X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_8.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_8.md;h=2d1934dd0be7d8231797cf3576be1b277ef8c198;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=0000000000000000000000000000000000000000;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/help/markdown/releases/release-2_8.md b/help/markdown/releases/release-2_8.md new file mode 100644 index 0000000..2d1934d --- /dev/null +++ b/help/markdown/releases/release-2_8.md @@ -0,0 +1,110 @@ +--- +channel: release +version: 2.8 +date: 2012-11-12 +--- + +## New Features + + + +### Application +- Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega) +- JABAWS server status indicator in Web Services preferences +- VARNA (http://varna.lri.fr) viewer for RNA structures in Jalview alignment window +- Updated Jalview build and deploy framework for OSX mountain lion, windows 7, and 8 +- Nucleotide substitution matrix for PCA that supports RNA and ambiguity codes +- Improved sequence database retrieval GUI +- Support fetching and database reference look up against multiple DAS sources (Fetch all from in 'fetch db refs') +- Jalview project improvements + - Store and retrieve the 'belowAlignment' flag for annotation + - calcId attribute to group annotation rows on the alignment + - Store AACon calculation settings for a view in Jalview project +- horizontal scrolling gesture support +- Visual progress indicator when PCA calculation is running +- Simpler JABA web services menus +- visual indication that web service results are still being retrieved from server +- Serialise the dialogs that are shown when Jalview starts up for first time +- Jalview user agent string for interacting with HTTP services +- DAS 1.6 and DAS 2.0 source support using new JDAS client library +- Examples directory and Groovy library included in InstallAnywhere distribution + + +### Applet +- RNA alignment and secondary structure annotation visualization applet example + + +### General +- Normalise option for consensus sequence logo +- Reset button in PCA window to return dimensions to defaults +- Allow seqspace or Jalview variant of alignment PCA calculation +- PCA with either nucleic acid and protein substitution matrices +- Allow windows containing HTML reports to be exported in HTML +- Interactive display and editing of RNA secondary structure contacts +- RNA Helix Alignment Colouring +- RNA base pair logo consensus +- Parse sequence associated secondary structure information in Stockholm files +- HTML Export database accessions and annotation information presented in tooltip for sequences +- Import secondary structure from LOCARNA clustalw style RNA alignment files +- import and visualise T-COFFEE quality scores for an alignment +- 'colour by annotation' per sequence option to shade each sequence according to its associated alignment annotation +- New Jalview Logo + + +### Documentation and Development +- documentation for score matrices used in Jalview +- New Website! + + +## Issues Resolved + + + +### Application +- PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch REST service +- Stop windows being moved outside desktop on OSX +- Filetype associations not installed for webstart launch +- Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete +- revise SHMR RSBS definition to ensure alignment is uploaded via ali_file parameter +- Jalview 2.7 is incompatible with Jmol-12.2.2 +- View all structures superposed fails with exception +- Jnet job queues forever if a very short sequence is submitted for prediction +- Cut and paste menu not opened when mouse clicked on desktop window +- Putting fractional value into integer text box in alignment parameter dialog causes Jalview to hang +- Structure view highlighting doesn't work on windows 7 +- View all structures fails with exception shown in structure view +- Characters in filename associated with PDBEntry not escaped in a platform independent way +- Jalview desktop fails to launch with exception when using proxy +- Tree calculation reports 'you must have 2 or more sequences selected' when selection is empty +- Jalview desktop fails to launch with jar signature failure when java web start temporary file caching is disabled +- DAS Sequence retrieval with range qualification results in sequence xref which includes range qualification +- Errors during processing of command line arguments cause progress bar (JAL-898) to be removed +- Replace comma for semi-colon option not disabled for DAS sources in sequence fetcher +- Cannot close news reader when JABAWS server warning dialog is shown +- Option widgets not updated to reflect user settings +- Edited sequence not submitted to web service +- Jalview 2.7 Webstart does not launch on mountain lion +- InstallAnywhere installer doesn't unpack and run on OSX Mountain Lion +- Annotation panel not given a scroll bar when sequences with alignment annotation are pasted into the alignment +- Sequence associated annotation rows not associated when loaded from Jalview project +- Browser launch fails with NPE on java 1.7 +- JABAWS alignment marked as finished when job was cancelled or job failed due to invalid input +- NPE with v2.7 example when clicking on Tree associated with all views +- Exceptions when copy/paste sequences with grouped annotation rows to new window + + +### Applet +- Sequence features are momentarily displayed before they are hidden using hidefeaturegroups applet parameter +- loading features via javascript API automatically enables feature display +- scrollToColumnIn javascript API method doesn't work + + +### General +- Redundancy removal fails for rna alignment +- PCA calculation fails when sequence has been selected and then deselected +- PCA window shows grey box when first opened on OSX +- Letters coloured pink in sequence logo when alignment coloured with clustalx +- Choosing fonts without letter symbols defined causes exceptions and redraw errors +- Initial PCA plot view is not same as manually reconfigured view +- Grouped annotation graph label has incorrect line colour +- Grouped annotation graph label display is corrupted for lots of labels