X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=3fe08cb98b0c0dd5e045243a9ae29f365175b26e;hb=a012e2133484a7a43c7cb7ebe9897feaaa633ee1;hp=19fa2857ba807ec9052c2ee0274c24d9ed1c9cbd;hpb=0943de76f6a7435894e72479671642c05f2f3687;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 19fa285..3fe08cb 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -23,368 +23,1190 @@ Release History -

Release History

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-
- Release -
- 		-
- New Features -
- 		-
- Issues Resolved -
-
- 2.9
1/9/2015 -
General -
    -
Application -
    -
- Applet -
    -
- 		- General -
    -
  • Make selection for columns now works on marked columns - rather than columns in rubber-band selection region.
    • -
- - Application -
    -
- Deployment and Documentation -
    -
Application Known issues -
    -
Applet Known Issues -
    -
-
-
- 2.8.2b1
15/12/2014 -
- 		-
-
- 		-
-
  • Reinstated the display of default example file on startup
    • -
  • All pairs shown in Jalview window when viewing result of pairwise alignment
    • -
-
-
- 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
    • -
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
    • +

    + Release History +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - + + + + - + - - - + Applet +
      +
    • Remove group option is shown even when selection is + not a group
      • +
    • Apply to all groups ticked but colourscheme changes + don't affect groups
      • +
    • Documented RNA Helices and T-Coffee Scores as valid + colourscheme name
      • +
    • Annotation labels drawn on sequence IDs when + Annotation panel is not displayed
      • +
    • Increased font size for dropdown menus on OSX and + embedded windows
      • +
    Other +
      +
    • Consensus sequence for alignments/groups with a + single sequence were not calculated
      • +
    • annotation files that contain only groups imported as + annotation and junk sequences
      • +
    • Fasta files with sequences containing '*' incorrectly + recognised as PFAM or BLC
      • +
    • conservation/PID slider apply all groups option + doesn't affect background (2.8.0b1) +
    • +
    • redundancy highlighting is erratic at 0% and 100%
      • +
    • Remove gapped columns fails for sequences with ragged + trailing gaps
      • +
    • AMSA annotation row with leading spaces is not + registered correctly on import
      • +
    • Jalview crashes when selecting PCA analysis for + certain alignments
      • +
    • Opening the colour by annotation dialog for an + existing annotation based 'use original colours' + colourscheme loses original colours setting
      • +
    + + + + - - - + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - + + + + + - - - - - - - - - - +
  • 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.
      • +
    + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    +
    + Release +
    +     		+
    + New Features +
    +     		+
    + Issues Resolved +
    +
    +
    + 2.10.0b1
    + 25/10/2016     +
    +     		Application +
      +
    • 3D Structure chooser opens with 'Cached structures' + view if structures already loaded
      • +
    • Progress bar reports models as they are loaded to + structure views
      • +
    		+
    + General +
      +
    • Colour by conservation always enabled and no tick + shown in menu when BLOSUM or PID shading applied
      • +
    • FER1_ARATH and FER2_ARATH labels were switched in + example sequences/projects/trees
      • +
    + Application +
      +
    • Jalview projects with views of local PDB structure + files saved on Windows cannot be opened on OSX
      • +
    • Multiple structure views can be opened and + superposed without timeout for structures with multiple + models or multiple sequences in alignment
      • +
    • Cannot import or associated local PDB files without + a PDB ID HEADER line
      • +
    • RMSD is not output in Jmol console when + superposition is performed
      • +
    • Drag and drop of URL from Browser fails for Linux + and OSX versions earlier than El Capitan
      • +
    • ENA client ignores invalid content from ENA server
      • +
    • Exceptions are not raised in console when ENA + client attempts to fetch non-existent IDs via Fetch DB + Refs UI option
      • +
    • Exceptions are not raised in console when a new + view is created on the alignment
      • +
    • OSX right-click fixed for group selections: + CMD-click to insert/remove gaps in groups and CTRL-click + to open group pop-up menu
      • +
    + Build and deployment +
      +
    • URL link checker now copes with multi-line anchor + tags
      • +
    + New Known Issues +
      +
    • Drag and drop from URL links in browsers do not + work on Windows
      • +
    +
    +
    +
    + 2.10.0
    06/10/2016     +
    +     		General +
      +
    • + Updated Spanish translations. +
      • +
    • + Jmol now primary parser + for importing structure data to Jalview. Enables mmCIF and + better PDB parsing. +
      • +
    • + Alignment ruler shows positions relative to + reference sequence +
      • +
    • + Position/residue shown in status bar when + mousing over sequence associated annotation +
      • +
    • + Default RNA SS symbol to 'matching bracket' + for manual entry +
      • +
    • + RNA Structure consensus indicates wc-only + '()', canonical '[]' and invalid '{}' base pair populations + for each column +
      • +
    • + Feature settings popup menu options for + showing or hiding columns containing a feature +
      • +
    • + Edit selected group by double clicking on + group and sequence associated annotation labels +
      • +
    • + Sequence name added to annotation label in + select/hide columns by annotation and colour by annotation + dialogs +
      • + +
    Application +
      +
    • + Automatically hide introns when opening a + gene/transcript view +
      • +
    • + Uniprot Sequence fetcher Free Text Search + dialog +
      • +
    • + UniProt - PDB protein + structure mappings with the EMBL-EBI PDBe SIFTS database +
      • +
    • + Updated download sites used for Rfam and + Pfam sources to xfam.org +
      • +
    • + Disabled Rfam(Full) in the sequence fetcher +
      • +
    • + Show residue labels in Chimera when mousing + over sequences in Jalview +
      • +
    • + Support for reverse-complement coding + regions in ENA and EMBL +
      • +
    • + Upgrade to EMBL XML 1.2 + for record retrieval via ENA rest API +
      • +
    • + Support for ENA CDS records with reverse + complement operator +
      • +
    • + Update to groovy-2.4.6-indy - for faster + groovy script execution +
      • +
    • + New 'execute Groovy script' option in an + alignment window's Calculate menu +
      • +
    • + Allow groovy scripts that call + Jalview.getAlignFrames() to run in headless mode +
      • +
    • + Support for creating new alignment + calculation workers from groovy scripts +
      • +
    • + Store/restore reference sequence in + Jalview projects +
      • +
    • + Chain codes for a sequence's PDB + associations are now saved/restored from project +
      • +
    • + Database selection dialog always shown + before sequence fetcher is opened +
      • +
    • + Double click on an entry in Jalview's + database chooser opens a sequence fetcher +
      • +
    • + Free-text search client for UniProt using + the UniProt REST API +
      • +
    • + -nonews command line parameter to prevent + the news reader opening +
      • +
    • + Displayed columns for PDBe and Uniprot + querying stored in preferences +
      • +
    • + Pagination for displaying PDBe and Uniprot + search results +
      • +
    • + Tooltips shown on database chooser +
      • +
    • + Reverse complement function in calculate + menu for nucleotide sequences +
      • +
    • + Alignment sort by feature scores + and feature counts preserves alignment ordering (and + debugged for complex feature sets). +
      • +
    • + Chimera 1.11.1 minimum requirement for + viewing structures with Jalview 2.10 +
      • +
    • + Retrieve + genome, transcript CCDS and gene ids via the Ensembl and + Ensembl Genomes REST API +
      • +
    • + Protein sequence variant annotation + computed for 'sequence_variant' annotation on CDS regions + (Ensembl) +
      • +
    • + ENA CDS 'show cross references' for Uniprot + sequences +
      • +
    • + Improved warning messages when DB + Ref Fetcher fails to match, or otherwise updates sequence + data from external database records. +
      • +
    • + Revised Jalview Project format for + efficient recovery of sequence coding and alignment + annotation relationships. +
      • +
    		+
    + General +
      +
    • + reinstate CTRL-click for opening pop-up + menu on OSX +
      • +
    • + Export features in Jalview format (again) + includes graduated colourschemes +
      • +
    • + More responsive when + working with big alignments and lots of hidden columns +
      • +
    • + Hidden column markers not always rendered + at right of alignment window +
      • +
    • + Tidied up links in help file table of + contents +
      • +
    • + Feature based tree calculation not shown + for DNA alignments +
      • +
    • + Hidden columns ignored during feature + based tree calculation +
      • +
    • + Alignment view stops updating when show + unconserved enabled for group on alignment +
      • +
    • + Cannot insert gaps into sequence when + set as reference +
      • +
    • + Alignment column in status incorrectly + shown as "Sequence position" when mousing over + annotation +
      • +
    • + Incorrect column numbers in ruler when + hidden columns present +
      • +
    • + Colour by RNA Helices not enabled when + user created annotation added to alignment +
      • +
    • + RNA Structure consensus only computed for + '()' base pair annotation +
      • +
    • + Enabling 'Ignore Gaps' results + in zero scores for all base pairs in RNA Structure + Consensus +
      • +
    • + Extend selection with columns containing + feature not working +
      • +
    • + Pfam format writer puts extra space at + beginning of sequence +
      • +
    • + Incomplete sequence extracted from pdb + entry 3a6s +
      • +
    • + Cannot create groups on an alignment from + from a tree when t-coffee scores are shown +
      • +
    • + Cannot import and view PDB + structures with chains containing negative resnums (4q4h) +
      • +
    • + ArithmeticExceptions raised when parsing + some structures +
      • +
    • + 'Empty' alignment blocks added + to Clustal, PIR and PileUp output +
      • +
    • + Reordering sequence features that are + not visible causes alignment window to repaint +
      • +
    • + Threshold sliders don't work in + graduated colour and colour by annotation row for e-value + scores associated with features and annotation rows +
      • +
    • + amino acid physicochemical conservation + calculation should be case independent +
      • +
    • + Remove annotation also updates hidden + columns +
      • +
    • + FER1_ARATH and FER2_ARATH mislabelled in + example file (uniref50.fa, feredoxin.fa, unaligned.fa, + exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar) +
      • +
    • + Null pointer exceptions and redraw + problems when reference sequence defined and 'show + non-conserved' enabled +
      • +
    • + Quality and Conservation are now shown on + load even when Consensus calculation is disabled +
      • +
    + Application +
      +
    • + URLs and links can't be imported by + drag'n'drop on OSX when launched via webstart (note - not + yet fixed for El Capitan) +
      • +
    • + Corrupt preferences for SVG, EPS & HTML + output when running on non-gb/us i18n platforms +
      • +
    • + Error thrown when exporting a view with + hidden sequences as flat-file alignment +
      • +
    • + InstallAnywhere distribution fails when + launching Chimera +
      • +
    • + Jalview very slow to launch via webstart + (also hotfix for 2.9.0b2) +
      • +
    • + Cannot save project when view has a + reference sequence defined +
      • +
    • + Columns are suddenly selected in other + alignments and views when revealing hidden columns +
      • +
    • + Hide columns not mirrored in complement + view in a cDNA/Protein splitframe +
      • +
    • + Cannot save/restore representative + sequence from project when only one sequence is + represented +
      • +
    • + Disabled 'Best Uniprot Coverage' option + in Structure Chooser +
      • +
    • + Modifying 'Ignore Gaps' on consensus or + structure consensus didn't refresh annotation panel +
      • +
    • + View mapping in structure view shows + mappings between sequence and all chains in a PDB file +
      • +
    • + PDB and Uniprot FTS + dialogs format columns correctly, don't display array + data, sort columns according to type +
      • +
    • + Export complete shown after destination + file chooser is cancelled during an image export +
      • +
    • + Error when querying PDB Service with + sequence name containing special characters +
      • +
    • + Manual PDB structure querying should be + case insensitive +
      • +
    • + Large tooltips with broken HTML + formatting don't wrap +
      • +
    • + Figures exported from wrapped view are + truncated so L looks like I in consensus annotation +
      • +
    • + Export features should only export the + currently displayed features for the current selection or + view +
      • +
    • + Enable 'Get Cross-References' in menu + after fetching cross-references, and restoring from project +
      • +
    • + Mouseover of a copy of a sequence is not + followed in the structure viewer +
      • +
    • + Titles for individual alignments in + splitframe not restored from project +
      • +
    • + missing autocalculated annotation at + trailing end of protein alignment in transcript/product + splitview when pad-gaps not enabled by default +
      • +
    • + amino acid physicochemical conservation + is case dependent +
      • +
    • + RSS reader doesn't stay hidden after last + article has been read (reopened issue due to + internationalisation problems) +
      • +
    • + Only offer PDB structures in structure + viewer based on sequence name, PDB and UniProt + cross-references +
      • + +
    • + No progress bar shown during export of + alignment as HTML +
      • +
    • + Structures not always superimposed after + multiple structures are shown for one or more sequences. +
      • +
    • + Reference sequence characters should not + be replaced with '.' when 'Show unconserved' format option + is enabled. +
      • +
    • + Cannot specify chain code when entering + specific PDB id for sequence +
      • +
    • + File->Export->.. as doesn't work when + 'Export hidden sequences' is enabled, but 'export hidden + columns' is disabled. +
      • +
    • + Best Quality option in structure chooser + selects lowest rather than highest resolution structures + for each sequence +
      • +
    • + Incorrect start and end reported for PDB + to sequence mapping in 'View Mappings' report +
      • + +
    + Applet +
      +
    • + Incorrect columns are selected when + hidden columns present before start of sequence +
      • +
    • + Missing dependencies on applet pages + (JSON jars) +
      • +
    • + Overview pixel size changes when + sequences are hidden in applet +
      • +
    • + Updated instructions for applet + deployment on examples pages. +
      • +
    +
    +
    +
    + 2.9.0b2
    + 16/10/2015     +
    +     		General +
      +
    • Time stamps for signed Jalview application and applet + jars
      • +
    		+
    + Application +
      +
    • Duplicate group consensus and conservation rows + shown when tree is partitioned
      • +
    • Erratic behaviour when tree partitions made with + multiple cDNA/Protein split views
      • +
    +
    +
    +
    + 2.9.0b1
    + 8/10/2015     +
    +     		General +
      +
    • Updated Spanish translations of localized text for + 2.9
      • +
    Application +
      + +
    • Signed OSX InstallAnywhere installer
      • +
    • Support for per-sequence based annotations in BioJSON
      • +
    Applet +
      +
    • Split frame example added to applet examples page
      • +
    		+
    + 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
      • -
    • Sequence database accessions imported when fetching - alignments from Rfam
      • -
    • update VARNA version to 3.91
      • +
    • VARNA RNA viewer updated to v3.93
      • +
    • VARNA views are saved in Jalview Projects
      • +
    • Pseudoknots displayed as Jalview RNA annotation can + be shown in VARNA
      • + +
    • Make groups for selection uses marked columns as well + as the active selected region
      • + +
    • Calculate UPGMA and NJ trees using sequence feature + similarity
      • +
    • New Export options +
        +
      • New Export Settings dialog to control hidden + region export in flat file generation
        • + +
      • Export alignment views for display with the BioJS MSAViewer
        • + +
      • Export scrollable SVG in HTML page
        • +
      • Optional embedding of BioJSON data when exporting + alignment figures to HTML
        • + +
      • 3D structure retrieval and display +
          +
        • Free text and structured queries with the PDBe + Search API
          • +
        • PDBe Search API based discovery and selection of + PDB structures for a sequence set
          • +
        +
        • + +
      • JPred4 employed for protein secondary structure + predictions
        • +
      • Hide Insertions menu option to hide unaligned columns + for one or a group of sequences
        • +
      • Automatically hide insertions in alignments imported + from the JPred4 web server
        • +
      • (Nearly) Native 'Quaqua' dialogs for browsing file + system on OSX
        LGPL libraries courtesy of http://www.randelshofer.ch/quaqua/ +
        • +
      • changed 'View nucleotide structure' submenu to 'View + VARNA 2D Structure'
        • +
      • change "View protein structure" menu option to "3D + Structure ..."
        • + +
      Applet +
        +
      • New layout for applet example pages
        • +
      • New parameters to enable SplitFrame view + (file2,enableSplitFrame, scaleProteinAsCdna)
        • +
      • New example demonstrating linked viewing of cDNA and + Protein alignments
        • +
      Development and deployment +
        +
      • Java 1.7 minimum requirement for Jalview 2.9
        • +
      • Include installation type and git revision in build + properties and console log output
        • +
      • Jalview Github organisation, and new github site for + storing BioJsMSA Templates
        • +
      • Jalview's unit tests now managed with TestNG
        • +
    		+ Application +
      +
    • Escape should close any open find dialogs
      • +
    • Typo in select-by-features status report
      • +
    • Consensus RNA secondary secondary structure + predictions are not highlighted in amber
      • +
    • Missing gap character in v2.7 example file means + alignment appears unaligned when pad-gaps is not enabled
      • +
    • First switch to RNA Helices colouring doesn't colour + associated structure views
      • +
    • ID width preference option is greyed out when auto + width checkbox not enabled
      • +
    • Stopped a warning dialog from being shown when + creating user defined colours
      • +
    • 'View Mapping' in structure viewer shows sequence + mappings for just that viewer's sequences
      • +
    • Workaround for superposing PDB files containing + multiple models in Chimera
      • +
    • Report sequence position in status bar when hovering + over Jmol structure
      • +
    • Cannot output gaps as '.' symbols with Selection -> + output to text box
      • +
    • Flat file exports of alignments with hidden columns + have incorrect sequence start/end
      • +
    • 'Aligning' a second chain to a Chimera structure from + Jalview fails
      • +
    • Colour schemes applied to structure viewers don't + work for nucleotide
      • +
    • Loading/cut'n'pasting an empty or invalid file leads + to a grey/invisible alignment window
      • +
    • Exported Jpred annotation from a sequence region + imports to different position
      • +
    • Space at beginning of sequence feature tooltips shown + on some platforms
      • +
    • Chimera viewer 'View | Show Chain' menu is not + populated
      • +
    • 'New View' fails with a Null Pointer Exception in + console if Chimera has been opened
      • +
    • Mouseover to Chimera not working
      • +
    • Miscellaneous ENA XML feature qualifiers not + retrieved
      • +
    • NPE in annotation renderer after 'Extract Scores'
      • +
    • If two structures in one Chimera window, mouseover of + either sequence shows on first structure
      • +
    • 'Show annotations' options should not make + non-positional annotations visible
      • +
    • Subsequence secondary structure annotation not shown + in right place after 'view flanking regions'
      • +
    • File Save As type unset when current file format is + unknown
      • +
    • Save as '.jar' option removed for saving Jalview + projects
      • +
    • Colour by Sequence colouring in Chimera more + responsive
      • +
    • Cannot 'add reference annotation' for a sequence in + several views on same alignment
      • +
    • Cannot show linked products for EMBL / ENA records
      • +
    • Jalview's tooltip wraps long texts containing no + spaces
      • +
    Applet +
      +
    • Jmol to JalviewLite mouseover/link not working
      • +
    • JalviewLite can't import sequences with ID + descriptions containing angle brackets
      • +
    General +
      +
    • Cannot export and reimport RNA secondary structure + via jalview annotation file
      • +
    • Random helix colour palette for colour by annotation + with RNA secondary structure
      • +
    • Mouseover to cDNA from STOP residue in protein + translation doesn't work.
      • +
    • hints when using the select by annotation dialog box
      • +
    • Jmol alignment incorrect if PDB file has alternate CA + positions
      • +
    • FontChooser message dialog appears to hang after + choosing 1pt font
      • +
    • Peptide secondary structure incorrectly imported from + annotation file when annotation display text includes 'e' or + 'h'
      • +
    • Cannot set colour of new feature type whilst creating + new feature
      • +
    • cDNA translation alignment should not be sequence + order dependent
      • +
    • 'Show unconserved' doesn't work for lower case + sequences
      • +
    • Nucleotide ambiguity codes involving R not recognised
      • +
    Deployment and Documentation +
      +
    • Applet example pages appear different to the rest of + www.jalview.org
      • +
    Application Known issues +
      +
    • Incomplete sequence extracted from PDB entry 3a6s
      • +
    • Misleading message appears after trying to delete + solid column.
      • +
    • Jalview icon not shown in dock after InstallAnywhere + version launches
      • +
    • Fetching EMBL reference for an RNA sequence results + fails with a sequence mismatch
      • +
    • Corrupted or unreadable alignment display when + scrolling alignment to right
      • +
    • ArrayIndexOutOfBoundsException thrown when remove + empty columns called on alignment with ragged gapped ends
      • +
    • auto calculated alignment annotation rows do not get + placed above or below non-autocalculated rows
      • +
    • Jalview dekstop becomes sluggish at full screen in + ultra-high resolution
      • +
    • Cannot disable consensus calculation independently of + quality and conservation
      • +
    • Mouseover highlighting between cDNA and protein can + become sluggish with more than one splitframe shown
      • +
    Applet Known Issues +
      +
    • Core PDB parsing code requires Jmol
      • +
    • Sequence canvas panel goes white when alignment + window is being resized
      • + +
    +
    + 2.8.2
    3/12/2014     +
    		General +
      +
    • Updated Java code signing certificate donated by + Certum.PL.
      • +
    • Features and annotation preserved when performing + pairwise alignment
      • +
    • RNA pseudoknot annotation can be + imported/exported/displayed
      • +
    • 'colour by annotation' can colour by RNA and + protein secondary structure
      • +
    • Warn user if 'Find' regular expression is invalid (mentioned + post-hoc with 2.9 release) +
      • + +
    Application +
      +
    • Extract and display secondary structure for sequences + with 3D structures
      • +
    • Support for parsing RNAML
      • +
    • Annotations menu for layout +
        +
      • sort sequence annotation rows by alignment
        • +
      • place sequence annotation above/below alignment + annotation
        • +
      +
    • Output in Stockholm format
      • +
    • Internationalisation: improved Spanish (es) + translation
      • +
    • Structure viewer preferences tab
      • +
    • Disorder and Secondary Structure annotation tracks + shared between alignments
      • +
    • UCSF Chimera launch and linked highlighting from + Jalview
      • +
    • Show/hide all sequence associated annotation rows for + all or current selection
      • +
    • disorder and secondary structure predictions + available as dataset annotation
      • +
    • Per-sequence rna helices colouring
      • -
    • 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 -
      • -
    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 -
      • +
        +
      • 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: -
        +
      • Sort by annotation score doesn't reverse order + when selected
        • +
      +
    + 2.8.1
    4/6/2014     +
    		+ + General +
      +
    • Internationalisation of user interface (usually + called i18n support) and translation for Spanish locale
      • +
    • Define/Undefine group on current selection with + Ctrl-G/Shift Ctrl-G
      • +
    • Improved group creation/removal options in + alignment/sequence Popup menu
      • +
    • Sensible precision for symbol distribution + percentages shown in logo tooltip.
      • +
    • Annotation panel height set according to amount of + annotation when alignment first opened
      • +
    Application +
      +
    • Interactive consensus RNA secondary structure + prediction VIENNA RNAAliFold JABA 2.1 service
      • +
    • Select columns containing particular features from + Feature Settings dialog
      • +
    • View all 'representative' PDB structures for selected + sequences
      • +
    • Update Jalview project format: +
      • New file extension for Jalview projects '.jvp'
        • -
      • Preserve sequence and annotation dataset (to store - secondary structure annotation,etc)
        • -
      • Per group and alignment annotation and RNA helix - colouring
        • -
      -
      • -
    • New similarity measures for PCA and Tree calculation - (PAM250)
      • -
    • Experimental support for retrieval and viewing of flanking - regions for an alignment
      • -
    -     		- Application -
      -
    • logo keeps spinning and status remains at queued or - running after job is cancelled
      • -
    • cannot export features from alignments imported from - Jalview/VAMSAS projects
      • -
    • Buggy slider for web service parameters that take float - values
      • -
    • Newly created RNA secondary structure line doesn't have - 'display all symbols' flag set
      • -
    • T-COFFEE alignment score shading scheme and other - annotation shading not saved in Jalview project
      • -
    • Local file cannot be loaded in freshly downloaded Jalview
      • -
    • Jalview icon not shown on dock in Mountain Lion/Webstart
      • -
    • Load file from desktop file browser fails
      • -
    • Occasional NPE thrown when calculating large trees
      • -
    • Cannot reorder or slide sequences after dragging an - alignment onto desktop
      • -
    • Colour by annotation dialog throws NPE after using - 'extract scores' function
      • -
    • Loading/cut'n'pasting an empty file leads to a grey - alignment window
      • -
    • Disorder thresholds rendered incorrectly after performing - IUPred disorder prediction
      • -
    • Multiple group annotated consensus rows shown when - changing 'normalise logo' display setting
      • -
    • Find shows blank dialog after 'finished searching' if - nothing matches query
      • -
    • Null Pointer Exceptions raised when sorting by feature - with lots of groups -
      • -
    • Errors in Jmol console when structures in alignment don't - overlap -
      • -
    • Not all working JABAWS services are shown in Jalview's - menu
      • -
    • JAVAWS version of Jalview fails to launch with 'invalid - literal/length code'
      • -
    • Annotation/RNA Helix colourschemes cannot be applied to - alignment with groups (actually fixed in 2.8.0b1)
      • -
    • RNA Helices and T-Coffee Scores available as default colourscheme
      • +
    • Preserve sequence and annotation dataset (to + store secondary structure annotation,etc)
      • +
    • Per group and alignment annotation and RNA helix + colouring
      • +
    + +
  • New similarity measures for PCA and Tree calculation + (PAM250)
    • +
  • Experimental support for retrieval and viewing of + flanking regions for an alignment
    • + +     		+ Application +
      +
    • logo keeps spinning and status remains at queued or + running after job is cancelled
      • +
    • cannot export features from alignments imported from + Jalview/VAMSAS projects
      • +
    • Buggy slider for web service parameters that take + float values
      • +
    • Newly created RNA secondary structure line doesn't + have 'display all symbols' flag set
      • +
    • T-COFFEE alignment score shading scheme and other + annotation shading not saved in Jalview project
      • +
    • Local file cannot be loaded in freshly downloaded + Jalview
      • +
    • Jalview icon not shown on dock in Mountain + Lion/Webstart
      • +
    • Load file from desktop file browser fails
      • +
    • Occasional NPE thrown when calculating large trees
      • +
    • Cannot reorder or slide sequences after dragging an + alignment onto desktop
      • +
    • Colour by annotation dialog throws NPE after using + 'extract scores' function
      • +
    • Loading/cut'n'pasting an empty file leads to a grey + alignment window
      • +
    • Disorder thresholds rendered incorrectly after + performing IUPred disorder prediction
      • +
    • Multiple group annotated consensus rows shown when + changing 'normalise logo' display setting
      • +
    • Find shows blank dialog after 'finished searching' if + nothing matches query
      • +
    • Null Pointer Exceptions raised when sorting by + feature with lots of groups +
      • +
    • Errors in Jmol console when structures in alignment + don't overlap +
      • +
    • Not all working JABAWS services are shown in + Jalview's menu
      • +
    • JAVAWS version of Jalview fails to launch with + 'invalid literal/length code'
      • +
    • Annotation/RNA Helix colourschemes cannot be applied + to alignment with groups (actually fixed in 2.8.0b1)
      • +
    • RNA Helices and T-Coffee Scores available as default + colourscheme
      • -
    Applet -
      -
    • Remove group option is shown even when selection is not a - group
      • -
    • Apply to all groups ticked but colourscheme changes don't - affect groups
      • -
    • Documented RNA Helices and T-Coffee Scores as valid colourscheme name
      • -
    • Annotation labels drawn on sequence IDs when Annotation panel is not displayed
      • -
    • Increased font size for dropdown menus on OSX and embedded windows
      • -
    Other -
      -
    • Consensus sequence for alignments/groups with a single - sequence were not calculated
      • -
    • annotation files that contain only groups imported as - annotation and junk sequences
      • -
    • Fasta files with sequences containing '*' incorrectly - recognised as PFAM or BLC
      • -
    • conservation/PID slider apply all groups option doesn't - affect background (2.8.0b1) -
    • -
    • redundancy highlighting is erratic at 0% and 100%
      • -
    • Remove gapped columns fails for sequences with ragged - trailing gaps
      • -
    • AMSA annotation row with leading spaces is not registered - correctly on import
      • -
    • Jalview crashes when selecting PCA analysis for certain - alignments
      • -
    • Opening the colour by annotation dialog for an existing - annotation based 'use original colours' colourscheme loses - original colours setting
      • -
    -
    - 2.8.0b1
    30/1/2014     -
    -
    + 2.8.0b1
    + 30/1/2014     +
    • Trusted certificates for JalviewLite applet and @@ -392,7 +1214,7 @@ Certum to the Jalview open source project).
      • -
    • Jalview SRS links replaced by Uniprot and EBI-search +
    • Jalview SRS links replaced by UniProt and EBI-search
    • Output in Stockholm format
    • Allow import of data from gzipped files
      • @@ -472,1273 +1294,1359 @@
    • ClassCastException when generating EPS in headless mode
    • Adjusting sequence-associated shading threshold only - changes one row's threshold
      • + changes one row's threshold
    • Preferences and Feature settings panel panel doesn't open
      • -
    • hide consensus histogram also hides conservation and - quality histograms
      • -
    +
  • hide consensus histogram also hides conservation and + quality histograms
    • +
    - 2.8
    12/11/2012 -
    		Application -
    • Support for JABAWS 2.0 Services (AACon alignment - conservation, protein disorder and Clustal Omega)
      • -
    • JABAWS server status indicator in Web Services preferences -
      • -
    • VARNA (http://varna.lri.fr) viewer for RNA structures in - Jalview alignment window
      • -
    • Updated Jalview build and deploy framework for OSX mountain - lion, windows 7, and 8
      • -
    • Nucleotide substitution matrix for PCA that supports RNA - and ambiguity codes
      • +
    + 2.8
    12/11/2012 +
    		Application +
      +
    • Support for JABAWS 2.0 Services (AACon alignment + conservation, protein disorder and Clustal Omega)
      • +
    • JABAWS server status indicator in Web Services + preferences
      • +
    • VARNA (http://varna.lri.fr) viewer for RNA structures + in Jalview alignment window
      • +
    • Updated Jalview build and deploy framework for OSX + mountain lion, windows 7, and 8
      • +
    • Nucleotide substitution matrix for PCA that supports + RNA and ambiguity codes
      • -
    • Improved sequence database retrieval GUI
      • -
    • Support fetching and database reference look up against - multiple DAS sources (Fetch all from in 'fetch db refs')
      • -
    • Jalview project improvements -
        -
      • Store and retrieve the 'belowAlignment' flag for - annotation
        • -
      • calcId attribute to group annotation rows on the - alignment
        • -
      • Store AACon calculation settings for a view in Jalview - project
        • +
      • Improved sequence database retrieval GUI
        • +
      • Support fetching and database reference look up + against multiple DAS sources (Fetch all from in 'fetch db + refs')
        • +
      • Jalview project improvements +
          +
        • Store and retrieve the 'belowAlignment' + flag for annotation
          • +
        • calcId attribute to group annotation rows on the + alignment
          • +
        • Store AACon calculation settings for a view in + Jalview project
          • + +
        +
        • +
      • horizontal scrolling gesture support
        • +
      • Visual progress indicator when PCA calculation is + running
        • +
      • Simpler JABA web services menus
        • +
      • visual indication that web service results are still + being retrieved from server
        • +
      • Serialise the dialogs that are shown when Jalview + starts up for first time
        • +
      • Jalview user agent string for interacting with HTTP + services
        • +
      • DAS 1.6 and DAS 2.0 source support using new JDAS + client library
        • +
      • Examples directory and Groovy library included in + InstallAnywhere distribution
        • +
      Applet +
        +
      • RNA alignment and secondary structure annotation + visualization applet example
        • +
      General +
        +
      • Normalise option for consensus sequence logo
        • +
      • Reset button in PCA window to return dimensions to + defaults
        • +
      • Allow seqspace or Jalview variant of alignment PCA + calculation
        • +
      • PCA with either nucleic acid and protein substitution + matrices +
      • Allow windows containing HTML reports to be exported + in HTML
        • +
      • Interactive display and editing of RNA secondary + structure contacts
        • +
      • RNA Helix Alignment Colouring
        • +
      • RNA base pair logo consensus
        • +
      • Parse sequence associated secondary structure + information in Stockholm files
        • +
      • HTML Export database accessions and annotation + information presented in tooltip for sequences
        • +
      • Import secondary structure from LOCARNA clustalw + style RNA alignment files
        • +
      • import and visualise T-COFFEE quality scores for an + alignment
        • +
      • 'colour by annotation' per sequence option to + shade each sequence according to its associated alignment + annotation
        • +
      • New Jalview Logo
        • +
      Documentation and Development +
        +
      • documentation for score matrices used in Jalview
        • +
      • New Website!
        • +
    		Application +
      +
    • PDB, Unprot and EMBL (ENA) databases retrieved via + wsdbfetch REST service
      • +
    • Stop windows being moved outside desktop on OSX
      • +
    • Filetype associations not installed for webstart + launch
      • +
    • Jalview does not always retrieve progress of a JABAWS + job execution in full once it is complete
      • +
    • revise SHMR RSBS definition to ensure alignment is + uploaded via ali_file parameter
      • +
    • Jalview 2.7 is incompatible with Jmol-12.2.2
      • +
    • View all structures superposed fails with exception
      • +
    • Jnet job queues forever if a very short sequence is + submitted for prediction
      • +
    • Cut and paste menu not opened when mouse clicked on + desktop window
      • +
    • Putting fractional value into integer text box in + alignment parameter dialog causes Jalview to hang
      • +
    • Structure view highlighting doesn't work on + windows 7
      • +
    • View all structures fails with exception shown in + structure view
      • +
    • Characters in filename associated with PDBEntry not + escaped in a platform independent way
      • +
    • Jalview desktop fails to launch with exception when + using proxy
      • +
    • Tree calculation reports 'you must have 2 or more + sequences selected' when selection is empty
      • +
    • Jalview desktop fails to launch with jar signature + failure when java web start temporary file caching is + disabled
      • +
    • DAS Sequence retrieval with range qualification + results in sequence xref which includes range qualification
      • +
    • Errors during processing of command line arguments + cause progress bar (JAL-898) to be removed
      • +
    • Replace comma for semi-colon option not disabled for + DAS sources in sequence fetcher
      • +
    • Cannot close news reader when JABAWS server warning + dialog is shown
      • +
    • Option widgets not updated to reflect user settings
      • +
    • Edited sequence not submitted to web service
      • +
    • Jalview 2.7 Webstart does not launch on mountain lion
      • +
    • InstallAnywhere installer doesn't unpack and run + on OSX Mountain Lion
      • +
    • Annotation panel not given a scroll bar when + sequences with alignment annotation are pasted into the + alignment
      • +
    • Sequence associated annotation rows not associated + when loaded from Jalview project
      • +
    • Browser launch fails with NPE on java 1.7
      • +
    • JABAWS alignment marked as finished when job was + cancelled or job failed due to invalid input
      • +
    • NPE with v2.7 example when clicking on Tree + associated with all views
      • +
    • Exceptions when copy/paste sequences with grouped + annotation rows to new window
      • +
    Applet +
      +
    • Sequence features are momentarily displayed before + they are hidden using hidefeaturegroups applet parameter
      • +
    • loading features via javascript API automatically + enables feature display
      • +
    • scrollToColumnIn javascript API method doesn't + work
      • +
    General +
      +
    • Redundancy removal fails for rna alignment
      • +
    • PCA calculation fails when sequence has been selected + and then deselected
      • +
    • PCA window shows grey box when first opened on OSX
      • +
    • Letters coloured pink in sequence logo when alignment + coloured with clustalx
      • +
    • Choosing fonts without letter symbols defined causes + exceptions and redraw errors
      • +
    • Initial PCA plot view is not same as manually + reconfigured view
      • +
    • Grouped annotation graph label has incorrect line + colour
      • +
    • Grouped annotation graph label display is corrupted + for lots of labels
      • +
    +
    +
    + 2.7
    27/09/2011 +
    +     		Application +
      +
    • Jalview Desktop News Reader
      • +
    • Tweaked default layout of web services menu
      • +
    • View/alignment association menu to enable user to + easily specify which alignment a multi-structure view takes + its colours/correspondences from
      • +
    • Allow properties file location to be specified as URL
      • +
    • Extend Jalview project to preserve associations + between many alignment views and a single Jmol display
      • +
    • Store annotation row height in Jalview project file
      • +
    • Annotation row column label formatting attributes + stored in project file
      • +
    • Annotation row order for auto-calculated annotation + rows preserved in Jalview project file
      • +
    • Visual progress indication when Jalview state is + saved using Desktop window menu
      • +
    • Visual indication that command line arguments are + still being processed
      • +
    • Groovy script execution from URL
      • +
    • Colour by annotation default min and max colours in + preferences
      • +
    • Automatically associate PDB files dragged onto an + alignment with sequences that have high similarity and + matching IDs
      • +
    • Update JGoogleAnalytics to latest release (0.3)
      • +
    • 'view structures' option to open many + structures in same window
      • +
    • Sort associated views menu option for tree panel
      • +
    • Group all JABA and non-JABA services for a particular + analysis function in its own submenu
      • +
    Applet +
      +
    • Userdefined and autogenerated annotation rows for + groups
      • +
    • Adjustment of alignment annotation pane height
      • +
    • Annotation scrollbar for annotation panel
      • +
    • Drag to reorder annotation rows in annotation panel
      • +
    • 'automaticScrolling' parameter
      • +
    • Allow sequences with partial ID string matches to be + annotated from GFF/Jalview features files
      • +
    • Sequence logo annotation row in applet
      • +
    • Absolute paths relative to host server in applet + parameters are treated as such
      • +
    • New in the JalviewLite javascript API: +
        +
      • JalviewLite.js javascript library
        • +
      • Javascript callbacks for +
          +
        • 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
      • -
    - -
  • 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
          • +
        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
            • +
          +
        -
        • -
      • 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
      • -
    +
    +
    + 2.5
    30/4/2010 +
    +     		New Capabilities +
      +
    • URL links generated from description line for + regular-expression based URL links (applet and application) + - 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
      • +
    +
    +
    + 2.2.1
    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 + -
    -
    2.4.0.b2
    - 28/10/2009
    -     		-
      -
    • Experimental support for google analytics usage tracking.
      • -
    • Jalview privacy settings (user preferences and docs).
      • -
    -     		-
      -
    • Race condition in applet preventing startup in jre1.6.0u12+.
      • -
    • Exception when feature created from selection beyond length - of sequence.
      • -
    • Allow synthetic PDB files to be imported gracefully
      • -
    • Sequence associated annotation rows associate with all - sequences with a given id
      • -
    • Find function matches case-insensitively for sequence ID - string searches
      • -
    • Non-standard characters do not cause pairwise alignment to - fail with exception
      • -
    - Application Issues -
      -
    • Sequences are now validated against EMBL database
      • -
    • Sequence fetcher fetches multiple records for all data - sources
      • -
    - InstallAnywhere Issues -
      -
    • Dock icon works for Mac OS X java (Mac 1.6 update issue with - installAnywhere mechanism)
      • -
    • Command line launching of JARs from InstallAnywhere version - (java class versioning error fixed)
      • -
    -
    -
    2.4
    - 27/8/2008
    -     		User Interface -
      -
    • Linked highlighting of codon and amino acid from translation - and protein products
      • -
    • Linked highlighting of structure associated with residue - mapping to codon position
      • -
    • Sequence Fetcher provides example accession numbers and - 'clear' button
      • -
    • MemoryMonitor added as an option under Desktop's Tools menu
      • -
    • Extract score function to parse whitespace separated numeric - data in description line
      • -
    • Column labels in alignment annotation can be centred.
      • -
    • Tooltip for sequence associated annotation give name of - sequence
      • -
    - Web Services and URL fetching -
      -
    • JPred3 web service
      • -
    • Prototype sequence search client (no public services - available yet)
      • -
    • Fetch either seed alignment or full alignment from PFAM
      • -
    • URL Links created for matching database cross references as - well as sequence ID
      • -
    • URL Links can be created using regular-expressions
      • -
    - Sequence Database Connectivity -
      -
    • Retrieval of cross-referenced sequences from other databases -
      • -
    • Generalised database reference retrieval and validation to - all fetchable databases
      • -
    • Fetch sequences from DAS sources supporting the sequence - command
      • -
    - Import and Export -
  • export annotation rows as CSV for spreadsheet import
    • -
  • Jalview projects record alignment dataset associations, EMBL - products, and cDNA sequence mappings
    • -
  • Sequence Group colour can be specified in Annotation File
    • -
  • Ad-hoc colouring of group in Annotation File using RGB - triplet as name of colourscheme
    • - - VAMSAS Client capabilities (Experimental) -
      -
    • treenode binding for VAMSAS tree exchange
      • -
    • local editing and update of sequences in VAMSAS alignments - (experimental)
      • -
    • Create new or select existing session to join
      • -
    • load and save of vamsas documents
      • -
    - Application command line -
      -
    • -tree parameter to open trees (introduced for passing from - applet)
      • -
    • -fetchfrom command line argument to specify nicknames of DAS - servers to query for alignment features
      • -
    • -dasserver command line argument to add new servers that are - also automatically queried for features
      • -
    • -groovy command line argument executes a given groovy script - after all input data has been loaded and parsed
      • -
    - Applet-Application data exchange -
      -
    • Trees passed as applet parameters can be passed to - application (when using "View in full application")
      • -
    - Applet Parameters -
      -
    • feature group display control parameter
      • -
    • debug parameter
      • -
    • showbutton parameter
      • -
    - Applet API methods -
      -
    • newView public method
      • -
    • Window (current view) specific get/set public methods
      • -
    • Feature display control methods
      • -
    • get list of currently selected sequences
      • -
    - New Jalview distribution features -
      -
    • InstallAnywhere Installer upgraded to IA 2008 VP1
      • -
    • RELEASE file gives build properties for the latest Jalview - release.
      • -
    • Java 1.1 Applet build made easier and donotobfuscate - property controls execution of obfuscator
      • -
    • Build target for generating source distribution
      • -
    • Debug flag for javacc
      • -
    • .jalview_properties file is documented (slightly) in - jalview.bin.Cache
      • -
    • Continuous Build Integration for stable and development - version of Application, Applet and source distribution
      • -
    -     		-
      -
    • selected region output includes visible annotations (for - certain formats)
      • -
    • edit label/displaychar contains existing label/char for - editing
      • -
    • update PDBEntries when DBRefEntries change (vamsas)
      • -
    • shorter peptide product names from EMBL records
      • -
    • Newick string generator makes compact representations
      • -
    • bootstrap values parsed correctly for tree files with - comments
      • -
    • pathological filechooser bug avoided by not allowing - filenames containing a ':'
      • -
    • Fixed exception when parsing GFF files containing global - sequence features
      • -
    • Alignment datasets are finalized only when number of - references from alignment sequences goes to zero
      • -
    • Close of tree branch colour box without colour selection - causes cascading exceptions
      • -
    • occasional negative imgwidth exceptions
      • -
    • better reporting of non-fatal warnings to user when file - parsing fails.
      • -
    • Save works when Jalview project is default format
      • -
    • Save as dialog opened if current alignment format is not a - valid output format
      • -
    • Uniprot canonical names introduced for both das and vamsas
      • -
    • Histidine should be midblue (not pink!) in Zappo
      • -
    • error messages passed up and output when data read fails
      • -
    • edit undo recovers previous dataset sequence when sequence - is edited
      • -
    • allow PDB files without pdb ID HEADER lines (like those - generated by MODELLER) to be read in properly
      • -
    • allow reading of JPred concise files as a normal filetype
      • -
    • Stockholm annotation parsing and alignment properties import - fixed for PFAM records
      • -
    • Structure view windows have correct name in Desktop window - list
      • -
    • annotation consisting of sequence associated scores can be - read and written correctly to annotation file
      • -
    • Aligned cDNA translation to aligned peptide works correctly
      • -
    • Fixed display of hidden sequence markers and non-italic font - for representatives in Applet
      • -
    • Applet Menus are always embedded in applet window on Macs.
      • -
    • Newly shown features appear at top of stack (in Applet)
      • -
    • Annotations added via parameter not drawn properly due to - null pointer exceptions
      • -
    • Secondary structure lines are drawn starting from first - column of alignment
      • -
    • Uniprot XML import updated for new schema release in July - 2008
      • -
    • Sequence feature to sequence ID match for Features file is - case-insensitive
      • -
    • Sequence features read from Features file appended to all - sequences with matching IDs
      • -
    • PDB structure coloured correctly for associated views - containing a sub-sequence
      • -
    • PDB files can be retrieved by applet from Jar files
      • -
    • feature and annotation file applet parameters referring to - different directories are retrieved correctly
      • - -
    • Fixed application hang whilst waiting for splash-screen - version check to complete
      • -
    • Applet properly URLencodes input parameter values when - passing them to the launchApp service
      • -
    • display name and local features preserved in results - retrieved from web service
      • -
    • Visual delay indication for sequence retrieval and sequence - fetcher initialisation
      • -
    • updated Application to use DAS 1.53e version of dasobert DAS - client
      • -
    • Re-instated Full AMSA support and .amsa file association
      • -
    • Fixed parsing of JNet Concise annotation sans - sequences
      • -
    -
    -
    2.3
    - 9/5/07
    -     		-
      -
    • Jmol 11.0.2 integration
      • -
    • PDB views stored in Jalview XML files
      • -
    • Slide sequences
      • -
    • Edit sequence in place
      • -
    • EMBL CDS features
      • -
    • DAS Feature mapping
      • -
    • Feature ordering
      • -
    • Alignment Properties
      • -
    • Annotation Scores
      • -
    • Sort by scores
      • -
    • Feature/annotation editing in applet
      • -
    -     		-
      -
    • Headless state operation in 2.2.1
      • -
    • Incorrect and unstable DNA pairwise alignment
      • -
    • Cut and paste of sequences with annotation
      • -
    • Feature group display state in XML
      • -
    • Feature ordering in XML
      • -
    • blc file iteration selection using filename # suffix
      • -
    • Stockholm alignment properties
      • -
    • Stockhom alignment secondary structure annotation
      • -
    • 2.2.1 applet had no feature transparency
      • -
    • Number pad keys can be used in cursor mode
      • -
    • Structure Viewer mirror image resolved
      • -
    -
    -
    2.2.1
    - 12/2/07
    -     		-
      -
    • Non standard characters can be read and displayed -
    • Annotations/Features can be imported/exported to the applet - via textbox -
    • Applet allows editing of sequence/annotation/group name - & description -
    • Preference setting to display sequence name in italics -
    • Annotation file format extended to allow Sequence_groups to - be defined -
    • Default opening of alignment overview panel can be specified - in preferences -
    • PDB residue numbering annotation added to associated - sequences -
    -     		-
      -
    • Applet crash under certain Linux OS with Java 1.6 installed -
    • Annotation file export / import bugs fixed -
    • PNG / EPS image output bugs fixed -
    -
    -
    2.2
    - 27/11/06
    -     		-
      -
    • Multiple views on alignment -
    • Sequence feature editing -
    • "Reload" alignment -
    • "Save" to current filename -
    • Background dependent text colour -
    • Right align sequence ids -
    • User-defined lower case residue colours -
    • Format Menu -
    • Select Menu -
    • Menu item accelerator keys -
    • Control-V pastes to current alignment -
    • Cancel button for DAS Feature Fetching -
    • PCA and PDB Viewers zoom via mouse roller -
    • User-defined sub-tree colours and sub-tree selection -
    • 'New Window' button on the 'Output to Text box' -
    -     		-
      -
    • New memory efficient Undo/Redo System -
    • Optimised symbol lookups and conservation/consensus - calculations -
    • Region Conservation/Consensus recalculated after edits -
    • Fixed Remove Empty Columns Bug (empty columns at end of - alignment) -
    • Slowed DAS Feature Fetching for increased robustness. -
    • Made angle brackets in ASCII feature descriptions display - correctly -
    • Re-instated Zoom function for PCA -
    • Sequence descriptions conserved in web service analysis - results -
    • Uniprot ID discoverer uses any word separated by ∣ -
    • WsDbFetch query/result association resolved -
    • Tree leaf to sequence mapping improved -
    • Smooth fonts switch moved to FontChooser dialog box. -
    -
    -
    2.1.1
    - 12/9/06
    -     		-
      -
    • Copy consensus sequence to clipboard
      • -
    -     		-
      -
    • Image output - rightmost residues are rendered if sequence - id panel has been resized
      • -
    • Image output - all offscreen group boundaries are rendered
      • -
    • Annotation files with sequence references - all elements in - file are relative to sequence position
      • -
    • Mac Applet users can use Alt key for group editing
      • -
    -
    -
    2.1
    - 22/8/06
    -     		-
      -
    • MAFFT Multiple Alignment in default Web Service list
      • -
    • DAS Feature fetching
      • -
    • Hide sequences and columns
      • -
    • Export Annotations and Features
      • -
    • GFF file reading / writing
      • -
    • Associate structures with sequences from local PDB files
      • -
    • Add sequences to exisiting alignment
      • -
    • Recently opened files / URL lists
      • -
    • Applet can launch the full application
      • -
    • Applet has transparency for features (Java 1.2 required)
      • -
    • Applet has user defined colours parameter
      • -
    • Applet can load sequences from parameter "sequencex"
      • -
    -     		-
      -
    • Redundancy Panel reinstalled in the Applet
      • -
    • Monospaced font - EPS / rescaling bug fixed
      • -
    • Annotation files with sequence references bug fixed
      • -
    -
    -
    2.08.1
    - 2/5/06
    -     		-
      -
    • Change case of selected region from Popup menu
      • -
    • Choose to match case when searching
      • -
    • Middle mouse button and mouse movement can compress / expand - the visible width and height of the alignment
      • -
    -     		-
      -
    • Annotation Panel displays complete JNet results
      • -
    -
    -
    2.08b
    - 18/4/06
    -     		  -
      -
    • Java 1.5 bug - InternalMessageDialog fix for threads
      • -
    • Righthand label on wrapped alignments shows correct value
      • -
    -
    -
    2.08
    - 10/4/06
    -     		-
      -
    • Editing can be locked to the selection area
      • -
    • Keyboard editing
      • -
    • Create sequence features from searches
      • -
    • Precalculated annotations can be loaded onto alignments
      • -
    • Features file allows grouping of features
      • -
    • Annotation Colouring scheme added
      • -
    • Smooth fonts off by default - Faster rendering
      • -
    • Choose to toggle Autocalculate Consensus On/Off
      • -
    -     		-
      -
    • Drag & Drop fixed on Linux
      • -
    • Jalview Archive file faster to load/save, sequence - descriptions saved.
      • -
    -
    -
    2.07
    - 12/12/05
    -     		-
      -
    • PDB Structure Viewer enhanced
      • -
    • Sequence Feature retrieval and display enhanced
      • -
    • Choose to output sequence start-end after sequence name for - file output
      • -
    • Sequence Fetcher WSDBFetch@EBI
      • -
    • Applet can read feature files, PDB files and can be used for - HTML form input
      • -
    -     		-
      -
    • HTML output writes groups and features
      • -
    • Group editing is Control and mouse click
      • -
    • File IO bugs
      • -
    -
    -
    2.06
    - 28/9/05
    -     		-
      -
    • View annotations in wrapped mode
      • -
    • More options for PCA viewer
      • -
    -     		-
      -
    • GUI bugs resolved
      • -
    • Runs with -nodisplay from command line
      • -
    -
    -
    2.05b
    - 15/9/05
    -     		-
      -
    • Choose EPS export as lineart or text
      • -
    • Jar files are executable
      • -
    • Can read in Uracil - maps to unknown residue
      • -
    -     		-
      -
    • Known OutOfMemory errors give warning message
      • -
    • Overview window calculated more efficiently
      • -
    • Several GUI bugs resolved
      • -
    -
    -
    2.05
    - 30/8/05
    -     		-
      -
    • Edit and annotate in "Wrapped" view
      • -
    -     		-
      -
    • Several GUI bugs resolved
      • -
    -
    -
    2.04
    - 24/8/05
    -     		-
      -
    • Hold down mouse wheel & scroll to change font size
      • -
    -     		-
      -
    • Improved JPred client reliability
      • -
    • Improved loading of Jalview files
      • -
    -
    -
    2.03
    - 18/8/05
    -     		-
      -
    • Set Proxy server name and port in preferences
      • -
    • Multiple URL links from sequence ids
      • -
    • User Defined Colours can have a scheme name and added to - Colour Menu
      • -
    • Choose to ignore gaps in consensus calculation
      • -
    • Unix users can set default web browser
      • -
    • Runs without GUI for batch processing
      • -
    • Dynamically generated Web Service Menus
      • -
    -     		-
      -
    • InstallAnywhere download for Sparc Solaris
      • -
    -
    -
    2.02
    - 18/7/05
    -     		  -
      -
    • Copy & Paste order of sequences maintains alignment - order.
      • -
    -
    -
    2.01
    - 12/7/05
    -     		-
      -
    • Use delete key for deleting selection.
      • -
    • Use Mouse wheel to scroll sequences.
      • -
    • Help file updated to describe how to add alignment - annotations.
      • -
    • Version and build date written to build properties file.
      • -
    • InstallAnywhere installation will check for updates at - launch of Jalview.
      • -
    -     		-
      -
    • Delete gaps bug fixed.
      • -
    • FileChooser sorts columns.
      • -
    • Can remove groups one by one.
      • -
    • Filechooser icons installed.
      • -
    • Finder ignores return character when searching. Return key - will initiate a search.
      -
      • -
    -
    -
    2.0
    - 20/6/05
    -     		-
      -
    • New codebase
      • -
    -     		 
    -

     

    + +
  • '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
    • +
+ 		 
+