X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_10_0.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_10_0.md;h=3d8f593b2de211a499729055169608c6f5f3c339;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=0000000000000000000000000000000000000000;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/help/markdown/releases/release-2_10_0.md b/help/markdown/releases/release-2_10_0.md new file mode 100644 index 0000000..3d8f593 --- /dev/null +++ b/help/markdown/releases/release-2_10_0.md @@ -0,0 +1,135 @@ +--- +channel: release +version: 2.10.0 +date: 2016-10-06 +--- + +## New Features + + + +### General +- Updated Spanish translations. +- Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing. +- Alignment ruler shows positions relative to reference sequence +- Position/residue shown in status bar when mousing over sequence associated annotation +- Default RNA SS symbol to 'matching bracket' for manual entry +- RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column +- Feature settings popup menu options for showing or hiding columns containing a feature +- Edit selected group by double clicking on group and sequence associated annotation labels +- Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs + + +### Application +- Automatically hide introns when opening a gene/transcript view +- Uniprot Sequence fetcher Free Text Search dialog +- UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database +- Updated download sites used for Rfam and Pfam sources to xfam.org +- Disabled Rfam(Full) in the sequence fetcher +- Show residue labels in Chimera when mousing over sequences in Jalview +- Support for reverse-complement coding regions in ENA and EMBL +- Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API +- Support for ENA CDS records with reverse complement operator +- Update to groovy-2.4.6-indy - for faster groovy script execution +- New 'execute Groovy script' option in an alignment window's Calculate menu +- Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode +- Support for creating new alignment calculation workers from groovy scripts +- Store/restore reference sequence in Jalview projects +- Chain codes for a sequence's PDB associations are now saved/restored from project +- Database selection dialog always shown before sequence fetcher is opened +- Double click on an entry in Jalview's database chooser opens a sequence fetcher +- Free-text search client for UniProt using the UniProt REST API +- -nonews command line parameter to prevent the news reader opening +- Displayed columns for PDBe and Uniprot querying stored in preferences +- Pagination for displaying PDBe and Uniprot search results +- Tooltips shown on database chooser +- Reverse complement function in calculate menu for nucleotide sequences +- Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets). +- Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10 +- Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API +- Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl) +- ENA CDS 'show cross references' for Uniprot sequences +- Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records. +- Revised Jalview Project format for efficient recovery of sequence coding and alignment annotation relationships. + + +## Issues Resolved + + + +### General + - reinstate CTRL-click for opening pop-up menu on OSX + - Export features in Jalview format (again) includes graduated colourschemes + - More responsive when working with big alignments and lots of hidden columns + - Hidden column markers not always rendered at right of alignment window + - Tidied up links in help file table of contents + - Feature based tree calculation not shown for DNA alignments + - Hidden columns ignored during feature based tree calculation + - Alignment view stops updating when show unconserved enabled for group on alignment + - Cannot insert gaps into sequence when set as reference + - Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation + - Incorrect column numbers in ruler when hidden columns present + - Colour by RNA Helices not enabled when user created annotation added to alignment + - RNA Structure consensus only computed for '()' base pair annotation + - Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus + - Extend selection with columns containing feature not working + - Pfam format writer puts extra space at beginning of sequence + - Incomplete sequence extracted from pdb entry 3a6s + - Cannot create groups on an alignment from from a tree when t-coffee scores are shown + - Cannot import and view PDB structures with chains containing negative resnums (4q4h) + - ArithmeticExceptions raised when parsing some structures + - 'Empty' alignment blocks added to Clustal, PIR and PileUp output + - Reordering sequence features that are not visible causes alignment window to repaint + - Threshold sliders don't work in graduated colour and colour by annotation row for e-value scores associated with features and annotation rows + - amino acid physicochemical conservation calculation should be case independent + - Remove annotation also updates hidden columns + - FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar) + - Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled + - Quality and Conservation are now shown on load even when Consensus calculation is disabled + - Remove right on penultimate column of alignment does nothing + + +### Application + - URLs and links can't be imported by drag'n'drop on OSX when launched via webstart (note - not yet fixed for El Capitan) + - Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms + - Error thrown when exporting a view with hidden sequences as flat-file alignment + - InstallAnywhere distribution fails when launching Chimera + - Jalview very slow to launch via webstart (also hotfix for 2.9.0b2) + - Cannot save project when view has a reference sequence defined + - Columns are suddenly selected in other alignments and views when revealing hidden columns + - Hide columns not mirrored in complement view in a cDNA/Protein splitframe + - Cannot save/restore representative sequence from project when only one sequence is represented + - Disabled 'Best Uniprot Coverage' option in Structure Chooser + - Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel + - View mapping in structure view shows mappings between sequence and all chains in a PDB file + - PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type + - Export complete shown after destination file chooser is cancelled during an image export + - Error when querying PDB Service with sequence name containing special characters + - Manual PDB structure querying should be case insensitive + - Large tooltips with broken HTML formatting don't wrap + - Figures exported from wrapped view are truncated so L looks like I in consensus annotation + - Export features should only export the currently displayed features for the current selection or view + - Enable 'Get Cross-References' in menu after fetching cross-references, and restoring from project + - Mouseover of a copy of a sequence is not followed in the structure viewer + - Titles for individual alignments in splitframe not restored from project + - missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default + - amino acid physicochemical conservation is case dependent + - RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems) + - Only offer PDB structures in structure viewer based on sequence name, PDB and UniProt cross-references + - No progress bar shown during export of alignment as HTML + - Structures not always superimposed after multiple structures are shown for one or more sequences. + - Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled. + - Cannot specify chain code when entering specific PDB id for sequence + - File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled. + - Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence + - Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report + - Unable to read old Jalview projects that contain non-XML data added after Jalvew wrote project. + - Newly created annotation row reorders after clicking on it to create new annotation for a column. + - Null Pointer Exception raised when pressing Add on an orphaned cut'n'paste window. + + +### Applet + - Incorrect columns are selected when hidden columns present before start of sequence + - Missing dependencies on applet pages (JSON jars) + - Overview pixel size changes when sequences are hidden in applet + - Updated instructions for applet deployment on examples pages.