X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=6eb42bc7d90a51d5a90ec2ac2a6fc7dcd20f919e;hb=e5ff0544866ec954e311b7401f5c3989c0016a5e;hp=08ea3eb4294a42796e9a3795dcb144ab17cad6d4;hpb=6e23a164b465e79b78230d042159f4c8cc1fa9f0;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 08ea3eb..6eb42bc 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,1479 +1,2308 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Release History -

Release History

- - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
-
Release
- 		-
New Features
- 		-
Issues Resolved
-
- 2.8
08/11/2012 -
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 -
      • +

      + Release History +

      + + + + + + + + + + - - - - + + + + + + + + + + + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + - - - - - + + + + + + + + + + + + + + + + + + + + - - + 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
          • +
        +
        • +
      + + + - - - +
    • 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.
        • +
      + + + + + + + + + + + + + + + + - - - - - - - - + + + + + + + + - + - - - - - - + +
    • 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. -
      • - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
      +
      + Release +
      +       		+
      + New Features +
      +       		+
      + Issues Resolved +
      +
      +
      + 2.10.0
      04/10/2016       +
      +       		General +
        +
      • Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.
        • +
      • Alignment ruler shows positions relative to reference sequence
        • +
      • Position/residue shown in status bar when mousing over sequence associated annotation
        • +
      • Default RNA SS symbol to 'matching bracket' for manual entry
        • +
      • RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column
        • +
      • Feature settings popup menu options for showing or hiding columns containing a feature
        • +
      • Edit selected group by double clicking on group and sequence associated annotation labels
        • +
      • 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
        • +
      • + +
        • +
      • + +
        • + + +
      Applet +
        +
        • +
      		+
      + 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
        • +
      • + +
        • +
      • + +
        • +
      • + +
        • +
      + Application +
        +
        • +
      • Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
        • +
      • URLs and links can imported by drag'n'drop on OSX webstart
        • +
      • InstallAnywhere distribution fails when launching Chimera
        • +
      • Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
        • +
      • Cannot save project when view has a reference sequence defined
        • +
      • Columns are suddenly selected in other alignments and views when revealing hidden columns
        • +
      • Hide columns not mirrored in complement view in a cDNA/Protein splitframe
        • +
      • Cannot save/restore representative sequence from project when only one sequence is represented
        • +
      • Disabled 'Best Uniprot Coverage' option in Structure Chooser
        • +
      • Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
        • +
      • 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
        • +
      • 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 +
        • +
      • + Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records. +
        • +
      • + 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 +
        • +
      • + +
        • +
      • + +
        • -
      - -
    • - 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: + +
      + 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
        -
      • JalviewLite.js javascript library
        • -
      • Javascript callbacks for + +
      • Signed OSX InstallAnywhere installer
        • +
      • Support for per-sequence based annotations in BioJSON
        • +
      Applet +
        +
      • Split frame example added to applet examples page
        • +
      		+
      + 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
        -
      • Applet initialisation
        • -
      • Sequence/alignment mouse-overs and selections
        • +
      • 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
        • +
      - -
    • 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 +
      + 2.8.2
      3/12/2014       +
      		General +
        +
      • Updated Java code signing certificate donated by + Certum.PL.
        • +
      • Features and annotation preserved when performing + pairwise alignment
        • +
      • RNA pseudoknot annotation can be + imported/exported/displayed
        • +
      • 'colour by annotation' can colour by RNA and + protein secondary structure
        • +
      • Warn user if 'Find' regular expression is invalid (mentioned + post-hoc with 2.9 release) +
        • + +
      Application +
        +
      • Extract and display secondary structure for sequences + with 3D structures
        • +
      • Support for parsing RNAML
        • +
      • Annotations menu for layout +
          +
        • sort sequence annotation rows by alignment
          • +
        • place sequence annotation above/below alignment + annotation
          • +
        +
      • Output in Stockholm format
        • +
      • Internationalisation: improved Spanish (es) + translation
        • +
      • Structure viewer preferences tab
        • +
      • Disorder and Secondary Structure annotation tracks + shared between alignments
        • +
      • UCSF Chimera launch and linked highlighting from + Jalview
        • +
      • Show/hide all sequence associated annotation rows for + all or current selection
        • +
      • disorder and secondary structure predictions + available as dataset annotation
        • +
      • Per-sequence rna helices colouring
        • + + +
      • Sequence database accessions imported when fetching + alignments from Rfam
        • +
      • update VARNA version to 3.91
        • + +
      • New groovy scripts for exporting aligned positions, + conservation values, and calculating sum of pairs scores.
        • +
      • Command line argument to set default JABAWS server
        • +
      • include installation type in build properties and + console log output
        • +
      • Updated Jalview project format to preserve dataset + annotation
        • +
      		+ Application +
        +
      • Distinguish alignment and sequence associated RNA + structure in structure->view->VARNA
        • +
      • Raise dialog box if user deletes all sequences in an + alignment
        • +
      • Pressing F1 results in documentation opening twice
        • +
      • Sequence feature tooltip is wrapped
        • +
      • Double click on sequence associated annotation + selects only first column
        • +
      • Redundancy removal doesn't result in unlinked + leaves shown in tree
        • +
      • Undos after several redundancy removals don't undo + properly
        • +
      • Hide sequence doesn't hide associated annotation
        • +
      • User defined colours dialog box too big to fit on + screen and buttons not visible
        • +
      • author list isn't updated if already written to + Jalview properties
        • +
      • Popup menu won't open after retrieving sequence + from database
        • +
      • File open window for associate PDB doesn't open
        • +
      • Left-then-right click on a sequence id opens a + browser search window
        • +
      • Cannot open sequence feature shading/sort popup menu + in feature settings dialog
        • +
      • better tooltip placement for some areas of Jalview + desktop
        • +
      • Allow addition of JABAWS Server which doesn't + pass validation
        • +
      • Web services parameters dialog box is too large to + fit on screen
        • +
      • Muscle nucleotide alignment preset obscured by + tooltip
        • +
      • JABAWS preset submenus don't contain newly + defined user preset
        • +
      • MSA web services warns user if they were launched + with invalid input
        • +
      • Jalview cannot contact DAS Registy when running on + Java 8
        • +
      • + + 'Superpose with' submenu not shown when new view + created +
        • + +
      Deployment and Documentation +
        +
      • 2G and 1G options in launchApp have no effect on + memory allocation
        • +
      • launchApp service doesn't automatically open + www.jalview.org/examples/exampleFile.jar if no file is given
        • +
      • + + InstallAnywhere reports cannot find valid JVM when Java + 1.7_055 is available +
        • +
      Application Known issues +
        +
      • + + corrupted or unreadable alignment display when scrolling + alignment to right +
        • +
      • + + retrieval fails but progress bar continues for DAS retrieval + with large number of ID +
        • +
      • + + flatfile output of visible region has incorrect sequence + start/end +
        • +
      • + + rna structure consensus doesn't update when secondary + structure tracks are rearranged +
        • +
      • + + invalid rna structure positional highlighting does not + highlight position of invalid base pairs +
        • +
      • + + out of memory errors are not raised when saving Jalview + project from alignment window file menu +
        • +
      • + + Switching to RNA Helices colouring doesn't propagate to + structures +
        • +
      • + + colour by RNA Helices not enabled when user created + annotation added to alignment +
        • +
      • + + Jalview icon not shown on dock in Mountain Lion/Webstart +
        • +
      Applet Known Issues +
        +
      • + + JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies +
        • +
      • + + Jalview and Jmol example not compatible with IE9 +
        • + +
      • Sort by annotation score doesn't reverse order + when selected
        • +
      +
      + 2.8.1
      4/6/2014       +
      		+ + General +
        +
      • Internationalisation of user interface (usually + called i18n support) and translation for Spanish locale
        • +
      • Define/Undefine group on current selection with + Ctrl-G/Shift Ctrl-G
        • +
      • Improved group creation/removal options in + alignment/sequence Popup menu
        • +
      • Sensible precision for symbol distribution + percentages shown in logo tooltip.
        • +
      • Annotation panel height set according to amount of + annotation when alignment first opened
        • +
      Application +
        +
      • Interactive consensus RNA secondary structure + prediction VIENNA RNAAliFold JABA 2.1 service
        • +
      • Select columns containing particular features from + Feature Settings dialog
        • +
      • View all 'representative' PDB structures for selected + sequences
        • +
      • Update Jalview project format: +
          +
        • New file extension for Jalview projects '.jvp'
          • +
        • Preserve sequence and annotation dataset (to + store secondary structure annotation,etc)
          • +
        • Per group and alignment annotation and RNA helix + colouring
          • +
        +
        • +
      • New similarity measures for PCA and Tree calculation + (PAM250)
        • +
      • Experimental support for retrieval and viewing of + flanking regions for an alignment
        • +
      +       		+ Application +
        +
      • logo keeps spinning and status remains at queued or + running after job is cancelled
        • +
      • cannot export features from alignments imported from + Jalview/VAMSAS projects
        • +
      • Buggy slider for web service parameters that take + float values
        • +
      • Newly created RNA secondary structure line doesn't + have 'display all symbols' flag set
        • +
      • T-COFFEE alignment score shading scheme and other + annotation shading not saved in Jalview project
        • +
      • Local file cannot be loaded in freshly downloaded + Jalview
        • +
      • Jalview icon not shown on dock in Mountain + Lion/Webstart
        • +
      • Load file from desktop file browser fails
        • +
      • Occasional NPE thrown when calculating large trees
        • +
      • Cannot reorder or slide sequences after dragging an + alignment onto desktop
        • +
      • Colour by annotation dialog throws NPE after using + 'extract scores' function
        • +
      • Loading/cut'n'pasting an empty file leads to a grey + alignment window
        • +
      • Disorder thresholds rendered incorrectly after + performing IUPred disorder prediction
        • +
      • Multiple group annotated consensus rows shown when + changing 'normalise logo' display setting
        • +
      • Find shows blank dialog after 'finished searching' if + nothing matches query
        • +
      • Null Pointer Exceptions raised when sorting by + feature with lots of groups +
        • +
      • Errors in Jmol console when structures in alignment + don't overlap +
        • +
      • Not all working JABAWS services are shown in + Jalview's menu
        • +
      • JAVAWS version of Jalview fails to launch with + 'invalid literal/length code'
        • +
      • Annotation/RNA Helix colourschemes cannot be applied + to alignment with groups (actually fixed in 2.8.0b1)
        • +
      • RNA Helices and T-Coffee Scores available as default + colourscheme
        • + +
      Applet +
        +
      • Remove group option is shown even when selection is + not a group
        • +
      • Apply to all groups ticked but colourscheme changes + don't affect groups
        • +
      • Documented RNA Helices and T-Coffee Scores as valid + colourscheme name
        • +
      • Annotation labels drawn on sequence IDs when + Annotation panel is not displayed
        • +
      • Increased font size for dropdown menus on OSX and + embedded windows
        • +
      Other +
        +
      • Consensus sequence for alignments/groups with a + single sequence were not calculated
        • +
      • annotation files that contain only groups imported as + annotation and junk sequences
        • +
      • Fasta files with sequences containing '*' incorrectly + recognised as PFAM or BLC
        • +
      • conservation/PID slider apply all groups option + doesn't affect background (2.8.0b1) +
      • +
      • redundancy highlighting is erratic at 0% and 100%
        • +
      • Remove gapped columns fails for sequences with ragged + trailing gaps
        • +
      • AMSA annotation row with leading spaces is not + registered correctly on import
        • +
      • Jalview crashes when selecting PCA analysis for + certain alignments
        • +
      • Opening the colour by annotation dialog for an + existing annotation based 'use original colours' + colourscheme loses original colours setting
        • +
      +
      + 2.8.0b1
      + 30/1/2014       +
      		+
        +
      • Trusted certificates for JalviewLite applet and + Jalview Desktop application
        Certificate was donated by + Certum to the Jalview + open source project). +
        • +
      • Jalview SRS links replaced by UniProt and EBI-search +
        • +
      • Output in Stockholm format
        • +
      • Allow import of data from gzipped files
        • +
      • Export/import group and sequence associated line + graph thresholds
        • +
      • Nucleotide substitution matrix that supports RNA and + ambiguity codes
        • +
      • Allow disorder predictions to be made on the current + selection (or visible selection) in the same way that JPred + works
        • +
      • Groovy scripting for headless Jalview operation
        • +
      Other improvements +
        +
      • Upgrade desktop installer to InstallAnywhere 2013
        • +
      • COMBINE statement uses current SEQUENCE_REF and + GROUP_REF scope to group annotation rows
        • +
      • Support '' style escaping of quotes in Newick + files
        • +
      • Group options for JABAWS service by command line name
        • +
      • Empty tooltip shown for JABA service options with a + link but no description
        • +
      • Select primary source when selecting authority in + database fetcher GUI
        • +
      • Add .mfa to FASTA file extensions recognised by + Jalview
        • +
      • Annotation label tooltip text wrap
        • +
      +       		+
        +
      • Slow scrolling when lots of annotation rows are + displayed
        • +
      • Lots of NPE (and slowness) after creating RNA + secondary structure annotation line
        • +
      • Sequence database accessions not imported when + fetching alignments from Rfam
        • +
      • Incorrect SHMR submission for sequences with + identical IDs
        • +
      • View all structures does not always superpose + structures
        • +
      • Option widgets in service parameters not updated to + reflect user or preset settings
        • +
      • Null pointer exceptions for some services without + presets or adjustable parameters
        • +
      • Discover PDB IDs entry in structure menu doesn't + discover PDB xRefs
        • +
      • Exception encountered while trying to retrieve + features with DAS
        • +
      • Lowest value in annotation row isn't coloured + when colour by annotation (per sequence) is coloured
        • +
      • Keyboard mode P jumps to start of gapped region when + residue follows a gap
        • +
      • Jalview appears to hang importing an alignment with + Wrap as default or after enabling Wrap
        • +
      • 'Right click to add annotations' message + shown in wrap mode when no annotations present
        • +
      • Disorder predictions fail with NPE if no automatic + annotation already exists on alignment
        • +
      • oninit javascript function should be called after + initialisation completes
        • +
      • Remove redundancy after disorder prediction corrupts + alignment window display
        • +
      • Example annotation file in documentation is invalid
        • +
      • Grouped line graph annotation rows are not exported + to annotation file
        • +
      • Multi-harmony analysis cannot be run when only two + groups created
        • +
      • Cannot create multiple groups of line graphs with + several 'combine' statements in annotation file
        • +
      • Pressing return several times causes Number Format + exceptions in keyboard mode
        • +
      • Multi-harmony (SHMMR) method doesn't submit + correct partitions for input data
        • +
      • Translation from DNA to Amino Acids fails
        • +
      • Jalview fail to load newick tree with quoted label
        • +
      • --headless flag isn't understood
        • +
      • ClassCastException when generating EPS in headless + mode
        • +
      • Adjusting sequence-associated shading threshold only + changes one row's threshold
        • +
      • Preferences and Feature settings panel panel + doesn't open
        • +
      • hide consensus histogram also hides conservation and + quality histograms
        • +
      +
      + 2.8
      12/11/2012 +
      		Application +
        +
      • Support for JABAWS 2.0 Services (AACon alignment + conservation, protein disorder and Clustal Omega)
        • +
      • JABAWS server status indicator in Web Services + preferences
        • +
      • VARNA (http://varna.lri.fr) viewer for RNA structures + in Jalview alignment window
        • +
      • Updated Jalview build and deploy framework for OSX + mountain lion, windows 7, and 8
        • +
      • Nucleotide substitution matrix for PCA that supports + RNA and ambiguity codes
        • + +
      • Improved sequence database retrieval GUI
        • +
      • Support fetching and database reference look up + against multiple DAS sources (Fetch all from in 'fetch db + refs')
        • +
      • Jalview project improvements +
          +
        • Store and retrieve the 'belowAlignment' + flag for annotation
          • +
        • calcId attribute to group annotation rows on the + alignment
          • +
        • Store AACon calculation settings for a view in + Jalview project
          • - 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
        • +
      + +
    • horizontal scrolling gesture support
      • +
    • Visual progress indicator when PCA calculation is + running
      • +
    • Simpler JABA web services menus
      • +
    • visual indication that web service results are still + being retrieved from server
      • +
    • Serialise the dialogs that are shown when Jalview + starts up for first time
      • +
    • Jalview user agent string for interacting with HTTP + services
      • +
    • DAS 1.6 and DAS 2.0 source support using new JDAS + client library
      • +
    • Examples directory and Groovy library included in + InstallAnywhere distribution
      • + Applet +
        +
      • RNA alignment and secondary structure annotation + visualization applet example
        • +
      General +
        +
      • Normalise option for consensus sequence logo
        • +
      • Reset button in PCA window to return dimensions to + defaults
        • +
      • Allow seqspace or Jalview variant of alignment PCA + calculation
        • +
      • PCA with either nucleic acid and protein substitution + matrices +
      • Allow windows containing HTML reports to be exported + in HTML
        • +
      • Interactive display and editing of RNA secondary + structure contacts
        • +
      • RNA Helix Alignment Colouring
        • +
      • RNA base pair logo consensus
        • +
      • Parse sequence associated secondary structure + information in Stockholm files
        • +
      • HTML Export database accessions and annotation + information presented in tooltip for sequences
        • +
      • Import secondary structure from LOCARNA clustalw + style RNA alignment files
        • +
      • import and visualise T-COFFEE quality scores for an + alignment
        • +
      • 'colour by annotation' per sequence option to + shade each sequence according to its associated alignment + annotation
        • +
      • New Jalview Logo
        • +
      Documentation and Development +
        +
      • documentation for score matrices used in Jalview
        • +
      • New Website!
        • +
      		Application +
        +
      • PDB, Unprot and EMBL (ENA) databases retrieved via + wsdbfetch REST service
        • +
      • Stop windows being moved outside desktop on OSX
        • +
      • Filetype associations not installed for webstart + launch
        • +
      • Jalview does not always retrieve progress of a JABAWS + job execution in full once it is complete
        • +
      • revise SHMR RSBS definition to ensure alignment is + uploaded via ali_file parameter
        • +
      • Jalview 2.7 is incompatible with Jmol-12.2.2
        • +
      • View all structures superposed fails with exception
        • +
      • Jnet job queues forever if a very short sequence is + submitted for prediction
        • +
      • Cut and paste menu not opened when mouse clicked on + desktop window
        • +
      • Putting fractional value into integer text box in + alignment parameter dialog causes Jalview to hang
        • +
      • Structure view highlighting doesn't work on + windows 7
        • +
      • View all structures fails with exception shown in + structure view
        • +
      • Characters in filename associated with PDBEntry not + escaped in a platform independent way
        • +
      • Jalview desktop fails to launch with exception when + using proxy
        • +
      • Tree calculation reports 'you must have 2 or more + sequences selected' when selection is empty
        • +
      • Jalview desktop fails to launch with jar signature + failure when java web start temporary file caching is + disabled
        • +
      • DAS Sequence retrieval with range qualification + results in sequence xref which includes range qualification
        • +
      • Errors during processing of command line arguments + cause progress bar (JAL-898) to be removed
        • +
      • Replace comma for semi-colon option not disabled for + DAS sources in sequence fetcher
        • +
      • Cannot close news reader when JABAWS server warning + dialog is shown
        • +
      • Option widgets not updated to reflect user settings
        • +
      • Edited sequence not submitted to web service
        • +
      • Jalview 2.7 Webstart does not launch on mountain lion
        • +
      • InstallAnywhere installer doesn't unpack and run + on OSX Mountain Lion
        • +
      • Annotation panel not given a scroll bar when + sequences with alignment annotation are pasted into the + alignment
        • +
      • Sequence associated annotation rows not associated + when loaded from Jalview project
        • +
      • Browser launch fails with NPE on java 1.7
        • +
      • JABAWS alignment marked as finished when job was + cancelled or job failed due to invalid input
        • +
      • NPE with v2.7 example when clicking on Tree + associated with all views
        • +
      • Exceptions when copy/paste sequences with grouped + annotation rows to new window
        • +
      Applet +
        +
      • Sequence features are momentarily displayed before + they are hidden using hidefeaturegroups applet parameter
        • +
      • loading features via javascript API automatically + enables feature display
        • +
      • scrollToColumnIn javascript API method doesn't + work
        • +
      General +
        +
      • Redundancy removal fails for rna alignment
        • +
      • PCA calculation fails when sequence has been selected + and then deselected
        • +
      • PCA window shows grey box when first opened on OSX
        • +
      • Letters coloured pink in sequence logo when alignment + coloured with clustalx
        • +
      • Choosing fonts without letter symbols defined causes + exceptions and redraw errors
        • +
      • Initial PCA plot view is not same as manually + reconfigured view
        • +
      • Grouped annotation graph label has incorrect line + colour
        • +
      • Grouped annotation graph label display is corrupted + for lots of labels
        • +
      +
      +
      + 2.7
      27/09/2011 +
      +       		Application +
        +
      • Jalview Desktop News Reader
        • +
      • Tweaked default layout of web services menu
        • +
      • View/alignment association menu to enable user to + easily specify which alignment a multi-structure view takes + its colours/correspondences from
        • +
      • Allow properties file location to be specified as URL
        • +
      • Extend Jalview project to preserve associations + between many alignment views and a single Jmol display
        • +
      • Store annotation row height in Jalview project file
        • +
      • Annotation row column label formatting attributes + stored in project file
        • +
      • Annotation row order for auto-calculated annotation + rows preserved in Jalview project file
        • +
      • Visual progress indication when Jalview state is + saved using Desktop window menu
        • +
      • Visual indication that command line arguments are + still being processed
        • +
      • Groovy script execution from URL
        • +
      • Colour by annotation default min and max colours in + preferences
        • +
      • Automatically associate PDB files dragged onto an + alignment with sequences that have high similarity and + matching IDs
        • +
      • Update JGoogleAnalytics to latest release (0.3)
        • +
      • 'view structures' option to open many + structures in same window
        • +
      • Sort associated views menu option for tree panel
        • +
      • Group all JABA and non-JABA services for a particular + analysis function in its own submenu
        • +
      Applet +
        +
      • Userdefined and autogenerated annotation rows for + groups
        • +
      • Adjustment of alignment annotation pane height
        • +
      • Annotation scrollbar for annotation panel
        • +
      • Drag to reorder annotation rows in annotation panel
        • +
      • 'automaticScrolling' parameter
        • +
      • Allow sequences with partial ID string matches to be + annotated from GFF/Jalview features files
        • +
      • Sequence logo annotation row in applet
        • +
      • Absolute paths relative to host server in applet + parameters are treated as such
        • +
      • New in the JalviewLite javascript API: +
          +
        • JalviewLite.js javascript library
          • +
        • Javascript callbacks for +
            +
          • Applet initialisation
            • +
          • Sequence/alignment mouse-overs and selections
            • +
          +
          • +
        • scrollTo row and column alignment scrolling + functions
          • +
        • Select sequence/alignment regions from javascript
          • +
        • javascript structure viewer harness to pass + messages between Jmol and Jalview when running as + distinct applets
          • +
        • sortBy method
          • +
        • Set of applet and application examples shipped + with documentation
          • +
        • New example to demonstrate JalviewLite and Jmol + javascript message exchange
          • +
        +
      General +
        +
      • Enable Jmol displays to be associated with multiple + multiple alignments
        • +
      • Option to automatically sort alignment with new tree
        • +
      • User configurable link to enable redirects to a + www.Jalview.org mirror
        • +
      • Jmol colours option for Jmol displays
        • +
      • Configurable newline string when writing alignment + and other flat files
        • +
      • Allow alignment annotation description lines to + contain html tags
        • +
      Documentation and Development +
        +
      • Add groovy test harness for bulk load testing to + examples
        • +
      • Groovy script to load and align a set of sequences + using a web service before displaying the result in the + Jalview desktop
        • +
      • Restructured javascript and applet api documentation
        • +
      • Ant target to publish example html files with applet + archive
        • +
      • Netbeans project for building Jalview from source
        • +
      • ant task to create online javadoc for Jalview source
        • +
      		Application +
        +
      • User defined colourscheme throws exception when + current built in colourscheme is saved as new scheme
        • +
      • AlignFrame->Save in application pops up save + dialog for valid filename/format
        • +
      • Cannot view associated structure for UniProt sequence
        • +
      • PDB file association breaks for UniProt sequence + P37173
        • +
      • Associate PDB from file dialog does not tell you + which sequence is to be associated with the file
        • +
      • Find All raises null pointer exception when query + only matches sequence IDs
        • +
      • Pre 2.6 Jalview project cannot be loaded into v2.6
        • +
      • Jalview project with Jmol views created with Jalview + 2.4 cannot be loaded
        • +
      • Filetype associations not installed for webstart + launch
        • +
      • Two or more chains in a single PDB file associated + with sequences in different alignments do not get coloured + by their associated sequence
        • +
      • Visibility status of autocalculated annotation row + not preserved when project is loaded
        • +
      • Annotation row height and visibility attributes not + stored in Jalview project
        • +
      • Tree bootstraps are not preserved when saved as a + Jalview project
        • +
      • Envision2 workflow tooltips are corrupted
        • +
      • Enabling show group conservation also enables colour + by conservation
        • +
      • Duplicate group associated conservation or consensus + created on new view
        • +
      • Annotation scrollbar not displayed after 'show + all hidden annotation rows' option selected
        • +
      • Alignment quality not updated after alignment + annotation row is hidden then shown
        • +
      • Preserve colouring of structures coloured by + sequences in pre Jalview 2.7 projects
        • +
      • Web service job parameter dialog is not laid out + properly
        • +
      • Web services menu not refreshed after 'reset + services' button is pressed in preferences
        • +
      • Annotation off by one in Jalview v2_3 example project
        • +
      • Structures imported from file and saved in project + get name like jalview_pdb1234.txt when reloaded
        • +
      • Jalview does not always retrieve progress of a JABAWS + job execution in full once it is complete
        • +
      Applet +
        +
      • Alignment height set incorrectly when lots of + annotation rows are displayed
        • +
      • Relative URLs in feature HTML text not resolved to + codebase
        • +
      • View follows highlighting does not work for positions + in sequences
        • +
      • <= shown as = in tooltip
        • +
      • Export features raises exception when no features + exist
        • +
      • Separator string used for serialising lists of IDs + for javascript api is modified when separator string + provided as parameter
        • +
      • Null pointer exception when selecting tree leaves for + alignment with no existing selection
        • +
      • Relative URLs for datasources assumed to be relative + to applet's codebase
        • +
      • Status bar not updated after finished searching and + search wraps around to first result
        • +
      • StructureSelectionManager instance shared between + several Jalview applets causes race conditions and memory + leaks
        • +
      • Hover tooltip and mouseover of position on structure + not sent from Jmol in applet
        • +
      • Certain sequences of javascript method calls to + applet API fatally hang browser
        • +
      General +
        +
      • View follows structure mouseover scrolls beyond + position with wrapped view and hidden regions
        • +
      • Find sequence position moves to wrong residue + with/without hidden columns
        • +
      • Sequence length given in alignment properties window + is off by 1
        • +
      • InvalidNumberFormat exceptions thrown when trying to + import PDB like structure files
        • +
      • Positional search results are only highlighted + between user-supplied sequence start/end bounds
        • +
      • End attribute of sequence is not validated
        • +
      • Find dialog only finds first sequence containing a + given sequence position
        • +
      • Sequence numbering not preserved in MSF alignment + output
        • +
      • Jalview PDB file reader does not extract sequence + from nucleotide chains correctly
        • +
      • Structure colours not updated when tree partition + changed in alignment
        • +
      • Sequence associated secondary structure not correctly + parsed in interleaved stockholm
        • +
      • Colour by annotation dialog does not restore current + state
        • +
      • Hiding (nearly) all sequences doesn't work + properly
        • +
      • Sequences containing lowercase letters are not + properly associated with their pdb files
        • +
      Documentation and Development +
        +
      • schemas/JalviewWsParamSet.xsd corrupted by + ApplyCopyright tool
        • +
      +
      + 2.6.1
      15/11/2010 +
      +       		Application +
        +
      • New warning dialog when the Jalview Desktop cannot + contact web services
        • +
      • JABA service parameters for a preset are shown in + service job window
        • +
      • JABA Service menu entries reworded
        • +
      		+
        +
      • Modeller PIR IO broken - cannot correctly import a + pir file emitted by Jalview
        • +
      • Existing feature settings transferred to new + alignment view created from cut'n'paste
        • +
      • Improved test for mixed amino/nucleotide chains when + parsing PDB files
        • +
      • Consensus and conservation annotation rows + occasionally become blank for all new windows
        • +
      • Exception raised when right clicking above sequences + in wrapped view mode
        • +
      Application +
        +
      • multiple multiply aligned structure views cause cpu + usage to hit 100% and computer to hang
        • +
      • Web Service parameter layout breaks for long user + parameter names
        • +
      • Jaba service discovery hangs desktop if Jaba server + is down
        • +
      +
      +
      + 2.6
      26/9/2010 +
      +       		Application +
        +
      • Support for Java bioinformatics + analysis web services + (JABAWS) +
        • +
      • Web Services preference tab
        • +
      • Analysis parameters dialog box and user defined + preferences
        • +
      • Improved speed and layout of Envision2 service menu
        • +
      • Superpose structures using associated sequence + alignment
        • +
      • Export coordinates and projection as CSV from PCA + viewer
        • +
      Applet +
        +
      • enable javascript: execution by the applet via the + link out mechanism
        • +
      Other +
        +
      • Updated the Jmol Jalview interface to work with Jmol + series 12
        • +
      • The Jalview Desktop and JalviewLite applet now + require Java 1.5
        • +
      • Allow Jalview feature colour specification for GFF + sequence annotation files
        • +
      • New 'colour by label' keword in Jalview feature file + type colour specification
        • +
      • New Jalview Desktop Groovy API method that allows a + script to check if it being run in an interactive session or + in a batch operation from the Jalview command line
        • +
      		+
        +
      • clustalx colourscheme colours Ds preferentially when + both D+E are present in over 50% of the column
        • +
      Application +
        +
      • typo in AlignmentFrame->View->Hide->all but + selected Regions menu item
        • +
      • sequence fetcher replaces ',' for ';' when the ',' is + part of a valid accession ID
        • +
      • fatal OOM if object retrieved by sequence fetcher + runs out of memory
        • +
      • unhandled Out of Memory Error when viewing pca + analysis results
        • +
      • InstallAnywhere builds fail to launch on OS X java + 10.5 update 4 (due to apple Java 1.6 update)
        • +
      • Installanywhere Jalview silently fails to launch
        • +
      Applet +
        +
      • Jalview.getFeatureGroups() raises an + ArrayIndexOutOfBoundsException if no feature groups are + defined.
        • +
      +
      +
      + 2.5.1
      14/6/2010 +
      +       		+
        +
      • Alignment prettyprinter doesn't cope with long + sequence IDs
        • +
      • clustalx colourscheme colours Ds preferentially when + both D+E are present in over 50% of the column
        • +
      • nucleic acid structures retrieved from PDB do not + import correctly
        • +
      • More columns get selected than were clicked on when a + number of columns are hidden
        • +
      • annotation label popup menu not providing correct + add/hide/show options when rows are hidden or none are + present
        • +
      • Stockholm format shown in list of readable formats, + and parser copes better with alignments from RFAM.
        • +
      • CSV output of consensus only includes the percentage + of all symbols if sequence logo display is enabled
        • -
      - Applet -
        -
      • annotation panel disappears when annotation is - hidden/removed
        • -
      - Application -
        -
      • Alignment view not redrawn properly when new alignment - opened where annotation panel is visible but no annotations are - present on alignment
        • -
      • pasted region containing hidden columns is incorrectly - displayed in new alignment window
        • -
      • Jalview slow to complete operations when stdout is flooded - (fix is to close the Jalview console)
        • -
      • typo in AlignmentFrame->View->Hide->all but - selected Rregions menu item.
        • -
      • inconsistent group submenu and Format submenu entry 'Un' or - 'Non'conserved
        • -
      • Sequence feature settings are being shared by multiple - distinct alignments
        • -
      • group annotation not recreated when tree partition is - changed
        • -
      • double click on group annotation to select sequences does - not propagate to associated trees
        • -
      • Mac OSX specific issues: -
          -
        • exception raised when mouse clicked on desktop window - background
          • -
        • Desktop menu placed on menu bar and application name set - correctly
          • -
        • sequence feature settings not wide enough for the save - feature colourscheme button
          • -
        -
        • -
      -
      -
      2.5
      - 30/4/2010
      -       		New Capabilities -
        -
      • URL links generated from description line for - regular-expression based URL links (applet and application) -
      • Non-positional feature URL links are shown in link menu
        • -
      • Linked viewing of nucleic acid sequences and structures
        • -
      • Automatic Scrolling option in View menu to display the - currently highlighted region of an alignment.
        • -
      • Order an alignment by sequence length, or using the average - score or total feature count for each sequence.
        • -
      • Shading features by score or associated description
        • -
      • Subdivide alignment and groups based on identity of selected - subsequence (Make Groups from Selection).
        • -
      • New hide/show options including Shift+Control+H to hide - everything but the currently selected region.
        • - -
      - Application -
        -
      • Fetch DB References capabilities and UI expanded to support - retrieval from DAS sequence sources
        • -
      • Local DAS Sequence sources can be added via the command line - or via the Add local source dialog box.
        • -
      • DAS Dbref and DbxRef feature types are parsed as database - references and protein_name is parsed as description line (BioSapiens - terms).
        • -
      • Enable or disable non-positional feature and database - references in sequence ID tooltip from View menu in application.
        • - +
      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.
          • -
        -
        • -
      -       		+
        +
      • Source field in GFF files parsed as feature source + rather than description
        • +
      • Non-positional features are now included in sequence + feature and gff files (controlled via non-positional feature + visibility in tooltip).
        • +
      • URL links generated for all feature links (bugfix)
        • +
      • Added URL embedding instructions to features file + documentation.
        • +
      • Codons containing ambiguous nucleotides translated as + 'X' in peptide product
        • +
      • Match case switch in find dialog box works for both + sequence ID and sequence string and query strings do not + have to be in upper case to match case-insensitively.
        • +
      • AMSA files only contain first column of + multi-character column annotation labels
        • +
      • Jalview Annotation File generation/parsing consistent + with documentation (e.g. Stockholm annotation can be + exported and re-imported)
        • +
      • PDB files without embedded PDB IDs given a friendly + name
        • +
      • Find incrementally searches ID string matches as well + as subsequence matches, and correctly reports total number + of both.
        • +
      • Application: +
          +
        • Better handling of exceptions during sequence + retrieval
          • +
        • Dasobert generated non-positional feature URL + link text excludes the start_end suffix
          • +
        • DAS feature and source retrieval buttons disabled + when fetch or registry operations in progress.
          • +
        • PDB files retrieved from URLs are cached properly
          • +
        • Sequence description lines properly shared via + VAMSAS
          • +
        • Sequence fetcher fetches multiple records for all + data sources
          • +
        • Ensured that command line das feature retrieval + completes before alignment figures are generated.
          • +
        • Reduced time taken when opening file browser for + first time.
          • +
        • isAligned check prior to calculating tree, PCA or + submitting an MSA to JNet now excludes hidden sequences.
          • +
        • User defined group colours properly recovered + from Jalview projects.
          • +
        +
        • +
      +
      +
      + 2.4.0.b2
      28/10/2009 +
      +       		+
        +
      • Experimental support for google analytics usage + tracking.
        • +
      • Jalview privacy settings (user preferences and docs).
        • +
      +       		+
        +
      • Race condition in applet preventing startup in + jre1.6.0u12+.
        • +
      • Exception when feature created from selection beyond + length of sequence.
        • +
      • Allow synthetic PDB files to be imported gracefully
        • +
      • Sequence associated annotation rows associate with + all sequences with a given id
        • +
      • Find function matches case-insensitively for sequence + ID string searches
        • +
      • Non-standard characters do not cause pairwise + alignment to fail with exception
        • +
      Application Issues +
        +
      • Sequences are now validated against EMBL database
        • +
      • Sequence fetcher fetches multiple records for all + data sources
        • +
      InstallAnywhere Issues +
        +
      • Dock icon works for Mac OS X java (Mac 1.6 update + issue with installAnywhere mechanism)
        • +
      • Command line launching of JARs from InstallAnywhere + version (java class versioning error fixed)
        • +
      +
      + +
      + 2.4
      27/8/2008 +
      +       		User Interface +
        +
      • Linked highlighting of codon and amino acid from + translation and protein products
        • +
      • Linked highlighting of structure associated with + residue mapping to codon position
        • +
      • Sequence Fetcher provides example accession numbers + and 'clear' button
        • +
      • MemoryMonitor added as an option under Desktop's + Tools menu
        • +
      • Extract score function to parse whitespace separated + numeric data in description line
        • +
      • Column labels in alignment annotation can be centred.
        • +
      • Tooltip for sequence associated annotation give name + of sequence
        • +
      Web Services and URL fetching +
        +
      • JPred3 web service
        • +
      • Prototype sequence search client (no public services + available yet)
        • +
      • Fetch either seed alignment or full alignment from + PFAM
        • +
      • URL Links created for matching database cross + references as well as sequence ID
        • +
      • URL Links can be created using regular-expressions
        • +
      Sequence Database Connectivity +
        +
      • Retrieval of cross-referenced sequences from other + databases
        • +
      • Generalised database reference retrieval and + validation to all fetchable databases
        • +
      • Fetch sequences from DAS sources supporting the + sequence command
        • +
      Import and Export +
    • export annotation rows as CSV for spreadsheet import
      • +
    • Jalview projects record alignment dataset associations, + EMBL products, and cDNA sequence mappings
      • +
    • Sequence Group colour can be specified in Annotation + File
      • +
    • Ad-hoc colouring of group in Annotation File using RGB + triplet as name of colourscheme
      • + VAMSAS Client capabilities (Experimental) +
        +
      • treenode binding for VAMSAS tree exchange
        • +
      • local editing and update of sequences in VAMSAS + alignments (experimental)
        • +
      • Create new or select existing session to join
        • +
      • load and save of vamsas documents
        • +
      Application command line +
        +
      • -tree parameter to open trees (introduced for passing + from applet)
        • +
      • -fetchfrom command line argument to specify nicknames + of DAS servers to query for alignment features
        • +
      • -dasserver command line argument to add new servers + that are also automatically queried for features
        • +
      • -groovy command line argument executes a given groovy + script after all input data has been loaded and parsed
        • +
      Applet-Application data exchange +
        +
      • Trees passed as applet parameters can be passed to + application (when using "View in full + application")
        • +
      Applet Parameters +
        +
      • feature group display control parameter
        • +
      • debug parameter
        • +
      • showbutton parameter
        • +
      Applet API methods +
        +
      • newView public method
        • +
      • Window (current view) specific get/set public methods
        • +
      • Feature display control methods
        • +
      • get list of currently selected sequences
        • +
      New Jalview distribution features +
        +
      • InstallAnywhere Installer upgraded to IA 2008 VP1
        • +
      • RELEASE file gives build properties for the latest + Jalview release.
        • +
      • Java 1.1 Applet build made easier and donotobfuscate + property controls execution of obfuscator
        • +
      • Build target for generating source distribution
        • +
      • Debug flag for javacc
        • +
      • .jalview_properties file is documented (slightly) in + jalview.bin.Cache
        • +
      • Continuous Build Integration for stable and + development version of Application, Applet and source + distribution
        • +
      		+
        +
      • selected region output includes visible annotations + (for certain formats)
        • +
      • edit label/displaychar contains existing label/char + for editing
        • +
      • update PDBEntries when DBRefEntries change (vamsas)
        • +
      • shorter peptide product names from EMBL records
        • +
      • Newick string generator makes compact representations
        • +
      • bootstrap values parsed correctly for tree files with + comments
        • +
      • pathological filechooser bug avoided by not allowing + filenames containing a ':'
        • +
      • Fixed exception when parsing GFF files containing + global sequence features
        • +
      • Alignment datasets are finalized only when number of + references from alignment sequences goes to zero
        • +
      • Close of tree branch colour box without colour + selection causes cascading exceptions
        • +
      • occasional negative imgwidth exceptions
        • +
      • better reporting of non-fatal warnings to user when + file parsing fails.
        • +
      • Save works when Jalview project is default format
        • +
      • Save as dialog opened if current alignment format is + not a valid output format
        • +
      • UniProt canonical names introduced for both das and + vamsas
        • +
      • Histidine should be midblue (not pink!) in Zappo
        • +
      • error messages passed up and output when data read + fails
        • +
      • edit undo recovers previous dataset sequence when + sequence is edited
        • +
      • allow PDB files without pdb ID HEADER lines (like + those generated by MODELLER) to be read in properly
        • +
      • allow reading of JPred concise files as a normal + filetype
        • +
      • Stockholm annotation parsing and alignment properties + import fixed for PFAM records
        • +
      • Structure view windows have correct name in Desktop + window list
        • +
      • annotation consisting of sequence associated scores + can be read and written correctly to annotation file
        • +
      • Aligned cDNA translation to aligned peptide works + correctly
        • +
      • Fixed display of hidden sequence markers and + non-italic font for representatives in Applet
        • +
      • Applet Menus are always embedded in applet window on + Macs.
        • +
      • Newly shown features appear at top of stack (in + Applet)
        • +
      • Annotations added via parameter not drawn properly + due to null pointer exceptions
        • +
      • Secondary structure lines are drawn starting from + first column of alignment
        • +
      • UniProt XML import updated for new schema release in + July 2008
        • +
      • Sequence feature to sequence ID match for Features + file is case-insensitive
        • +
      • Sequence features read from Features file appended to + all sequences with matching IDs
        • +
      • PDB structure coloured correctly for associated views + containing a sub-sequence
        • +
      • PDB files can be retrieved by applet from Jar files
        • +
      • feature and annotation file applet parameters + referring to different directories are retrieved correctly
        • + +
      • Fixed application hang whilst waiting for + splash-screen version check to complete
        • +
      • Applet properly URLencodes input parameter values + when passing them to the launchApp service
        • +
      • display name and local features preserved in results + retrieved from web service
        • +
      • Visual delay indication for sequence retrieval and + sequence fetcher initialisation
        • +
      • updated Application to use DAS 1.53e version of + dasobert DAS client
        • +
      • Re-instated Full AMSA support and .amsa file + association
        • +
      • Fixed parsing of JNet Concise annotation sans + sequences +
        • +
      +
      +
      + 2.3
      9/5/07 +
      +       		+
        +
      • Jmol 11.0.2 integration
        • +
      • PDB views stored in Jalview XML files
        • +
      • Slide sequences
        • +
      • Edit sequence in place
        • +
      • EMBL CDS features
        • +
      • DAS Feature mapping
        • +
      • Feature ordering
        • +
      • Alignment Properties
        • +
      • Annotation Scores
        • +
      • Sort by scores
        • +
      • Feature/annotation editing in applet
        • +
      +       		+
        +
      • Headless state operation in 2.2.1
        • +
      • Incorrect and unstable DNA pairwise alignment
        • +
      • Cut and paste of sequences with annotation
        • +
      • Feature group display state in XML
        • +
      • Feature ordering in XML
        • +
      • blc file iteration selection using filename # suffix
        • +
      • Stockholm alignment properties
        • +
      • Stockhom alignment secondary structure annotation
        • +
      • 2.2.1 applet had no feature transparency
        • +
      • Number pad keys can be used in cursor mode
        • +
      • Structure Viewer mirror image resolved
        • +
      +
      -
      2.4.0.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)
        • -
      -
      +
      +
      + 2.2.1
      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 -
        2.4
        - 27/8/2008
        -
      		User Interface -
        -
      • Linked highlighting of codon and amino acid from translation - and protein products
        • -
      • Linked highlighting of structure associated with residue - mapping to codon position
        • -
      • Sequence Fetcher provides example accession numbers and - 'clear' button
        • -
      • MemoryMonitor added as an option under Desktop's Tools menu
        • -
      • Extract score function to parse whitespace separated numeric - data in description line
        • -
      • Column labels in alignment annotation can be centred.
        • -
      • Tooltip for sequence associated annotation give name of - sequence
        • -
      - Web Services and URL fetching -
        -
      • JPred3 web service
        • -
      • Prototype sequence search client (no public services - available yet)
        • -
      • Fetch either seed alignment or full alignment from PFAM
        • -
      • URL Links created for matching database cross references as - well as sequence ID
        • -
      • URL Links can be created using regular-expressions
        • -
      - Sequence Database Connectivity -
        -
      • Retrieval of cross-referenced sequences from other databases -
        • -
      • Generalised database reference retrieval and validation to - all fetchable databases
        • -
      • Fetch sequences from DAS sources supporting the sequence - command
        • -
      - Import and Export -
    • export annotation rows as CSV for spreadsheet import
      • -
    • Jalview projects record alignment dataset associations, EMBL - products, and cDNA sequence mappings
      • -
    • Sequence Group colour can be specified in Annotation File
      • -
    • Ad-hoc colouring of group in Annotation File using RGB - triplet as name of colourscheme
      • - - VAMSAS Client capabilities (Experimental) -
        -
      • treenode binding for VAMSAS tree exchange
        • -
      • local editing and update of sequences in VAMSAS alignments - (experimental)
        • -
      • Create new or select existing session to join
        • -
      • load and save of vamsas documents
        • -
      - Application command line -
        -
      • -tree parameter to open trees (introduced for passing from - applet)
        • -
      • -fetchfrom command line argument to specify nicknames of DAS - servers to query for alignment features
        • -
      • -dasserver command line argument to add new servers that are - also automatically queried for features
        • -
      • -groovy command line argument executes a given groovy script - after all input data has been loaded and parsed
        • -
      - Applet-Application data exchange -
        -
      • Trees passed as applet parameters can be passed to - application (when using "View in full application")
        • -
      - Applet Parameters -
        -
      • feature group display control parameter
        • -
      • debug parameter
        • -
      • showbutton parameter
        • -
      - Applet API methods -
        -
      • newView public method
        • -
      • Window (current view) specific get/set public methods
        • -
      • Feature display control methods
        • -
      • get list of currently selected sequences
        • -
      - New Jalview distribution features -
        -
      • InstallAnywhere Installer upgraded to IA 2008 VP1
        • -
      • RELEASE file gives build properties for the latest Jalview - release.
        • -
      • Java 1.1 Applet build made easier and donotobfuscate - property controls execution of obfuscator
        • -
      • Build target for generating source distribution
        • -
      • Debug flag for javacc
        • -
      • .jalview_properties file is documented (slightly) in - jalview.bin.Cache
        • -
      • Continuous Build Integration for stable and development - version of Application, Applet and source distribution
        • -
      + +
    • '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. -
      		-
        -
      • 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
        • -
      -       		 
      -

       

      + +
    +
    • +
    + 2.1.1
    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
      • +
    +     		 
    +