X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=a97c11cd83e9d7d2f6811511513945ca095c6ad1;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=c709a5f776764b1d1d50bf4da2497bdc0408ef66;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index c709a5f..a97c11c 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,57 +1,350 @@ + --> Release History

Release History

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-
Release
- 		-
New Features
- 		-
Issues Resolved
-
- 2.8.1
20/5/2014 -
- 		- -
    -
Other improvements -
    -
- 		-
    -
-
+
+ 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
@@ -143,10 +436,12 @@
  • 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
    • +