X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=07d05ea6db6f3e20caf2e179ef6d874a934376bb;hb=9f48318d26fe985ea5e0445abb6625fe1e788bd5;hp=b6fb83c328416c86714e818c7f5af7fb220eeec1;hpb=3c9a109fe89504b4713bfaf612275edc8c07e433;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index b6fb83c..07d05ea 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,86 +1,578 @@ + --> Release History

Release History

- - - - - - - - + + + + + + + - + + + + + + + + + + + + + + + + - - +
  • 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 + + + +
    -
    Release
    -     		-
    New Features
    -     		-
    Issues Resolved
    -
    - 2.8.1
    20/5/2014     -
    -     		- -
      -
    • i18n Internationalisation of user interface and translation for Spanish locale
      • -
    - Application
      -
    • Define/Undefine group on current selection with Ctrl-G
      • -
    • Select columns containing particular features from Feature Settings dialog
      • -
    • View all 'representative' PDB structures for selected sequences
      • -
    • Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service
      • -
    • -
    • Jalview v2.8.1 project preserves sequence dataset and dataset annotation (e.g. hidden secondary structure annotation rows)
      • -
    - Applet
      - -
    Other improvements +
    +
    + Release +
    +     		+
    + New Features +
    +     		+
    + Issues Resolved +
    +
    + 2.9
    9/9/2015     +
    		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
        • +
      • Add cDNA or Protein product sequences to Protein or + cDNA alignments
        • +
      • Reconstruct linked cDNA alignment from aligned + protein sequences +
      • + +
    • Update Jmol to v14.2n
      • + +
    • BioJSON data exchange
      • + +
    • New alignment annotation file statements for + reference sequences and marking hidden columns
      • + +
    • Alignments can be sorted by number of RNA helices
      • + +
    • Assign a reference sequence to highlight + variation and consensus analysis
      • + +
    • Select or hide columns according to alignment + annotation
      • +
    • Find option for locating sequences by + description
      • + +
    • Conserved physicochemical properties shown in amino + acid conservation row
      • + +
    Application +
      +
    • Optional embedding of BioJSON data when exporting + alignment figures to HTML
      • +
    • New Export Settings dialog to control hidden region export in flat file + generation
      • +
    • 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
        • +
      • support '*' in amino acid sequences to indicate stop + codon
        • +
      • + +
    • Use REST API to talk to Chimera
      • +
    • Selected regions in Chimera are highlighted in linked Jalview windows
      • + +
    • Calculate UPGMA and NJ trees using sequence feature + similarity
      • + +
    • 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
      • + +
    • changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'
      • +
    • change "View protein structure" menu option to "3D + Structure ..."
      • + +
    • Make groups for selection uses marked columns as well + as the active selected region
      • + +
    • allow different similarity matrix calculations for + tree building and PCA
      • + +
    • Export alignment views for display with the BioJS MSAViewer
      • +
    • Scrollable SVG for HTML export
      • + +
    • Novel data discovery and retrieval mechanism using + PDBe Search API
      • +
    • Smarter technique for selecting PDB structures to + view in Jalview
      • + +
    • 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
      • +
    Applet
      +
    • Parameter to enable SplitFrame view
      • ? check other + parameters in applet ? +
    • New example demonstrating linked viewing of cDNA and + Protein alignments
      • +
    • New layout for applet example pages
    -     		- Application
      + 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
      • +
    • Github project and web URL for storing BioJsMSA + Templates
      • +
    • Jalview's unit tests now managed with TestNG
    		General +
      +
    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 means v2.7 example file appears + unaligned REVIEW
      • +
    • 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 mouseover + tooltip on some platforms
      • +
    • Chimera viewer 'View | Show Chain' menu is not + populated
      • +
    • 'New View' fails with a Null Pointer Exception 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
      • +
    • Native 'Quaqua' dialogs for saving and loading files + on OSX
      • +
    • Save as '.jar' option removed for saving Jalview + projects
      • +
    • Colour by Sequence colouring in Chimera more + responsive
      • +
    • Can disable consensus calculation independently of + quality and conservation
      • +
    • 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 +
      + +
    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
      • +
    Applet Known Issues +
      +
    • Core PDB parsing code requires Jmol
      • +
    • Sequence canvas panel goes white when alignment + window is being resized +
    • +
    +
    + 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
      • +
    • Warn user if 'Find' regular expression is invalid (mentioned post-hoc with 2.9 release)
      • + +
    Application +
      +
    • Extract and display secondary structure for sequences with + 3D structures
      • +
    • Support for parsing RNAML
      • +
    • Annotations menu for layout +
        +
      • sort sequence annotation rows by alignment
        • +
      • place sequence annotation above/below alignment + annotation
        • +
      +
    • Output in Stockholm format
      • +
    • Internationalisation: improved Spanish (es) translation
      • +
    • Structure viewer preferences tab
      • +
    • Disorder and Secondary Structure annotation tracks shared + between alignments
      • +
    • UCSF Chimera launch and linked highlighting from Jalview
      • +
    • Show/hide all sequence associated annotation rows for all + or current selection
      • +
    • disorder and secondary structure predictions available as + dataset annotation
      • +
    • Per-sequence rna helices colouring
      • + + +
    • Sequence database accessions imported when fetching + alignments from Rfam
      • +
    • update VARNA version to 3.91
      • + +
    • New groovy scripts for exporting aligned positions, + conservation values, and calculating sum of pairs scores.
      • +
    • Command line argument to set default JABAWS server
      • +
    • include installation type in build properties and console + log output
      • +
    • Updated Jalview project format to preserve dataset annotation
      • +
    		+ Application +
      +
    • Distinguish alignment and sequence associated RNA + structure in structure->view->VARNA
      • +
    • Raise dialog box if user deletes all sequences in an + alignment
      • +
    • Pressing F1 results in documentation opening twice
      • +
    • Sequence feature tooltip is wrapped
      • +
    • Double click on sequence associated annotation selects + only first column
      • +
    • Redundancy removal doesn't result in unlinked leaves + shown in tree
      • +
    • Undos after several redundancy removals don't undo + properly
      • +
    • Hide sequence doesn't hide associated annotation
      • +
    • User defined colours dialog box too big to fit on screen + and buttons not visible
      • +
    • author list isn't updated if already written to Jalview + properties
      • +
    • Popup menu won't open after retrieving sequence from + database
      • +
    • File open window for associate PDB doesn't open
      • +
    • Left-then-right click on a sequence id opens a browser + search window
      • +
    • Cannot open sequence feature shading/sort popup menu in + feature settings dialog
      • +
    • better tooltip placement for some areas of Jalview desktop
      • +
    • Allow addition of JABAWS Server which doesn't pass + validation
      • +
    • Web services parameters dialog box is too large to fit on + screen
      • +
    • Muscle nucleotide alignment preset obscured by tooltip
      • +
    • JABAWS preset submenus don't contain newly defined + user preset
      • +
    • MSA web services warns user if they were launched with + invalid input
      • +
    • Jalview cannot contact DAS Registy when running on Java 8
      • +
    • + + 'Superpose with' submenu not shown when new view created +
      • + +
    Deployment and Documentation +
      +
    • 2G and 1G options in launchApp have no effect on memory + allocation
      • +
    • launchApp service doesn't automatically open + www.jalview.org/examples/exampleFile.jar if no file is given
      • +
    • + + InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is + available +
      • +
    Application Known issues +
      +
    • + + corrupted or unreadable alignment display when scrolling alignment + to right +
      • +
    • + + retrieval fails but progress bar continues for DAS retrieval with + large number of ID +
      • +
    • + + flatfile output of visible region has incorrect sequence start/end +
      • +
    • + + rna structure consensus doesn't update when secondary + structure tracks are rearranged +
      • +
    • + + invalid rna structure positional highlighting does not highlight + position of invalid base pairs +
      • +
    • + + out of memory errors are not raised when saving Jalview project + from alignment window file menu +
      • +
    • + + Switching to RNA Helices colouring doesn't propagate to + structures +
      • +
    • + + colour by RNA Helices not enabled when user created annotation + added to alignment +
      • +
    • + + Jalview icon not shown on dock in Mountain Lion/Webstart +
      • +
    Applet Known Issues +
      +
    • + + JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies +
      • +
    • + + Jalview and Jmol example not compatible with IE9 +
      • + +
    • Sort by annotation score doesn't reverse order when + selected
      • +
    +
    + 2.8.1
    4/6/2014     +
    		+ + General +
      +
    • Internationalisation of user interface (usually called + i18n support) and translation for Spanish locale
      • +
    • Define/Undefine group on current selection with + Ctrl-G/Shift Ctrl-G
      • +
    • Improved group creation/removal options in + alignment/sequence Popup menu
      • +
    • Sensible precision for symbol distribution percentages + shown in logo tooltip.
      • +
    • Annotation panel height set according to amount of + annotation when alignment first opened
      • +
    Application +
      +
    • Interactive consensus RNA secondary structure prediction + VIENNA RNAAliFold JABA 2.1 service
      • +
    • Select columns containing particular features from Feature + Settings dialog
      • +
    • View all 'representative' PDB structures for selected + sequences
      • +
    • Update Jalview project format: +
        +
      • New file extension for Jalview projects '.jvp'
        • +
      • Preserve sequence and annotation dataset (to store + secondary structure annotation,etc)
        • +
      • Per group and alignment annotation and RNA helix + colouring
        • +
      +
      • +
    • New similarity measures for PCA and Tree calculation + (PAM250)
      • +
    • Experimental support for retrieval and viewing of flanking + regions for an alignment
      • +
    +     		+ Application +
      +
    • logo keeps spinning and status remains at queued or + running after job is cancelled
      • +
    • cannot export features from alignments imported from + Jalview/VAMSAS projects
      • +
    • Buggy slider for web service parameters that take float + values
    • Newly created RNA secondary structure line doesn't have 'display all symbols' flag set
      • -
    • T-COFFEE alignment score shading scheme not saved in - jalview project
      • +
    • T-COFFEE alignment score shading scheme and other + annotation shading not saved in Jalview project
    • Local file cannot be loaded in freshly downloaded Jalview
      • -
    • ??? unresolved ??? Jalview icon not shown on dock in - Mountain Lion/Webstart
      • +
    • Jalview icon not shown on dock in Mountain Lion/Webstart
    • Load file from desktop file browser fails
    • Occasional NPE thrown when calculating large trees
      • -
    - Applet -
      +
    • 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
      • -
    - Other
      -
    • -
    -
    2.8.0b1
    30/1/2014
    @@ -103,7 +595,7 @@
  • Allow disorder predictions to be made on the current selection (or visible selection) in the same way that JPred works
    • -
  • Groovy scripting for headless jalview operation
    • +
  • Groovy scripting for headless Jalview operation
    • Other improvements
    • Upgrade desktop installer to InstallAnywhere 2013
      • @@ -172,10 +664,12 @@
    • 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
    • +