X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=a97c11cd83e9d7d2f6811511513945ca095c6ad1;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=69b009e0e76d81527c964e0b7524eb9e178c2cf6;hpb=9eff2c2a7aeb98617fb6e55179f53c66ac1ecd82;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 69b009e..a97c11c 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,39 +1,232 @@ + --> Release History

Release History

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Release
- 		-
New Features
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Issues Resolved
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+
+ 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