X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=49d4c3f98f0f18b39693912d50c340231fee6aee;hb=71881f2cf715e6143cd594e20bd41db538282f81;hp=a240a49344a3e4c6f4872fac18ff111a52468cb8;hpb=7a75fae1d4cc6136494716bfaa2b1edb26ca76be;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index a240a49..49d4c3f 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,118 +1,363 @@ + --> 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
- 20/5/2014 + 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
    • +
  • 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
    • - +
  • 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:
      • - 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
      • -
    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
    • +
  • 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 +
    • 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
      • +
    • 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
      • -
    • cannot reorder or slide sequences after dragging an +
    • 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
      • + IUPred disorder prediction
    • Multiple group annotated consensus rows shown when changing 'normalise logo' display setting
      • -
    • Annotation/RNA Helix colourschemes cannot be applied to alignment - with groups (2.8.0b1)
      • -
    • 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'
      • +
    • 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 shown in applet when selection is not a group
      • +
    • 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
      • +
        +
      • 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 @@ -121,15 +366,19 @@ affect background (2.8.0b1)
      • redundancy highlighting is erratic at 0% and 100%
        • -
      • remove gapped columns fails for sequences with ragged +
      • 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
        • +
      • 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