X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=3c7c0c07756732d0e13d8d63e3a6bc4dd8a6da87;hb=13068d0d1b32754d76b488313cdf3af8b35e3dd1;hp=6b92a2c6b40295f16922c73be927b6e2b4fd15f9;hpb=e5cbd35e13f46ae1d59a08b0af1086677418141d;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 6b92a2c..54740d6 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,7 +1,7 @@ Release History + -

Release History

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-
Release
- 		-
New Features
- 		-
Issues Resolved
-
- 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: -
      +

      + Release History +

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - + 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
        • +
      + + + + - - - + + - - - - + - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + - - + 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
          • +
        +
        • +
      + + + - - - - - - - - + + -
      2.4
      - 27/8/2008
      - - + + + + + + + - - - - - - +
      + 2.4
      27/8/2008 +
      + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
      +
      + Release +
      +       		+
      + New Features +
      +       		+
      + Issues Resolved +
      +
      +
      + 2.10.2
      8/8/2017       +
      +
      + 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 +
        • + +
      +
      + +
      +
      + 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. +
        • + +
      + 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
        • +
      • 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       -
      -
      + 2.8.0b1
      + 30/1/2014       +
      • Trusted certificates for JalviewLite applet and @@ -165,8 +1979,7 @@ Certum to the Jalview open source project).
        • -
      • Jalview SRS links replaced by Uniprot and EBI-search -
        • +
      • Jalview SRS links replaced by UniProt and EBI-search
      • Output in Stockholm format
      • Allow import of data from gzipped files
      • Export/import group and sequence associated line @@ -176,7 +1989,7 @@
      • 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
        • +
      • Groovy scripting for headless Jalview operation
      Other improvements
      • Upgrade desktop installer to InstallAnywhere 2013
        • @@ -245,1273 +2058,1339 @@
      • ClassCastException when generating EPS in headless mode
      • Adjusting sequence-associated shading threshold only - changes one row's threshold
        • + changes one row's threshold
      • Preferences and Feature settings panel panel doesn't open
        • -
      • hide consensus histogram also hides conservation and - quality histograms
        • -
      +
    • 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
        • +
      + 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
          • +
        • 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 +
        +
        • +
      • 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
        -
      • Applet initialisation
        • -
      • Sequence/alignment mouse-overs and selections
        • +
      • 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
      - -
    • 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
          • -
        -
        • -
      -
      +
      + 2.7
      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
        • -
      		-
      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)
        • -
      -
      + +
      + 2.5
      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.
          • +
        +
        • +
      +       		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
        • -
      +
      +
      + 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)
        • +
      +
      - -
        -
      • 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
        • -
      -       		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
        • -
      -       		 
      -

       

      +
+
+ 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
    • +
+ 		 
+