Release History

+ General +

+ 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 +
+
+ Tree/PCA calculation menu items merged to + a calculation dialog box +
+ More robust colours and shader + model for alignments and groups +
+ Custom shading schemes created via groovy + scripts +
+ linked scrolling of CDS/Protein views + via Overview or sequence motif search operations +
+ Efficiency improvements for interacting + with alignment and overview windows +
+ Hidden columns and sequences can be + omitted in Overview +
+ Posterior probability annotation from + Stockholm files imported as sequence associated annotation +
+ Sequence names don't include file + extension when importing structure files without embedded + names or PDB accessions +
+ Amend sequence features dialog box can be + opened by double clicking gaps within sequence feature + extent +
+ Graduated feature colour style example + included in the example feature file +
+ Occupancy annotation row shows number of + ungapped positions in each column of the alignment. +
+ File extension pruned from Sequence ID + for sequences derived from structure files without + embedded database accession +
+ Status bar message shown when not enough + aligned positions were available to create a 3D structure + superposition. +
+ More robust per-sequence positional + annotation input/output via stockholm flatfile +

+ Application +

+ Experimental Features Checkbox in + Desktop's Tools menu to hide or show untested features in + the application. +
+ Warning in alignment status bar when + there are not enough columns to superimpose structures in + Chimera +
+ Faster Chimera/Jalview communication by + file-based command exchange +
+ URLs for viewing database + cross-references provided by identifiers.org and the + EMBL-EBI's MIRIAM DB +
+ Updated JABAWS client to v2.2 +
+ Drag and drop load of AAIndex and NCBI + format sequence substitution matrices +
+ 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. +

+ Experimental features +

+ New entries in the Chimera menu + to transfer Chimera's structure attributes as Jalview + features, and vice-versa. +

+ Applet +

+ Test Suite +

+ Added PrivilegedAccessor to test suite +
+ Prevent or clear modal dialogs raised + during tests +
+ External service integration tests for + Uniprot REST Free Text Search Client +
+ 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) +
+

+ General +

+ 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). To restore pre-2.10.2 + behaviour
+ jalview.viewmodel.PCAModel.scoreGapAsAny=true // for + 2.10.1 mode
+ jalview.viewmodel.PCAModel.scoreGapAsAny=false // to + restore 2.10.2 mode +
+ Fixed off-by-one bug that affected + scaling of branch lengths for trees computed using + Sequence Feature Similarity. +
+ Reopening Colour by annotation dialog + doesn't reselect a specific sequence's associated + annotation after it was used for colouring a view +
+ Hidden regions in alignment views are not + coloured in linked structure views +
+ Current selection lost if popup menu + opened on a region of alignment without groups +
+ 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 +
+ PCA calculation could hang when + generating output report when working with highly + redundant alignments +
+ Cannot configure feature colours with + lightGray or darkGray via features file +
+ Overview window visible region moves + erratically when hidden rows or columns are present +
+ Per-residue colourschemes applied via the + Structure Viewer's colour menu don't correspond to + sequence colouring +
+ Protein specific colours only offered in + colour and group colour menu for protein alignments +
+ 'Apply to all groups' setting when + changing colour does not apply Conservation slider value + to all groups +
+ Colour threshold slider doesn't update to + reflect currently selected view or group's shading + thresholds +
+ Percentage identity and conservation menu + items do not show a tick or allow shading to be disabled +
+ 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 +
+ Very large alignments take a long time to + load +
+ Graduated feature colour threshold not + restored to UI when feature colour is edited +
+ Feature colour thresholds not respected + when rendered on overview and structures when opacity at + 100% +
+ Structure and alignment overview update + as graduate feature colour settings are modified via the + dialog box +
+ Vertical scrollbar jumps one page-width at + a time when scrolling vertically in wrapped mode. +
+ Overview window doesn't always update + when a group defined on the alignment is resized +
+ Mouseovers on left/right scale region in + wrapped view result in positional status updates +
+ Status bar shows position for ambiguous + amino acid and nucleotide symbols +
+ Copy consensus sequence failed if + alignment included gapped columns +
+ User defined gap colour not shown in + overview when features overlaid on alignment +
+ 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) +
+ Gap colours in user-defined colourschemes + are not shown +
+ Exception thrown if trying to create a + sequence feature on gaps only +
+ Sort by features includes features to + right of selected region when gaps present on right-hand + boundary +
+ 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 +
+ 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 +
+ 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 +
+ +
+ +
+ +

+ Documentation +

+ Release notes reformatted for readibility + with the built-in Java help viewer +
+ Find documentation updated with 'search + sequence description' option +

+ Application +

+ Sequence Database chooser doesn't show + available databases panel on Linux +
+ EnsemblGenomes example failing after + release of Ensembl v.88 +
+ 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 +
+ Proxy server address and port always + appear enabled in Preferences->Connections +
+ 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' +
+ DAS registry not found exceptions + removed from console output +
+ Above PID colour threshold not recovered + when alignment view imported from project +
+ No mappings generated between + structure and sequences extracted from structure files + imported via URL 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 +
+ Trackpad horizontal scroll gesture + adjusts start position in wrap mode +
+ Status bar doesn't show positions for + ambiguous amino acids +
+ Hide insertions in PopUp menu excludes + gaps in selection, current sequence and only within + selected columns +
+ Cannot retrieve protein products from + Ensembl by Peptide ID +
+ cDNA Consensus annotation not shown in + CDS/Protein view after CDS sequences added for aligned + proteins +
+ Incorrect PDB-Uniprot mappings created + from SIFTs for April 2017 update due to 'null' strings in + RESNUM mapping field +

+ 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 +

+ 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 Newick trees from eggnog + ortholog database +

+ 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 +

+ 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 +

+ +

+ 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. +

+ 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. +

- General + General

Mapping of cDNA to protein in split frames incorrect when sequence start > 1
Broken images in filter column by annotation dialog documentation
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
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

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