X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_9.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_9.md;h=d03f0b4d1f190a9fe2d381efa20a9a1ae73763e5;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=0000000000000000000000000000000000000000;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/help/markdown/releases/release-2_9.md b/help/markdown/releases/release-2_9.md new file mode 100644 index 0000000..d03f0b4 --- /dev/null +++ b/help/markdown/releases/release-2_9.md @@ -0,0 +1,145 @@ +--- +channel: release +version: 2.9 +date: 2015-09-10 +--- + +## New Features + + + +### General +- Linked visualisation and analysis of DNA and Protein alignments: + - Translated cDNA alignments shown as split protein and DNA alignment views + - Codon consensus annotation for linked protein and cDNA alignment views + - Link cDNA or Protein product sequences by loading them onto Protein or cDNA alignments + - Reconstruct linked cDNA alignment from aligned protein sequences +- Jmol integration updated to Jmol v14.2.14 +- Import and export of Jalview alignment views as [BioJSON](features/bioJsonFormat.html) +- New alignment annotation file statements for reference sequences and marking hidden columns +- Reference sequence based alignment shading to highlight variation +- Select or hide columns according to alignment annotation +- Find option for locating sequences by description +- Conserved physicochemical properties shown in amino acid conservation row +- Alignments can be sorted by number of RNA helices + + +### Application +- New cDNA/Protein analysis capabilities + - Get Cross-References should open a Split Frame view with cDNA/Protein + - Detect when nucleotide sequences and protein sequences are placed in the same alignment + - Split cDNA/Protein views are saved in Jalview projects +- Use REST API to talk to Chimera +- Selected regions in Chimera are highlighted in linked Jalview windows +- VARNA RNA viewer updated to v3.93 +- VARNA views are saved in Jalview Projects +- Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA +- Make groups for selection uses marked columns as well as the active selected region +- Calculate UPGMA and NJ trees using sequence feature similarity +- New Export options + - New Export Settings dialog to control hidden region export in flat file generation + - Export alignment views for display with the [BioJS MSAViewer](http://msa.biojs.net/) + - Export scrollable SVG in HTML page + - Optional embedding of BioJSON data when exporting alignment figures to HTML +- 3D structure retrieval and display + - Free text and structured queries with the PDBe Search API + - PDBe Search API based discovery and selection of PDB structures for a sequence set +- JPred4 employed for protein secondary structure predictions +- Hide Insertions menu option to hide unaligned columns for one or a group of sequences +- Automatically hide insertions in alignments imported from the JPred4 web server +- (Nearly) Native 'Quaqua' dialogs for browsing file system on OSX
+LGPL libraries courtesy of [http://www.randelshofer.ch/quaqua/](http://www.randelshofer.ch/quaqua/) +- changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure' +- change "View protein structure" menu option to "3D Structure ..." + + +### Applet +- New layout for applet example pages +- New parameters to enable SplitFrame view (file2,enableSplitFrame, scaleProteinAsCdna) +- New example demonstrating linked viewing of cDNA and Protein alignments + + +### Development and deployment +- Java 1.7 minimum requirement for Jalview 2.9 +- Include installation type and git revision in build properties and console log output +- Jalview Github organisation, and new github site for storing BioJsMSA Templates +- Jalview's unit tests now managed with TestNG + + +## Issues Resolved + + + +### Application +- Escape should close any open find dialogs +- Typo in select-by-features status report +- Consensus RNA secondary secondary structure predictions are not highlighted in amber +- Missing gap character in v2.7 example file means alignment appears unaligned when pad-gaps is not enabled +- First switch to RNA Helices colouring doesn't colour associated structure views +- ID width preference option is greyed out when auto width checkbox not enabled +- Stopped a warning dialog from being shown when creating user defined colours +- 'View Mapping' in structure viewer shows sequence mappings for just that viewer's sequences +- Workaround for superposing PDB files containing multiple models in Chimera +- Report sequence position in status bar when hovering over Jmol structure +- Cannot output gaps as '.' symbols with Selection -> output to text box +- Flat file exports of alignments with hidden columns have incorrect sequence start/end +- 'Aligning' a second chain to a Chimera structure from Jalview fails +- Colour schemes applied to structure viewers don't work for nucleotide +- Loading/cut'n'pasting an empty or invalid file leads to a grey/invisible alignment window +- Exported Jpred annotation from a sequence region imports to different position +- Space at beginning of sequence feature tooltips shown on some platforms +- Chimera viewer 'View | Show Chain' menu is not populated +- 'New View' fails with a Null Pointer Exception in console if Chimera has been opened +- Mouseover to Chimera not working +- Miscellaneous ENA XML feature qualifiers not retrieved +- NPE in annotation renderer after 'Extract Scores' +- If two structures in one Chimera window, mouseover of either sequence shows on first structure +- 'Show annotations' options should not make non-positional annotations visible +- Subsequence secondary structure annotation not shown in right place after 'view flanking regions' +- File Save As type unset when current file format is unknown +- Save as '.jar' option removed for saving Jalview projects +- Colour by Sequence colouring in Chimera more responsive +- Cannot 'add reference annotation' for a sequence in several views on same alignment +- Cannot show linked products for EMBL / ENA records +- Jalview's tooltip wraps long texts containing no spaces + + +### Applet +- Jmol to JalviewLite mouseover/link not working +- JalviewLite can't import sequences with ID descriptions containing angle brackets + + +### General +- Cannot export and reimport RNA secondary structure via jalview annotation file +- Random helix colour palette for colour by annotation with RNA secondary structure +- Mouseover to cDNA from STOP residue in protein translation doesn't work. +- hints when using the select by annotation dialog box +- Jmol alignment incorrect if PDB file has alternate CA positions +- FontChooser message dialog appears to hang after choosing 1pt font +- Peptide secondary structure incorrectly imported from annotation file when annotation display text includes 'e' or 'h' +- Cannot set colour of new feature type whilst creating new feature +- cDNA translation alignment should not be sequence order dependent +- 'Show unconserved' doesn't work for lower case sequences +- Nucleotide ambiguity codes involving R not recognised + + +### Deployment and Documentation +- Applet example pages appear different to the rest of www.jalview.org + + +### Application Known issues +- Incomplete sequence extracted from PDB entry 3a6s +- Misleading message appears after trying to delete solid column. +- Jalview icon not shown in dock after InstallAnywhere version launches +- Fetching EMBL reference for an RNA sequence results fails with a sequence mismatch +- Corrupted or unreadable alignment display when scrolling alignment to right +- ArrayIndexOutOfBoundsException thrown when remove empty columns called on alignment with ragged gapped ends +- auto calculated alignment annotation rows do not get placed above or below non-autocalculated rows +- Jalview dekstop becomes sluggish at full screen in ultra-high resolution +- Cannot disable consensus calculation independently of quality and conservation +- Mouseover highlighting between cDNA and protein can become sluggish with more than one splitframe shown + + +### Applet Known Issues +- Core PDB parsing code requires Jmol +- Sequence canvas panel goes white when alignment window is being resized