X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=49d4c3f98f0f18b39693912d50c340231fee6aee;hb=a31a2a6912d40a3ebde6c07aeecb481119b4afc6;hp=1eb7abf98a6756a8f3404753f6ead31e67ba60c9;hpb=3f73b03257d72cbdd8cbe8889a6fc4fcab747dd3;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 1eb7abf..49d4c3f 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,45 +1,273 @@ + --> Release History

Release History

- - - - - + + + + + + + + + + + + + + + + + + + +
-
Release
- 		-
New Features
- 		-
Issues Resolved
-
+
+ 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
    • +
+
+
- 2.8.1
3/6/2014 + 2.8.3
13/4/2015 +
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 +
    +
+
+ 2.8.2
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
    • @@ -47,7 +275,10 @@ 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 @@ -58,6 +289,7 @@ 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 @@ -68,14 +300,6 @@ (PAM250)
    • Experimental support for retrieval and viewing of flanking regions for an alignment
      • -
    Applet -
      - -
    Other improvements -
  • Sensible precision for symbol distribution percentages - shown in logo tooltip.
    • -
  • Annotation panel height set according to amount of - annotation when alignment first opened