted for lots of labels

2.7
27/09/2011

Application

Jalview Desktop News Reader
Tweaked default layout of web services menu
View/alignment association menu to enable user to easily specify which alignment a multi-structure view takes its colours/correspondences from
Allow properties file location to be specified as URL
Extend Jalview project to preserve associations between many alignment views and a single Jmol display
Store annotation row height in Jalview project file
Annotation row column label formatting attributes stored in project file
Annotation row order for auto-calculated annotation rows preserved in Jalview project file
Visual progress indication when Jalview state is saved using Desktop window menu
Visual indication that command line arguments are still being processed
Groovy script execution from URL
Colour by annotation default min and max colours in preferences
Automatically associate PDB files dragged onto an alignment with sequences that have high similarity and matching IDs
Update JGoogleAnalytics to latest release (0.3)
'view structures' option to open many structures in same window
Sort associated views menu option for tree panel
Group all JABA and non-JABA services for a particular analysis function in its own submenu

Applet

Userdefined and autogenerated annotation rows for groups
Adjustment of alignment annotation pane height
Annotation scrollbar for annotation panel
Drag to reorder annotation rows in annotation panel
'automaticScrolling' parameter
Allow sequences with partial ID string matches to be annotated from GFF/Jalview features files
Sequence logo annotation row in applet
Absolute paths relative to host server in applet parameters are treated as such
New in the JalviewLite javascript API:
- JalviewLite.js javascript library
- Javascript callbacks for
  - Applet initialisation
  - Sequence/alignment mouse-overs and selections
- scrollTo row and column alignment scrolling functions
- Select sequence/alignment regions from javascript
- javascript structure viewer harness to pass messages between Jmol and Jalview when running as distinct applets
- sortBy method
- Set of applet and application examples shipped with documentation
- New example to demonstrate JalviewLite and Jmol javascript message exchange

General

Enable Jmol displays to be associated with multiple multiple alignments
Option to automatically sort alignment with new tree
User configurable link to enable redirects to a www.Jalview.org mirror
Jmol colours option for Jmol displays
Configurable newline string when writing alignment and other flat files
Allow alignment annotation description lines to contain html tags

Documentation and Development

Add groovy test harness for bulk load testing to examples
Groovy script to load and align a set of sequences using a web service before displaying the result in the Jalview desktop
Restructured javascript and applet api documentation
Ant target to publish example html files with applet archive
Netbeans project for building Jalview from source
ant task to create online javadoc for Jalview source

Application

User defined colourscheme throws exception when current built in colourscheme is saved as new scheme
AlignFrame->Save in application pops up save dialog for valid filename/format
Cannot view associated structure for UniProt sequence
PDB file association breaks for UniProt sequence P37173
Associate PDB from file dialog does not tell you which sequence is to be associated with the file
Find All raises null pointer exception when query only matches sequence IDs
Pre 2.6 Jalview project cannot be loaded into v2.6
Jalview project with Jmol views created with Jalview 2.4 cannot be loaded
Filetype associations not installed for webstart launch
Two or more chains in a single PDB file associated with sequences in different alignments do not get coloured by their associated sequence
Visibility status of autocalculated annotation row not preserved when project is loaded
Annotation row height and visibility attributes not stored in Jalview project
Tree bootstraps are not preserved when saved as a Jalview project
Envision2 workflow tooltips are corrupted
Enabling show group conservation also enables colour by conservation
Duplicate group associated conservation or consensus created on new view
Annotation scrollbar not displayed after 'show all hidden annotation rows' option selected
Alignment quality not updated after alignment annotation row is hidden then shown
Preserve colouring of structures coloured by sequences in pre Jalview 2.7 projects
Web service job parameter dialog is not laid out properly
Web services menu not refreshed after 'reset services' button is pressed in preferences
Annotation off by one in Jalview v2_3 example project
Structures imported from file and saved in project get name like jalview_pdb1234.txt when reloaded
Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete

Applet

Alignment height set incorrectly when lots of annotation rows are displayed
Relative URLs in feature HTML text not resolved to codebase
View follows highlighting does not work for positions in sequences
<= shown as = in tooltip
Export features raises exception when no features exist
Separator string used for serialising lists of IDs for javascript api is modified when separator string provided as parameter
Null pointer exception when selecting tree leaves for alignment with no existing selection
Relative URLs for datasources assumed to be relative to applet's codebase
Status bar not updated after finished searching and search wraps around to first result
StructureSelectionManager instance shared between several Jalview applets causes race conditions and memory leaks
Hover tooltip and mouseover of position on structure not sent from Jmol in applet
Certain sequences of javascript method calls to applet API fatally hang browser

General

View follows structure mouseover scrolls beyond position with wrapped view and hidden regions
Find sequence position moves to wrong residue with/without hidden columns
Sequence length given in alignment properties window is off by 1
InvalidNumberFormat exceptions thrown when trying to import PDB like structure files
Positional search results are only highlighted between user-supplied sequence start/end bounds
End attribute of sequence is not validated
Find dialog only finds first sequence containing a given sequence position
Sequence numbering not preserved in MSF alignment output
Jalview PDB file reader does not extract sequence from nucleotide chains correctly
Structure colours not updated when tree partition changed in alignment
Sequence associated secondary structure not correctly parsed in interleaved stockholm
Colour by annotation dialog does not restore current state
Hiding (nearly) all sequences doesn't work properly
Sequences containing lowercase letters are not properly associated with their pdb files

Documentation and Development

schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright tool

2.6.1
15/11/2010

Application

New warning dialog when the Jalview Desktop cannot contact web services
JABA service parameters for a preset are shown in service job window
JABA Service menu entries reworded

Modeller PIR IO broken - cannot correctly import a pir file emitted by Jalview
Existing feature settings transferred to new alignment view created from cut'n'paste
Improved test for mixed amino/nucleotide chains when parsing PDB files
Consensus and conservation annotation rows occasionally become blank for all new windows
Exception raised when right clicking above sequences in wrapped view mode

Application

multiple multiply aligned structure views cause cpu usage to hit 100% and computer to hang
Web Service parameter layout breaks for long user parameter names
Jaba service discovery hangs desktop if Jaba server is down

2.6
26/9/2010

Application

Support for Java bioinformatics analysis web services (JABAWS)
Web Services preference tab
Analysis parameters dialog box and user defined preferences
Improved speed and layout of Envision2 service menu
Superpose structures using associated sequence alignment
Export coordinates and projection as CSV from PCA viewer

Applet

enable javascript: execution by the applet via the link out mechanism

Other

Updated the Jmol Jalview interface to work with Jmol series 12
The Jalview Desktop and JalviewLite applet now require Java 1.5
Allow Jalview feature colour specification for GFF sequence annotation files
New 'colour by label' keword in Jalview feature file type colour specification
New Jalview Desktop Groovy API method that allows a script to check if it being run in an interactive session or in a batch operation from the Jalview command line

clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column

Application

typo in AlignmentFrame->View->Hide->all but selected Regions menu item
sequence fetcher replaces ',' for ';' when the ',' is part of a valid accession ID
fatal OOM if object retrieved by sequence fetcher runs out of memory
unhandled Out of Memory Error when viewing pca analysis results
InstallAnywhere builds fail to launch on OS X java 10.5 update 4 (due to apple Java 1.6 update)
Installanywhere Jalview silently fails to launch

Applet

Jalview.getFeatureGroups() raises an ArrayIndexOutOfBoundsException if no feature groups are defined.

2.5.1
14/6/2010

Alignment prettyprinter doesn't cope with long sequence IDs
clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column
nucleic acid structures retrieved from PDB do not import correctly
More columns get selected than were clicked on when a number of columns are hidden
annotation label popup menu not providing correct add/hide/show options when rows are hidden or none are present
Stockholm format shown in list of readable formats, and parser copes better with alignments from RFAM.
CSV output of consensus only includes the percentage of all symbols if sequence logo display is enabled

Applet

annotation panel disappears when annotation is hidden/removed

Application

Alignment view not redrawn properly when new alignment opened where annotation panel is visible but no annotations are present on alignment
pasted region containing hidden columns is incorrectly displayed in new alignment window
Jalview slow to complete operations when stdout is flooded (fix is to close the Jalview console)
typo in AlignmentFrame->View->Hide->all but selected Rregions menu item.
inconsistent group submenu and Format submenu entry 'Un' or 'Non'conserved
Sequence feature settings are being shared by multiple distinct alignments
group annotation not recreated when tree partition is changed
double click on group annotation to select sequences does not propagate to associated trees
Mac OSX specific issues:
- exception raised when mouse clicked on desktop window background
- Desktop menu placed on menu bar and application name set correctly
- sequence feature settings not wide enough for the save feature colourscheme button

2.5
30/4/2010

New Capabilities

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
Linked viewing of nucleic acid sequences and structures
Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
Order an alignment by sequence length, or using the average score or total feature count for each sequence.
Shading features by score or associated description
Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).
New hide/show options including Shift+Control+H to hide everything but the currently selected region.

Application

Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources
Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.
DAS Dbref and DbxRef feature types are parsed as database references and protein_name is parsed as description line (BioSapiens terms).
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 and visualized as sequence logos
Optionally scale multi-character column labels to fit within each column of annotation row
Optional automatic sort of associated alignment view when a new tree is opened.
Jalview Java Console
Better placement of desktop window when moving between different screens.
New preference items for sequence ID tooltip and consensus annotation
Client to submit sequences and IDs to Envision2 Workflows
Vamsas Capabilities
- Improved VAMSAS synchronization (Jalview archive used to preserve views, structures, and tree display settings)
- Import of vamsas documents from disk or URL via command line
- Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)
- Updated API to VAMSAS version 0.2

Applet

Middle button resizes annotation row height
New Parameters
- sortByTree (true/false) - automatically sort the associated alignment view by the tree when a new tree is opened.
- showTreeBootstraps (true/false) - show or hide branch bootstraps (default is to show them if available)
- showTreeDistances (true/false) - show or hide branch lengths (default is to show them if available)
- showUnlinkedTreeNodes (true/false) - indicate if unassociated nodes should be highlighted in the tree view
- heightScale and widthScale (1.0 or more) - increase the height or width of a cell in the alignment grid relative to the current font size.
Non-positional features displayed in sequence ID tooltip

Other

Features format: graduated colour definitions and specification of feature scores
Alignment Annotations format: new keywords for group associated annotation (GROUP_REF) and annotation row display properties (ROW_PROPERTIES)
XML formats extended to support graduated feature colourschemes, group associated annotation, and profile visualization settings.

Source field in GFF files parsed as feature source rather than description
Non-positional features are now included in sequence feature and gff files (controlled via non-positional feature visibility in tooltip).
URL links generated for all feature links (bugfix)
Added URL embedding instructions to features file documentation.
Codons containing ambiguous nucleotides translated as 'X' in peptide product
Match case switch in find dialog box works for both sequence ID and sequence string and query strings do not have to be in upper case to match case-insensitively.
AMSA files only contain first column of multi-character column annotation labels
Jalview Annotation File generation/parsing consistent with documentation (e.g. Stockholm annotation can be exported and re-imported)
PDB files without embedded PDB IDs given a friendly name
Find incrementally searches ID string matches as well as subsequence matches, and correctly reports total number of both.
Application:
- Better handling of exceptions during sequence retrieval
- Dasobert generated non-positional feature URL link text excludes the start_end suffix
- DAS feature and source retrieval buttons disabled when fetch or registry operations in progress.
- PDB files retrieved from URLs are cached properly
- Sequence description lines properly shared via VAMSAS
- Sequence fetcher fetches multiple records for all data sources
- Ensured that command line das feature retrieval completes before alignment figures are generated.
- Reduced time taken when opening file browser for first time.
- isAligned check prior to calculating tree, PCA or submitting an MSA to JNet now excludes hidden sequences.
- User defined group colours properly recovered from Jalview projects.

2.4.0.b2
28/10/2009

Experimental support for google analytics usage tracking.
Jalview privacy settings (user preferences and docs).

Race condition in applet preventing startup in jre1.6.0u12+.
Exception when feature created from selection beyond length of sequence.
Allow synthetic PDB files to be imported gracefully
Sequence associated annotation rows associate with all sequences with a given id
Find function matches case-insensitively for sequence ID string searches
Non-standard characters do not cause pairwise alignment to fail with exception

Application Issues

Sequences are now validated against EMBL database
Sequence fetcher fetches multiple records for all data sources

InstallAnywhere Issues

Dock icon works for Mac OS X java (Mac 1.6 update issue with installAnywhere mechanism)
Command line launching of JARs from InstallAnywhere version (java class versioning error fixed)

2.4
27/8/2008

User Interface

Linked highlighting of codon and amino acid from translation and protein products
Linked highlighting of structure associated with residue mapping to codon position
Sequence Fetcher provides example accession numbers and 'clear' button
MemoryMonitor added as an option under Desktop's Tools menu
Extract score function to parse whitespace separated numeric data in description line
Column labels in alignment annotation can be centred.
Tooltip for sequence associated annotation give name of sequence

Web Services and URL fetching

JPred3 web service
Prototype sequence search client (no public services available yet)
Fetch either seed alignment or full alignment from PFAM
URL Links created for matching database cross references as well as sequence ID
URL Links can be created using regular-expressions

Sequence Database Connectivity

Retrieval of cross-referenced sequences from other databases
Generalised database reference retrieval and validation to all fetchable databases
Fetch sequences from DAS sources supporting the sequence command

Import and Export

export annotation rows as CSV for spreadsheet import

Jalview projects record alignment dataset associations, EMBL products, and cDNA sequence mappings

Sequence Group colour can be specified in Annotation File

Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme

VAMSAS Client capabilities (Experimental)

treenode binding for VAMSAS tree exchange
local editing and update of sequences in VAMSAS alignments (experimental)
Create new or select existing session to join
load and save of vamsas documents

Application command line

-tree parameter to open trees (introduced for passing from applet)
-fetchfrom command line argument to specify nicknames of DAS servers to query for alignment features
-dasserver command line argument to add new servers that are also automatically queried for features
-groovy command line argument executes a given groovy script after all input data has been loaded and parsed

Applet-Application data exchange

Trees passed as applet parameters can be passed to application (when using "View in full application")

Applet Parameters

feature group display control parameter
debug parameter
showbutton parameter

Applet API methods

newView public method
Window (current view) specific get/set public methods
Feature display control methods
get list of currently selected sequences

New Jalview distribution features

InstallAnywhere Installer upgraded to IA 2008 VP1
RELEASE file gives build properties for the latest Jalview release.
Java 1.1 Applet build made easier and donotobfuscate property controls execution of obfuscator
Build target for generating source distribution
Debug flag for javacc
.jalview_properties file is documented (slightly) in jalview.bin.Cache
Continuous Build Integration for stable and development version of Application, Applet and source distribution

selected region output includes visible annotations (for certain formats)
edit label/displaychar contains existing label/char for editing
update PDBEntries when DBRefEntries change (vamsas)
shorter peptide product names from EMBL records
Newick string generator makes compact representations
bootstrap values parsed correctly for tree files with comments
pathological filechooser bug avoided by not allowing filenames containing a ':'
Fixed exception when parsing GFF files containing global sequence features
Alignment datasets are finalized only when number of references from alignment sequences goes to zero
Close of tree branch colour box without colour selection causes cascading exceptions
occasional negative imgwidth exceptions
better reporting of non-fatal warnings to user when file parsing fails.
Save works when Jalview project is default format
Save as dialog opened if current alignment format is not a valid output format
UniProt canonical names introduced for both das and vamsas
Histidine should be midblue (not pink!) in Zappo
error messages passed up and output when data read fails
edit undo recovers previous dataset sequence when sequence is edited
allow PDB files without pdb ID HEADER lines (like those generated by MODELLER) to be read in properly
allow reading of JPred concise files as a normal filetype
Stockholm annotation parsing and alignment properties import fixed for PFAM records
Structure view windows have correct name in Desktop window list
annotation consisting of sequence associated scores can be read and written correctly to annotation file
Aligned cDNA translation to aligned peptide works correctly
Fixed display of hidden sequence markers and non-italic font for representatives in Applet
Applet Menus are always embedded in applet window on Macs.
Newly shown features appear at top of stack (in Applet)
Annotations added via parameter not drawn properly due to null pointer exceptions
Secondary structure lines are drawn starting from first column of alignment
UniProt XML import updated for new schema release in July 2008
Sequence feature to sequence ID match for Features file is case-insensitive
Sequence features read from Features file appended to all sequences with matching IDs
PDB structure coloured correctly for associated views containing a sub-sequence
PDB files can be retrieved by applet from Jar files
feature and annotation file applet parameters referring to different directories are retrieved correctly
Fixed application hang whilst waiting for splash-screen version check to complete
Applet properly URLencodes input parameter values when passing them to the launchApp service
display name and local features preserved in results retrieved from web service
Visual delay indication for sequence retrieval and sequence fetcher initialisation
updated Application to use DAS 1.53e version of dasobert DAS client
Re-instated Full AMSA support and .amsa file association
Fixed parsing of JNet Concise annotation sans sequences

2.3
9/5/07

Jmol 11.0.2 integration
PDB views stored in Jalview XML files
Slide sequences
Edit sequence in place
EMBL CDS features
DAS Feature mapping
Feature ordering
Alignment Properties
Annotation Scores
Sort by scores
Feature/annotation editing in applet

Headless state operation in 2.2.1
Incorrect and unstable DNA pairwise alignment
Cut and paste of sequences with annotation
Feature group display state in XML
Feature ordering in XML
blc file iteration selection using filename # suffix
Stockholm alignment properties
Stockhom alignment secondary structure annotation
2.2.1 applet had no feature transparency
Number pad keys can be used in cursor mode
Structure Viewer mirror image resolved

2.2.1
12/2/07

Non standard characters can be read and displayed
Annotations/Features can be imported/exported to the applet via textbox
Applet allows editing of sequence/annotation/group name & description
Preference setting to display sequence name in italics
Annotation file format extended to allow Sequence_groups to be defined
Default opening of alignment overview panel can be specified in preferences
PDB residue numbering annotation added to associated sequences

Applet crash under certain Linux OS with Java 1.6 installed
Annotation file export / import bugs fixed
PNG / EPS image output bugs fixed

2.2
27/11/06

Multiple views on alignment
Sequence feature editing
"Reload" alignment
"Save" to current filename
Background dependent text colour
Right align sequence ids
User-defined lower case residue colours
Format Menu
Select Menu
Menu item accelerator keys
Control-V pastes to current alignment
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'

New memory efficient Undo/Redo System
Optimised symbol lookups and conservation/consensus calculations
Region Conservation/Consensus recalculated after edits
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
Re-instated Zoom function for PCA
Sequence descriptions conserved in web service analysis results
UniProt ID discoverer uses any word separated by ∣
WsDbFetch query/result association resolved
Tree leaf to sequence mapping improved
Smooth fonts switch moved to FontChooser dialog box.

2.1.1
12/9/06

Copy consensus sequence to clipboard

Image output - rightmost residues are rendered if sequence id panel has been resized
Image output - all offscreen group boundaries are rendered
Annotation files with sequence references - all elements in file are relative to sequence position
Mac Applet users can use Alt key for group editing

2.1
22/8/06

MAFFT Multiple Alignment in default Web Service list
DAS Feature fetching
Hide sequences and columns
Export Annotations and Features
GFF file reading / writing
Associate structures with sequences from local PDB files
Add sequences to exisiting alignment
Recently opened files / URL lists
Applet can launch the full application
Applet has transparency for features (Java 1.2 required)
Applet has user defined colours parameter
Applet can load sequences from parameter "sequencex"

Redundancy Panel reinstalled in the Applet
Monospaced font - EPS / rescaling bug fixed
Annotation files with sequence references bug fixed

2.08.1
2/5/06

Change case of selected region from Popup menu
Choose to match case when searching
Middle mouse button and mouse movement can compress / expand the visible width and height of the alignment

Annotation Panel displays complete JNet results

2.08b
18/4/06

Java 1.5 bug - InternalMessageDialog fix for threads
Righthand label on wrapped alignments shows correct value

2.08
10/4/06

Editing can be locked to the selection area
Keyboard editing
Create sequence features from searches
Precalculated annotations can be loaded onto alignments
Features file allows grouping of features
Annotation Colouring scheme added
Smooth fonts off by default - Faster rendering
Choose to toggle Autocalculate Consensus On/Off

Drag & Drop fixed on Linux
Jalview Archive file faster to load/save, sequence descriptions saved.

2.07
12/12/05

PDB Structure Viewer enhanced
Sequence Feature retrieval and display enhanced
Choose to output sequence start-end after sequence name for file output
Sequence Fetcher WSDBFetch@EBI
Applet can read feature files, PDB files and can be used for HTML form input

HTML output writes groups and features
Group editing is Control and mouse click
File IO bugs

2.06
28/9/05

View annotations in wrapped mode
More options for PCA viewer

GUI bugs resolved
Runs with -nodisplay from command line

2.05b
15/9/05

Choose EPS export as lineart or text
Jar files are executable
Can read in Uracil - maps to unknown residue

Known OutOfMemory errors give warning message
Overview window calculated more efficiently
Several GUI bugs resolved

2.05
30/8/05

Edit and annotate in "Wrapped" view

Several GUI bugs resolved

2.04
24/8/05

Hold down mouse wheel & scroll to change font size

Improved JPred client reliability
Improved loading of Jalview files

2.03
18/8/05

Set Proxy server name and port in preferences
Multiple URL links from sequence ids
User Defined Colours can have a scheme name and added to Colour Menu
Choose to ignore gaps in consensus calculation
Unix users can set default web browser
Runs without GUI for batch processing
Dynamically generated Web Service Menus

InstallAnywhere download for Sparc Solaris

2.02
18/7/05

Copy & Paste order of sequences maintains alignment order.

2.01
12/7/05

Use delete key for deleting selection.
Use Mouse wheel to scroll sequences.
Help file updated to describe how to add alignment annotations.
Version and build date written to build properties file.
InstallAnywhere installation will check for updates at launch of Jalview.

Delete gaps bug fixed.
FileChooser sorts columns.
Can remove groups one by one.
Filechooser icons installed.
Finder ignores return character when searching. Return key will initiate a search.

2.0
20/6/05

New codebase