X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=a97c11cd83e9d7d2f6811511513945ca095c6ad1;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=3bce79e137f3a0962c02189e6778508e29260460;hpb=75963e12376e3dbfc94e6324461024baea68178f;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 3bce79e..a97c11c 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,36 +1,897 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Release History

Release History

- - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -51,7 +912,11 @@ 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.
    • +
  • 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 - +
  • 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 + +
    • + + Applet + + Other + @@ -314,523 +1183,525 @@
  • 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) - -Application command line - -Applet-Application data exchange - -Applet Parameters - -Applet API methods - -New Jalview distribution features - + + VAMSAS Client capabilities (Experimental) + + Application command line + + Applet-Application data exchange + + Applet Parameters + + Applet API methods + + New Jalview distribution features + - - - - - - - + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    -
    Release
    -
    +
    + Release +
    +     		+
    + New Features +
    +     		+
    + Issues Resolved +
    +
    +
    + 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
      • + + +
    • Sequence database accessions imported when fetching + alignments from Rfam
      • +
    • update VARNA version to 3.91
      • + +
    • New groovy scripts for exporting aligned positions, + conservation values, and calculating sum of pairs scores.
      • +
    • Command line argument to set default JABAWS server
      • +
    • include installation type in build properties and console + log output
      • +
    • Updated Jalview project format to preserve dataset annotation
      • +
    		+ Application +
      +
    • Distinguish alignment and sequence associated RNA + structure in structure->view->VARNA
      • +
    • Raise dialog box if user deletes all sequences in an + alignment
      • +
    • Pressing F1 results in documentation opening twice
      • +
    • Sequence feature tooltip is wrapped
      • +
    • Double click on sequence associated annotation selects + only first column
      • +
    • Redundancy removal doesn't result in unlinked leaves + shown in tree
      • +
    • Undos after several redundancy removals don't undo + properly
      • +
    • Hide sequence doesn't hide associated annotation
      • +
    • User defined colours dialog box too big to fit on screen + and buttons not visible
      • +
    • author list isn't updated if already written to jalview + properties
      • +
    • Popup menu won't open after retrieving sequence from + database
      • +
    • File open window for associate PDB doesn't open
      • +
    • Left-then-right click on a sequence id opens a browser + search window
      • +
    • Cannot open sequence feature shading/sort popup menu in + feature settings dialog
      • +
    • better tooltip placement for some areas of Jalview desktop
      • +
    • Allow addition of JABAWS Server which doesn't pass + validation
      • +
    • Web services parameters dialog box is too large to fit on + screen
      • +
    • Muscle nucleotide alignment preset obscured by tooltip
      • +
    • JABAWS preset submenus don't contain newly defined + user preset
      • +
    • MSA web services warns user if they were launched with + invalid input
      • +
    • Jalview cannot contact DAS Registy when running on Java 8
      • +
    • + + 'Superpose with' submenu not shown when new view created +
      • + +
    Deployment and Documentation +
      +
    • 2G and 1G options in launchApp have no effect on memory + allocation
      • +
    • launchApp service doesn't automatically open + www.jalview.org/examples/exampleFile.jar if no file is given
      • +
    • + + InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is + available +
      • +
    Application Known issues +
      +
    • + + corrupted or unreadable alignment display when scrolling alignment + to right +
      • +
    • + + retrieval fails but progress bar continues for DAS retrieval with + large number of ID +
      • +
    • + + flatfile output of visible region has incorrect sequence start/end +
      • +
    • + + rna structure consensus doesn't update when secondary + structure tracks are rearranged +
      • +
    • + + invalid rna structure positional highlighting does not highlight + position of invalid base pairs +
      • +
    • + + out of memory errors are not raised when saving jalview project + from alignment window file menu +
      • +
    • + + Switching to RNA Helices colouring doesn't propagate to + structures +
      • +
    • + + colour by RNA Helices not enabled when user created annotation + added to alignment +
      • +
    • + + Jalview icon not shown on dock in Mountain Lion/Webstart +
      • +
    Applet Known Issues +
      +
    • + + JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies +
      • +
    • + + Jalview and Jmol example not compatible with IE9 +
      • + +
    • Sort by annotation score doesn't reverse order when + selected
      • +
    +
    + 2.8.1
    4/6/2014     +
    		+ + General +
      +
    • Internationalisation of user interface (usually called + i18n support) and translation for Spanish locale
      • +
    • Define/Undefine group on current selection with + Ctrl-G/Shift Ctrl-G
      • +
    • Improved group creation/removal options in + alignment/sequence Popup menu
      • +
    • Sensible precision for symbol distribution percentages + shown in logo tooltip.
      • +
    • Annotation panel height set according to amount of + annotation when alignment first opened
      • +
    Application +
      +
    • Interactive consensus RNA secondary structure prediction + VIENNA RNAAliFold JABA 2.1 service
      • +
    • Select columns containing particular features from Feature + Settings dialog
      • +
    • View all 'representative' PDB structures for selected + sequences
      • +
    • Update Jalview project format: +
        +
      • New file extension for Jalview projects '.jvp'
        • +
      • Preserve sequence and annotation dataset (to store + secondary structure annotation,etc)
        • +
      • Per group and alignment annotation and RNA helix + colouring
        • +
      +
      • +
    • New similarity measures for PCA and Tree calculation + (PAM250)
      • +
    • Experimental support for retrieval and viewing of flanking + regions for an alignment
      • +
    +     		+ Application +
      +
    • logo keeps spinning and status remains at queued or + running after job is cancelled
      • +
    • cannot export features from alignments imported from + Jalview/VAMSAS projects
      • +
    • Buggy slider for web service parameters that take float + values
      • +
    • Newly created RNA secondary structure line doesn't have + 'display all symbols' flag set
      • +
    • T-COFFEE alignment score shading scheme and other + annotation shading not saved in jalview project
      • +
    • Local file cannot be loaded in freshly downloaded Jalview
      • +
    • Jalview icon not shown on dock in Mountain Lion/Webstart
      • +
    • Load file from desktop file browser fails
      • +
    • Occasional NPE thrown when calculating large trees
      • +
    • Cannot reorder or slide sequences after dragging an + alignment onto desktop
      • +
    • Colour by annotation dialog throws NPE after using + 'extract scores' function
      • +
    • Loading/cut'n'pasting an empty file leads to a grey + alignment window
      • +
    • Disorder thresholds rendered incorrectly after performing + IUPred disorder prediction
      • +
    • Multiple group annotated consensus rows shown when + changing 'normalise logo' display setting
      • +
    • Find shows blank dialog after 'finished searching' if + nothing matches query
      • +
    • Null Pointer Exceptions raised when sorting by feature + with lots of groups +
      • +
    • Errors in Jmol console when structures in alignment don't + overlap +
      • +
    • Not all working JABAWS services are shown in Jalview's + menu
      • +
    • JAVAWS version of jalview fails to launch with 'invalid + literal/length code'
      • +
    • Annotation/RNA Helix colourschemes cannot be applied to + alignment with groups (actually fixed in 2.8.0b1)
      • +
    • RNA Helices and T-Coffee Scores available as default colourscheme
      • + +
    Applet +
      +
    • Remove group option is shown even when selection is not a + group
      • +
    • Apply to all groups ticked but colourscheme changes don't + affect groups
      • +
    • Documented RNA Helices and T-Coffee Scores as valid colourscheme name
      • +
    • Annotation labels drawn on sequence IDs when Annotation panel is not displayed
      • +
    • Increased font size for dropdown menus on OSX and embedded windows
      • +
    Other +
      +
    • Consensus sequence for alignments/groups with a single + sequence were not calculated
      • +
    • annotation files that contain only groups imported as + annotation and junk sequences
      • +
    • Fasta files with sequences containing '*' incorrectly + recognised as PFAM or BLC
      • +
    • conservation/PID slider apply all groups option doesn't + affect background (2.8.0b1) +
    • +
    • redundancy highlighting is erratic at 0% and 100%
      • +
    • Remove gapped columns fails for sequences with ragged + trailing gaps
      • +
    • AMSA annotation row with leading spaces is not registered + correctly on import
      • +
    • Jalview crashes when selecting PCA analysis for certain + alignments
      • +
    • Opening the colour by annotation dialog for an existing + annotation based 'use original colours' colourscheme loses + original colours setting
      • +
    +
    + 2.8.0b1
    30/1/2014     +
    +     		+
      +
    • Trusted certificates for JalviewLite applet and + Jalview Desktop application
      Certificate was donated by + Certum to the Jalview + open source project). +
      • +
    • Jalview SRS links replaced by Uniprot and EBI-search +
      • +
    • Output in Stockholm format
      • +
    • Allow import of data from gzipped files
      • +
    • Export/import group and sequence associated line + graph thresholds
      • +
    • Nucleotide substitution matrix that supports RNA and + ambiguity codes
      • +
    • Allow disorder predictions to be made on the current + selection (or visible selection) in the same way that JPred + works
      • +
    • Groovy scripting for headless jalview operation
      • +
    Other improvements +
      +
    • Upgrade desktop installer to InstallAnywhere 2013
      • +
    • COMBINE statement uses current SEQUENCE_REF and + GROUP_REF scope to group annotation rows
      • +
    • Support '' style escaping of quotes in Newick + files
      • +
    • Group options for JABAWS service by command line name
      • +
    • Empty tooltip shown for JABA service options with a + link but no description
      • +
    • Select primary source when selecting authority in + database fetcher GUI
      • +
    • Add .mfa to FASTA file extensions recognised by + Jalview
      • +
    • Annotation label tooltip text wrap
      • +
    +     		+
      +
    • Slow scrolling when lots of annotation rows are + displayed
      • +
    • Lots of NPE (and slowness) after creating RNA + secondary structure annotation line
      • +
    • Sequence database accessions not imported when + fetching alignments from Rfam
      • +
    • Incorrect SHMR submission for sequences with + identical IDs
      • +
    • View all structures does not always superpose + structures
      • +
    • Option widgets in service parameters not updated to + reflect user or preset settings
      • +
    • Null pointer exceptions for some services without + presets or adjustable parameters
      • +
    • Discover PDB IDs entry in structure menu doesn't + discover PDB xRefs
      • +
    • Exception encountered while trying to retrieve + features with DAS
      • +
    • Lowest value in annotation row isn't coloured + when colour by annotation (per sequence) is coloured
      • +
    • Keyboard mode P jumps to start of gapped region when + residue follows a gap
      • +
    • Jalview appears to hang importing an alignment with + Wrap as default or after enabling Wrap
      • +
    • 'Right click to add annotations' message + shown in wrap mode when no annotations present
      • +
    • Disorder predictions fail with NPE if no automatic + annotation already exists on alignment
      • +
    • oninit javascript function should be called after + initialisation completes
      • +
    • Remove redundancy after disorder prediction corrupts + alignment window display
      • +
    • Example annotation file in documentation is invalid
      • +
    • Grouped line graph annotation rows are not exported + to annotation file
      • +
    • Multi-harmony analysis cannot be run when only two + groups created
      • +
    • Cannot create multiple groups of line graphs with + several 'combine' statements in annotation file
      • +
    • Pressing return several times causes Number Format + exceptions in keyboard mode
      • +
    • Multi-harmony (SHMMR) method doesn't submit + correct partitions for input data
      • +
    • Translation from DNA to Amino Acids fails
      • +
    • Jalview fail to load newick tree with quoted label
      • +
    • --headless flag isn't understood
      • +
    • ClassCastException when generating EPS in headless + mode
      • +
    • Adjusting sequence-associated shading threshold only + changes one row's threshold
      • +
    • Preferences and Feature settings panel panel + doesn't open
      • +
    • hide consensus histogram also hides conservation and + quality histograms
      • +
    +
    + 2.8
    12/11/2012 +
    		Application +
    • Support for JABAWS 2.0 Services (AACon alignment + conservation, protein disorder and Clustal Omega)
      • +
    • JABAWS server status indicator in Web Services preferences +
      • +
    • VARNA (http://varna.lri.fr) viewer for RNA structures in + Jalview alignment window
      • +
    • Updated Jalview build and deploy framework for OSX mountain + lion, windows 7, and 8
      • +
    • Nucleotide substitution matrix for PCA that supports RNA + and ambiguity codes
      • + +
    • Improved sequence database retrieval GUI
      • +
    • Support fetching and database reference look up against + multiple DAS sources (Fetch all from in 'fetch db refs')
      • +
    • Jalview project improvements +
        +
      • Store and retrieve the 'belowAlignment' flag for + annotation
        • +
      • calcId attribute to group annotation rows on the + alignment
        • +
      • Store AACon calculation settings for a view in Jalview + project
        • + +
      +
      • +
    • horizontal scrolling gesture support
      • +
    • Visual progress indicator when PCA calculation is running
      • +
    • Simpler JABA web services menus
      • +
    • visual indication that web service results are still being + retrieved from server
      • +
    • Serialise the dialogs that are shown when Jalview starts up + for first time
      • +
    • Jalview user agent string for interacting with HTTP + services
      • +
    • DAS 1.6 and DAS 2.0 source support using new JDAS client + library
      • +
    • Examples directory and Groovy library included in + InstallAnywhere distribution
      • +
    Applet +
      +
    • RNA alignment and secondary structure annotation + visualization applet example
      • +
    General +
      +
    • Normalise option for consensus sequence logo
      • +
    • Reset button in PCA window to return dimensions to + defaults
      • +
    • Allow seqspace or Jalview variant of alignment PCA + calculation
      • +
    • PCA with either nucleic acid and protein substitution + matrices +
    • Allow windows containing HTML reports to be exported in + HTML
      • +
    • Interactive display and editing of RNA secondary structure + contacts
      • +
    • RNA Helix Alignment Colouring
      • +
    • RNA base pair logo consensus
      • +
    • Parse sequence associated secondary structure information + in Stockholm files
      • +
    • HTML Export database accessions and annotation information + presented in tooltip for sequences
      • +
    • Import secondary structure from LOCARNA clustalw style RNA + alignment files
      • +
    • import and visualise T-COFFEE quality scores for an + alignment
      • +
    • 'colour by annotation' per sequence option to + shade each sequence according to its associated alignment + annotation
      • +
    • New Jalview Logo
      • +
    Documentation and Development +
      +
    • documentation for score matrices used in Jalview
      • +
    • New Website!
      • +
    		Application +
      +
    • PDB, Unprot and EMBL (ENA) databases retrieved via + wsdbfetch REST service
      • +
    • Stop windows being moved outside desktop on OSX
      • +
    • Filetype associations not installed for webstart launch
      • +
    • Jalview does not always retrieve progress of a JABAWS job + execution in full once it is complete
      • +
    • revise SHMR RSBS definition to ensure alignment is + uploaded via ali_file parameter
      • +
    • Jalview 2.7 is incompatible with Jmol-12.2.2
      • +
    • View all structures superposed fails with exception
      • +
    • Jnet job queues forever if a very short sequence is + submitted for prediction
      • +
    • Cut and paste menu not opened when mouse clicked on + desktop window
      • +
    • Putting fractional value into integer text box in + alignment parameter dialog causes Jalview to hang
      • +
    • Structure view highlighting doesn't work on windows 7 +
      • +
    • View all structures fails with exception shown in + structure view
      • +
    • Characters in filename associated with PDBEntry not + escaped in a platform independent way
      • +
    • Jalview desktop fails to launch with exception when using + proxy
      • +
    • Tree calculation reports 'you must have 2 or more + sequences selected' when selection is empty
      • +
    • Jalview desktop fails to launch with jar signature failure + when java web start temporary file caching is disabled
      • +
    • DAS Sequence retrieval with range qualification results in + sequence xref which includes range qualification
      • +
    • Errors during processing of command line arguments cause + progress bar (JAL-898) to be removed
      • +
    • Replace comma for semi-colon option not disabled for DAS + sources in sequence fetcher
      • +
    • Cannot close news reader when JABAWS server warning dialog + is shown
      • +
    • Option widgets not updated to reflect user settings
      • +
    • Edited sequence not submitted to web service
      • +
    • Jalview 2.7 Webstart does not launch on mountain lion
      • +
    • InstallAnywhere installer doesn't unpack and run on + OSX Mountain Lion
      • +
    • Annotation panel not given a scroll bar when sequences + with alignment annotation are pasted into the alignment
      • +
    • Sequence associated annotation rows not associated when + loaded from Jalview project
      • +
    • Browser launch fails with NPE on java 1.7
      • +
    • JABAWS alignment marked as finished when job was cancelled + or job failed due to invalid input
      • +
    • NPE with v2.7 example when clicking on Tree associated + with all views
      • +
    • Exceptions when copy/paste sequences with grouped + annotation rows to new window
      • +
    Applet +
      +
    • Sequence features are momentarily displayed before they + are hidden using hidefeaturegroups applet parameter
      • +
    • loading features via javascript API automatically enables + feature display
      • +
    • scrollToColumnIn javascript API method doesn't work
      • +
    General +
      +
    • Redundancy removal fails for rna alignment
      • +
    • PCA calculation fails when sequence has been selected and + then deselected
      • +
    • PCA window shows grey box when first opened on OSX
      • +
    • Letters coloured pink in sequence logo when alignment + coloured with clustalx
      • +
    • Choosing fonts without letter symbols defined causes + exceptions and redraw errors
      • +
    • Initial PCA plot view is not same as manually reconfigured + view
      • +
    • Grouped annotation graph label has incorrect line colour
      • +
    • Grouped annotation graph label display is corrupted for + lots of labels
      • +
    +
    +
    + 2.7
    27/09/2011 +
    +     		Application +
      +
    • Jalview Desktop News Reader
      • +
    • Tweaked default layout of web services menu
      • +
    • View/alignment association menu to enable user to easily + specify which alignment a multi-structure view takes its + colours/correspondences from
      • +
    • Allow properties file location to be specified as URL
      • +
    • Extend Jalview project to preserve associations between + many alignment views and a single Jmol display
      • +
    • Store annotation row height in Jalview project file
      • +
    • Annotation row column label formatting attributes stored + in project file
      • +
    • Annotation row order for auto-calculated annotation rows + preserved in Jalview project file
      • +
    • Visual progress indication when Jalview state is saved + using Desktop window menu
      • +
    • Visual indication that command line arguments are still + being processed
      • +
    • Groovy script execution from URL
      • +
    • Colour by annotation default min and max colours in + preferences
      • +
    • Automatically associate PDB files dragged onto an + alignment with sequences that have high similarity and matching + IDs
      • +
    • Update JGoogleAnalytics to latest release (0.3)
      • +
    • 'view structures' option to open many structures + in same window
      • +
    • Sort associated views menu option for tree panel
      • +
    • Group all JABA and non-JABA services for a particular + analysis function in its own submenu
      • +
    Applet +
      +
    • Userdefined and autogenerated annotation rows for groups
      • +
    • Adjustment of alignment annotation pane height
      • +
    • Annotation scrollbar for annotation panel
      • +
    • Drag to reorder annotation rows in annotation panel
      • +
    • 'automaticScrolling' parameter
      • +
    • Allow sequences with partial ID string matches to be + annotated from GFF/Jalview features files
      • +
    • Sequence logo annotation row in applet
      • +
    • Absolute paths relative to host server in applet + parameters are treated as such
      • +
    • New in the JalviewLite javascript API: +
        +
      • JalviewLite.js javascript library
        • +
      • Javascript callbacks for +
          +
        • Applet initialisation
          • +
        • Sequence/alignment mouse-overs and selections
          • +
        +
        • +
      • scrollTo row and column alignment scrolling functions
        • +
      • Select sequence/alignment regions from javascript
        • +
      • javascript structure viewer harness to pass messages + between Jmol and Jalview when running as distinct applets
        • +
      • sortBy method
        • +
      • Set of applet and application examples shipped with + documentation
        • +
      • New example to demonstrate JalviewLite and Jmol + javascript message exchange
        • +
      +
    General +
      +
    • Enable Jmol displays to be associated with multiple + multiple alignments
      • +
    • Option to automatically sort alignment with new tree
      • +
    • User configurable link to enable redirects to a + www.Jalview.org mirror
      • +
    • Jmol colours option for Jmol displays
      • +
    • Configurable newline string when writing alignment and + other flat files
      • +
    • Allow alignment annotation description lines to contain + html tags
      • +
    Documentation and Development +
      +
    • Add groovy test harness for bulk load testing to examples +
      • +
    • Groovy script to load and align a set of sequences using a + web service before displaying the result in the Jalview desktop
      • +
    • Restructured javascript and applet api documentation
      • +
    • Ant target to publish example html files with applet + archive
      • +
    • Netbeans project for building Jalview from source
      • +
    • ant task to create online javadoc for Jalview source
      • +
    		Application +
      +
    • User defined colourscheme throws exception when current + built in colourscheme is saved as new scheme
      • +
    • AlignFrame->Save in application pops up save dialog for + valid filename/format
      • +
    • Cannot view associated structure for Uniprot sequence
      • +
    • PDB file association breaks for Uniprot sequence P37173
      • +
    • Associate PDB from file dialog does not tell you which + sequence is to be associated with the file
      • +
    • Find All raises null pointer exception when query only + matches sequence IDs
      • +
    • Pre 2.6 Jalview project cannot be loaded into v2.6
      • +
    • Jalview project with Jmol views created with Jalview 2.4 + cannot be loaded
      • +
    • Filetype associations not installed for webstart launch
      • +
    • Two or more chains in a single PDB file associated with + sequences in different alignments do not get coloured by their + associated sequence
      • +
    • Visibility status of autocalculated annotation row not + preserved when project is loaded
      • +
    • Annotation row height and visibility attributes not stored + in Jalview project
      • +
    • Tree bootstraps are not preserved when saved as a Jalview + project
      • +
    • Envision2 workflow tooltips are corrupted
      • +
    • Enabling show group conservation also enables colour by + conservation
      • +
    • Duplicate group associated conservation or consensus + created on new view
      • +
    • Annotation scrollbar not displayed after 'show all + hidden annotation rows' option selected
      • +
    • Alignment quality not updated after alignment annotation + row is hidden then shown
      • +
    • Preserve colouring of structures coloured by sequences in + pre Jalview 2.7 projects
      • +
    • Web service job parameter dialog is not laid out properly +
      • +
    • Web services menu not refreshed after 'reset + services' button is pressed in preferences
      • +
    • Annotation off by one in Jalview v2_3 example project
      • +
    • Structures imported from file and saved in project get + name like jalview_pdb1234.txt when reloaded
      • +
    • Jalview does not always retrieve progress of a JABAWS job + execution in full once it is complete
      • +
    Applet +
      +
    • Alignment height set incorrectly when lots of annotation + rows are displayed
      • +
    • Relative URLs in feature HTML text not resolved to + codebase
      • +
    • View follows highlighting does not work for positions in + sequences
      • +
    • <= shown as = in tooltip
      • +
    • Export features raises exception when no features exist
      • +
    • Separator string used for serialising lists of IDs for + javascript api is modified when separator string provided as + parameter
      • +
    • Null pointer exception when selecting tree leaves for + alignment with no existing selection
      • +
    • Relative URLs for datasources assumed to be relative to + applet's codebase
      • +
    • Status bar not updated after finished searching and search + wraps around to first result
      • +
    • StructureSelectionManager instance shared between several + Jalview applets causes race conditions and memory leaks
      • +
    • Hover tooltip and mouseover of position on structure not + sent from Jmol in applet
      • +
    • Certain sequences of javascript method calls to applet API + fatally hang browser
      • +
    General +
      +
    • View follows structure mouseover scrolls beyond position + with wrapped view and hidden regions
      • +
    • Find sequence position moves to wrong residue with/without + hidden columns
      • +
    • Sequence length given in alignment properties window is + off by 1
      • +
    • InvalidNumberFormat exceptions thrown when trying to + import PDB like structure files
      • +
    • Positional search results are only highlighted between + user-supplied sequence start/end bounds
      • +
    • End attribute of sequence is not validated
      • +
    • Find dialog only finds first sequence containing a given + sequence position
      • +
    • Sequence numbering not preserved in MSF alignment output
      • +
    • Jalview PDB file reader does not extract sequence from + nucleotide chains correctly
      • +
    • Structure colours not updated when tree partition changed + in alignment
      • +
    • Sequence associated secondary structure not correctly + parsed in interleaved stockholm
      • +
    • Colour by annotation dialog does not restore current state +
      • +
    • Hiding (nearly) all sequences doesn't work properly
      • +
    • Sequences containing lowercase letters are not properly + associated with their pdb files
      • +
    Documentation and Development +
      +
    • schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright + tool
      • +
    +
    + 2.6.1 +
    15/11/2010 +
    		Application +
      +
    • New warning dialog when the Jalview Desktop cannot contact + web services
      • +
    • JABA service parameters for a preset are shown in service + job window
      • +
    • JABA Service menu entries reworded
      • +
    		+
      +
    • Modeller PIR IO broken - cannot correctly import a pir + file emitted by Jalview
      • +
    • Existing feature settings transferred to new alignment + view created from cut'n'paste
      • +
    • Improved test for mixed amino/nucleotide chains when + parsing PDB files
      • +
    • Consensus and conservation annotation rows occasionally + become blank for all new windows
      • +
    • Exception raised when right clicking above sequences in + wrapped view mode
      • +
    Application +
      +
    • multiple multiply aligned structure views cause cpu usage + to hit 100% and computer to hang
      • +
    • Web Service parameter layout breaks for long user + parameter names
      • +
    • Jaba service discovery hangs desktop if Jaba server is + down
      • +
    -
    New Features
    +
    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
      • +
    		-
    Issues Resolved
    +
      +
    • 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.
      • +
    - New Capabilities + New Capabilities
    • URL links generated from description line for regular-expression based URL links (applet and application) @@ -107,125 +969,132 @@
    • 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.
      • +
    • 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.
      • +
    • Subdivide alignment and groups based on identity of selected + subsequence (Make Groups from Selection).
      • +
    • New hide/show options including Shift+Control+H to hide + everything but the currently selected region.
      • -
    -Application -
      -
    • Fetch DB References capabilities and UI expanded to support - retrieval from DAS sequence sources
      • -
    • Local DAS Sequence sources can be added via the command line - or via the Add local source dialog box.
      • -
    • DAS Dbref and DbxRef feature types are parsed as database - references and protein_name is parsed as description line (BioSapiens - terms).
      • -
    • Enable or disable non-positional feature and database - references in sequence ID tooltip from View menu in application.
      • - -
    • Group-associated consensus, sequence logos and conservation - plots
      • -
    • Symbol distributions for each column can be exported and - visualized as sequence logos
      • -
    • Optionally scale multi-character column labels to fit within - each column of annotation row
      • -
    • Optional automatic sort of associated alignment view when a - new tree is opened.
      • -
    • Jalview Java Console
      • -
    • Better placement of desktop window when moving between different screens.
      • -
    • New preference items for sequence ID tooltip and consensus - annotation
      • -
    • Client to submit sequences and IDs to Envision2 Workflows
      • -
    • Vamsas Capabilities -
        -
      • Improved VAMSAS synchronization (jalview archive used to - preserve views, structures, and tree display settings)
        • -
      • Import of vamsas documents from disk or URL via command line
        • -
      • Sharing of selected regions between views and with other - VAMSAS applications (Experimental feature!)
        • -
      • Updated API to VAMSAS version 0.2
        • -
      -
      • -
    -Applet -
      -
    • Middle button resizes annotation row height
      • -
    • New Parameters -
        -
      • sortByTree (true/false) - automatically sort the associated - alignment view by the tree when a new tree is opened.
        • -
      • showTreeBootstraps (true/false) - show or hide branch - bootstraps (default is to show them if available)
        • -
      • showTreeDistances (true/false) - show or hide branch lengths - (default is to show them if available)
        • -
      • showUnlinkedTreeNodes (true/false) - indicate if unassociated - nodes should be highlighted in the tree view
        • -
      • heightScale and widthScale (1.0 or more) - increase the - height or width of a cell in the alignment grid relative to the - current font size.
        • -
      -
      • -
    • Non-positional features displayed in sequence ID tooltip
      • -
    -Other -
      -
    • Features format: graduated colour definitions and - specification of feature scores
      • -
    • Alignment Annotations format: new keywords for group - associated annotation (GROUP_REF) and annotation row display properties - (ROW_PROPERTIES)
      • -
    • XML formats extended to support graduated feature - colourschemes, group associated annotation, and profile visualization - settings.
      • -
    		-
      -
    • Source field in GFF files parsed as feature source rather - than description
      • -
    • Non-positional features are now included in sequence feature - and gff files (controlled via non-positional feature visibility in - tooltip).
      • -
    • URL links generated for all feature links (bugfix)
      • -
    • Added URL embedding instructions to features file - documentation.
      • -
    • Codons containing ambiguous nucleotides translated as 'X' in - peptide product
      • -
    • Match case switch in find dialog box works for both sequence - ID and sequence string and query strings do not have to be in upper - case to match case-insensitively.
      • -
    • AMSA files only contain first column of multi-character - column annotation labels
      • -
    • Jalview Annotation File generation/parsing consistent with - documentation (e.g. Stockholm annotation can be exported and - re-imported)
      • -
    • PDB files without embedded PDB IDs given a friendly name
      • -
    • Find incrementally searches ID string matches as well as - subsequence matches, and correctly reports total number of both.
      • -
    • Application: -
        -
      • Better handling of exceptions during sequence retrieval
        • -
      • Dasobert generated non-positional feature URL link text - excludes the start_end suffix
        • -
      • DAS feature and source retrieval buttons disabled when fetch - or registry operations in progress.
        • -
      • PDB files retrieved from URLs are cached properly
        • -
      • Sequence description lines properly shared via VAMSAS
        • -
      • Sequence fetcher fetches multiple records for all data - sources
        • -
      • Ensured that command line das feature retrieval completes - before alignment figures are generated.
        • -
      • Reduced time taken when opening file browser for first time.
        • -
      • isAligned check prior to calculating tree, PCA or submitting - an MSA to JNet now excludes hidden sequences.
        • -
      • User defined group colours properly recovered from Jalview projects.
        • -
      -
      • -
    -     		+
      +
    • 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.
        • +
      +
      • +
    +
    -
      -
    • 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
      • -
    -     		+
      +
    • selected region output includes visible annotations (for + certain formats)
      • +
    • edit label/displaychar contains existing label/char for + editing
      • +
    • update PDBEntries when DBRefEntries change (vamsas)
      • +
    • shorter peptide product names from EMBL records
      • +
    • Newick string generator makes compact representations
      • +
    • bootstrap values parsed correctly for tree files with + comments
      • +
    • pathological filechooser bug avoided by not allowing + filenames containing a ':'
      • +
    • Fixed exception when parsing GFF files containing global + sequence features
      • +
    • Alignment datasets are finalized only when number of + references from alignment sequences goes to zero
      • +
    • Close of tree branch colour box without colour selection + causes cascading exceptions
      • +
    • occasional negative imgwidth exceptions
      • +
    • better reporting of non-fatal warnings to user when file + parsing fails.
      • +
    • Save works when Jalview project is default format
      • +
    • Save as dialog opened if current alignment format is not a + valid output format
      • +
    • Uniprot canonical names introduced for both das and vamsas
      • +
    • Histidine should be midblue (not pink!) in Zappo
      • +
    • error messages passed up and output when data read fails
      • +
    • edit undo recovers previous dataset sequence when sequence + is edited
      • +
    • allow PDB files without pdb ID HEADER lines (like those + generated by MODELLER) to be read in properly
      • +
    • allow reading of JPred concise files as a normal filetype
      • +
    • Stockholm annotation parsing and alignment properties import + fixed for PFAM records
      • +
    • Structure view windows have correct name in Desktop window + list
      • +
    • annotation consisting of sequence associated scores can be + read and written correctly to annotation file
      • +
    • Aligned cDNA translation to aligned peptide works correctly
      • +
    • Fixed display of hidden sequence markers and non-italic font + for representatives in Applet
      • +
    • Applet Menus are always embedded in applet window on Macs.
      • +
    • Newly shown features appear at top of stack (in Applet)
      • +
    • Annotations added via parameter not drawn properly due to + null pointer exceptions
      • +
    • Secondary structure lines are drawn starting from first + column of alignment
      • +
    • Uniprot XML import updated for new schema release in July + 2008
      • +
    • Sequence feature to sequence ID match for Features file is + case-insensitive
      • +
    • Sequence features read from Features file appended to all + sequences with matching IDs
      • +
    • PDB structure coloured correctly for associated views + containing a sub-sequence
      • +
    • PDB files can be retrieved by applet from Jar files
      • +
    • feature and annotation file applet parameters referring to + different directories are retrieved correctly
      • + +
    • Fixed application hang whilst waiting for splash-screen + version check to complete
      • +
    • Applet properly URLencodes input parameter values when + passing them to the launchApp service
      • +
    • display name and local features preserved in results + retrieved from web service
      • +
    • Visual delay indication for sequence retrieval and sequence + fetcher initialisation
      • +
    • updated Application to use DAS 1.53e version of dasobert DAS + client
      • +
    • Re-instated Full AMSA support and .amsa file association
      • +
    • Fixed parsing of JNet Concise annotation sans + sequences
      • +
    +
    +
    2.3
    + 9/5/07
    +     		+
      +
    • Jmol 11.0.2 integration
      • +
    • PDB views stored in Jalview XML files
      • +
    • Slide sequences
      • +
    • Edit sequence in place
      • +
    • EMBL CDS features
      • +
    • DAS Feature mapping
      • +
    • Feature ordering
      • +
    • Alignment Properties
      • +
    • Annotation Scores
      • +
    • Sort by scores
      • +
    • Feature/annotation editing in applet
      • +
    +     		+
      +
    • Headless state operation in 2.2.1
      • +
    • Incorrect and unstable DNA pairwise alignment
      • +
    • Cut and paste of sequences with annotation
      • +
    • Feature group display state in XML
      • +
    • Feature ordering in XML
      • +
    • blc file iteration selection using filename # suffix
      • +
    • Stockholm alignment properties
      • +
    • Stockhom alignment secondary structure annotation
      • +
    • 2.2.1 applet had no feature transparency
      • +
    • Number pad keys can be used in cursor mode
      • +
    • Structure Viewer mirror image resolved
      • +
    +
    -
    2.2.1
    - 12/2/07
    -     		-
      -
    • Non standard characters can be read and displayed -
    • Annotations/Features can be imported/exported to the applet - via textbox -
    • Applet allows editing of sequence/annotation/group name & - description -
    • Preference setting to display sequence name in italics -
    • Annotation file format extended to allow Sequence_groups to - be defined -
    • Default opening of alignment overview panel can be specified - in preferences -
    • PDB residue numbering annotation added to associated - sequences -
    -     		-
      -
    • Applet crash under certain Linux OS with Java 1.6 installed -
    • Annotation file export / import bugs fixed -
    • PNG / EPS image output bugs fixed -
    -
    -
    2.2
    - 27/11/06
    -     		-
      -
    • Multiple views on alignment -
    • Sequence feature editing -
    • "Reload" alignment -
    • "Save" to current filename -
    • Background dependent text colour -
    • Right align sequence ids -
    • User-defined lower case residue colours -
    • Format Menu -
    • Select Menu -
    • Menu item accelerator keys -
    • Control-V pastes to current alignment -
    • Cancel button for DAS Feature Fetching -
    • PCA and PDB Viewers zoom via mouse roller -
    • User-defined sub-tree colours and sub-tree selection -
    • 'New Window' button on the 'Output to Text box' -
    -     		-
      -
    • New memory efficient Undo/Redo System -
    • Optimised symbol lookups and conservation/consensus - calculations -
    • Region Conservation/Consensus recalculated after edits -
    • Fixed Remove Empty Columns Bug (empty columns at end of - alignment) -
    • Slowed DAS Feature Fetching for increased robustness. -
    • Made angle brackets in ASCII feature descriptions display - correctly -
    • Re-instated Zoom function for PCA -
    • Sequence descriptions conserved in web service analysis - results -
    • Uniprot ID discoverer uses any word separated by ∣ -
    • WsDbFetch query/result association resolved -
    • Tree leaf to sequence mapping improved -
    • Smooth fonts switch moved to FontChooser dialog box. -
    -
    -
    2.1.1
    - 12/9/06
    -     		-
      -
    • Copy consensus sequence to clipboard
      • -
    -     		-
      -
    • Image output - rightmost residues are rendered if sequence id - panel has been resized
      • -
    • Image output - all offscreen group boundaries are rendered
      • -
    • Annotation files with sequence references - all elements in - file are relative to sequence position
      • -
    • Mac Applet users can use Alt key for group editing
      • -
    -
    -
    2.1
    - 22/8/06
    -     		-
      -
    • MAFFT Multiple Alignment in default Web Service list
      • -
    • DAS Feature fetching
      • -
    • Hide sequences and columns
      • -
    • Export Annotations and Features
      • -
    • GFF file reading / writing
      • -
    • Associate structures with sequences from local PDB files
      • -
    • Add sequences to exisiting alignment
      • -
    • Recently opened files / URL lists
      • -
    • Applet can launch the full application
      • -
    • Applet has transparency for features (Java 1.2 required)
      • -
    • Applet has user defined colours parameter
      • -
    • Applet can load sequences from parameter "sequencex"
      • -
    -     		-
      -
    • Redundancy Panel reinstalled in the Applet
      • -
    • Monospaced font - EPS / rescaling bug fixed
      • -
    • Annotation files with sequence references bug fixed
      • -
    -
    -
    2.08.1
    - 2/5/06
    -     		-
      -
    • Change case of selected region from Popup menu
      • -
    • Choose to match case when searching
      • -
    • Middle mouse button and mouse movement can compress / expand - the visible width and height of the alignment
      • -
    -     		-
      -
    • Annotation Panel displays complete JNet results
      • -
    -
    -
    2.08b
    - 18/4/06
    -     		  -
      -
    • Java 1.5 bug - InternalMessageDialog fix for threads
      • -
    • Righthand label on wrapped alignments shows correct value
      • -
    -
    -
    2.08
    - 10/4/06
    -     		-
      -
    • Editing can be locked to the selection area
      • -
    • Keyboard editing
      • -
    • Create sequence features from searches
      • -
    • Precalculated annotations can be loaded onto alignments
      • -
    • Features file allows grouping of features
      • -
    • Annotation Colouring scheme added
      • -
    • Smooth fonts off by default - Faster rendering
      • -
    • Choose to toggle Autocalculate Consensus On/Off
      • -
    -     		-
      -
    • Drag & Drop fixed on Linux
      • -
    • Jalview Archive file faster to load/save, sequence - descriptions saved.
      • -
    -
    -
    2.07
    - 12/12/05
    -     		-
      -
    • PDB Structure Viewer enhanced
      • -
    • Sequence Feature retrieval and display enhanced
      • -
    • Choose to output sequence start-end after sequence name for - file output
      • -
    • Sequence Fetcher WSDBFetch@EBI
      • -
    • Applet can read feature files, PDB files and can be used for - HTML form input
      • -
    -     		-
      -
    • HTML output writes groups and features
      • -
    • Group editing is Control and mouse click
      • -
    • File IO bugs
      • -
    -
    -
    2.06
    - 28/9/05
    -     		-
      -
    • View annotations in wrapped mode
      • -
    • More options for PCA viewer
      • -
    -     		-
      -
    • GUI bugs resolved
      • -
    • Runs with -nodisplay from command line
      • -
    -
    -
    2.05b
    - 15/9/05
    -     		-
      -
    • Choose EPS export as lineart or text
      • -
    • Jar files are executable
      • -
    • Can read in Uracil - maps to unknown residue
      • -
    -     		-
      -
    • Known OutOfMemory errors give warning message
      • -
    • Overview window calculated more efficiently
      • -
    • Several GUI bugs resolved
      • -
    -
    -
    2.05
    - 30/8/05
    -     		-
      -
    • Edit and annotate in "Wrapped" view
      • -
    -     		-
      -
    • Several GUI bugs resolved
      • -
    -
    -
    2.04
    - 24/8/05
    -     		-
      -
    • Hold down mouse wheel & scroll to change font size
      • -
    -     		-
      -
    • Improved JPred client reliability
      • -
    • Improved loading of Jalview files
      • -
    -
    -
    2.03
    - 18/8/05
    -     		-
      -
    • Set Proxy server name and port in preferences
      • -
    • Multiple URL links from sequence ids
      • -
    • User Defined Colours can have a scheme name and added to - Colour Menu
      • -
    • Choose to ignore gaps in consensus calculation
      • -
    • Unix users can set default web browser
      • -
    • Runs without GUI for batch processing
      • -
    • Dynamically generated Web Service Menus
      • -
    -     		-
      -
    • InstallAnywhere download for Sparc Solaris
      • -
    -
    -
    2.02
    - 18/7/05
    -     		  -
      -
    • Copy & Paste order of sequences maintains alignment - order.
      • -
    -
    -
    2.01
    - 12/7/05
    -     		-
      -
    • Use delete key for deleting selection.
      • -
    • Use Mouse wheel to scroll sequences.
      • -
    • Help file updated to describe how to add alignment - annotations.
      • -
    • Version and build date written to build properties file.
      • -
    • InstallAnywhere installation will check for updates at launch - of Jalview.
      • -
    -     		-
      -
    • Delete gaps bug fixed.
      • -
    • FileChooser sorts columns.
      • -
    • Can remove groups one by one.
      • -
    • Filechooser icons installed.
      • -
    • Finder ignores return character when searching. Return key - will initiate a search.
      -
      • -
    -
    -
    2.0
    - 20/6/05
    -     		-
      -
    • New codebase
      • -
    -     		 
    +
    2.2.1
    + 12/2/07
    +     		+
      +
    • Non standard characters can be read and displayed +
    • Annotations/Features can be imported/exported to the applet + via textbox +
    • Applet allows editing of sequence/annotation/group name + & description +
    • Preference setting to display sequence name in italics +
    • Annotation file format extended to allow Sequence_groups to + be defined +
    • Default opening of alignment overview panel can be specified + in preferences +
    • PDB residue numbering annotation added to associated + sequences +
    +     		+
      +
    • Applet crash under certain Linux OS with Java 1.6 installed +
    • Annotation file export / import bugs fixed +
    • PNG / EPS image output bugs fixed +
    +
    +
    2.2
    + 27/11/06
    +     		+
      +
    • Multiple views on alignment +
    • Sequence feature editing +
    • "Reload" alignment +
    • "Save" to current filename +
    • Background dependent text colour +
    • Right align sequence ids +
    • User-defined lower case residue colours +
    • Format Menu +
    • Select Menu +
    • Menu item accelerator keys +
    • Control-V pastes to current alignment +
    • Cancel button for DAS Feature Fetching +
    • PCA and PDB Viewers zoom via mouse roller +
    • User-defined sub-tree colours and sub-tree selection +
    • 'New Window' button on the 'Output to Text box' +
    +     		+
      +
    • New memory efficient Undo/Redo System +
    • Optimised symbol lookups and conservation/consensus + calculations +
    • Region Conservation/Consensus recalculated after edits +
    • Fixed Remove Empty Columns Bug (empty columns at end of + alignment) +
    • Slowed DAS Feature Fetching for increased robustness. +
    • Made angle brackets in ASCII feature descriptions display + correctly +
    • Re-instated Zoom function for PCA +
    • Sequence descriptions conserved in web service analysis + results +
    • Uniprot ID discoverer uses any word separated by ∣ +
    • WsDbFetch query/result association resolved +
    • Tree leaf to sequence mapping improved +
    • Smooth fonts switch moved to FontChooser dialog box. +
    +
    +
    2.1.1
    + 12/9/06
    +     		+
      +
    • Copy consensus sequence to clipboard
      • +
    +     		+
      +
    • Image output - rightmost residues are rendered if sequence + id panel has been resized
      • +
    • Image output - all offscreen group boundaries are rendered
      • +
    • Annotation files with sequence references - all elements in + file are relative to sequence position
      • +
    • Mac Applet users can use Alt key for group editing
      • +
    +
    +
    2.1
    + 22/8/06
    +     		+
      +
    • MAFFT Multiple Alignment in default Web Service list
      • +
    • DAS Feature fetching
      • +
    • Hide sequences and columns
      • +
    • Export Annotations and Features
      • +
    • GFF file reading / writing
      • +
    • Associate structures with sequences from local PDB files
      • +
    • Add sequences to exisiting alignment
      • +
    • Recently opened files / URL lists
      • +
    • Applet can launch the full application
      • +
    • Applet has transparency for features (Java 1.2 required)
      • +
    • Applet has user defined colours parameter
      • +
    • Applet can load sequences from parameter "sequencex"
      • +
    +     		+
      +
    • Redundancy Panel reinstalled in the Applet
      • +
    • Monospaced font - EPS / rescaling bug fixed
      • +
    • Annotation files with sequence references bug fixed
      • +
    +
    +
    2.08.1
    + 2/5/06
    +     		+
      +
    • Change case of selected region from Popup menu
      • +
    • Choose to match case when searching
      • +
    • Middle mouse button and mouse movement can compress / expand + the visible width and height of the alignment
      • +
    +     		+
      +
    • Annotation Panel displays complete JNet results
      • +
    +
    +
    2.08b
    + 18/4/06
    +     		  +
      +
    • Java 1.5 bug - InternalMessageDialog fix for threads
      • +
    • Righthand label on wrapped alignments shows correct value
      • +
    +
    +
    2.08
    + 10/4/06
    +     		+
      +
    • Editing can be locked to the selection area
      • +
    • Keyboard editing
      • +
    • Create sequence features from searches
      • +
    • Precalculated annotations can be loaded onto alignments
      • +
    • Features file allows grouping of features
      • +
    • Annotation Colouring scheme added
      • +
    • Smooth fonts off by default - Faster rendering
      • +
    • Choose to toggle Autocalculate Consensus On/Off
      • +
    +     		+
      +
    • Drag & Drop fixed on Linux
      • +
    • Jalview Archive file faster to load/save, sequence + descriptions saved.
      • +
    +
    +
    2.07
    + 12/12/05
    +     		+
      +
    • PDB Structure Viewer enhanced
      • +
    • Sequence Feature retrieval and display enhanced
      • +
    • Choose to output sequence start-end after sequence name for + file output
      • +
    • Sequence Fetcher WSDBFetch@EBI
      • +
    • Applet can read feature files, PDB files and can be used for + HTML form input
      • +
    +     		+
      +
    • HTML output writes groups and features
      • +
    • Group editing is Control and mouse click
      • +
    • File IO bugs
      • +
    +
    +
    2.06
    + 28/9/05
    +     		+
      +
    • View annotations in wrapped mode
      • +
    • More options for PCA viewer
      • +
    +     		+
      +
    • GUI bugs resolved
      • +
    • Runs with -nodisplay from command line
      • +
    +
    +
    2.05b
    + 15/9/05
    +     		+
      +
    • Choose EPS export as lineart or text
      • +
    • Jar files are executable
      • +
    • Can read in Uracil - maps to unknown residue
      • +
    +     		+
      +
    • Known OutOfMemory errors give warning message
      • +
    • Overview window calculated more efficiently
      • +
    • Several GUI bugs resolved
      • +
    +
    +
    2.05
    + 30/8/05
    +     		+
      +
    • Edit and annotate in "Wrapped" view
      • +
    +     		+
      +
    • Several GUI bugs resolved
      • +
    +
    +
    2.04
    + 24/8/05
    +     		+
      +
    • Hold down mouse wheel & scroll to change font size
      • +
    +     		+
      +
    • Improved JPred client reliability
      • +
    • Improved loading of Jalview files
      • +
    +
    +
    2.03
    + 18/8/05
    +     		+
      +
    • Set Proxy server name and port in preferences
      • +
    • Multiple URL links from sequence ids
      • +
    • User Defined Colours can have a scheme name and added to + Colour Menu
      • +
    • Choose to ignore gaps in consensus calculation
      • +
    • Unix users can set default web browser
      • +
    • Runs without GUI for batch processing
      • +
    • Dynamically generated Web Service Menus
      • +
    +     		+
      +
    • InstallAnywhere download for Sparc Solaris
      • +
    +
    +
    2.02
    + 18/7/05
    +     		  +
      +
    • Copy & Paste order of sequences maintains alignment + order.
      • +
    +
    +
    2.01
    + 12/7/05
    +     		+
      +
    • Use delete key for deleting selection.
      • +
    • Use Mouse wheel to scroll sequences.
      • +
    • Help file updated to describe how to add alignment + annotations.
      • +
    • Version and build date written to build properties file.
      • +
    • InstallAnywhere installation will check for updates at + launch of Jalview.
      • +
    +     		+
      +
    • Delete gaps bug fixed.
      • +
    • FileChooser sorts columns.
      • +
    • Can remove groups one by one.
      • +
    • Filechooser icons installed.
      • +
    • Finder ignores return character when searching. Return key + will initiate a search.
      +
      • +
    +
    +
    2.0
    + 20/6/05
    +     		+
      +
    • New codebase
      • +
    +