X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_0.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_11_0.md;h=fdee5074ccf0ed3f0ec527038104789c94dc1b8a;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=0000000000000000000000000000000000000000;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/help/markdown/releases/release-2_11_0.md b/help/markdown/releases/release-2_11_0.md new file mode 100644 index 0000000..fdee507 --- /dev/null +++ b/help/markdown/releases/release-2_11_0.md @@ -0,0 +1,156 @@ +--- +channel: release +version: 2.11.0 +date: 2019-07-04 +--- + +## New Features + +- Jalview Native Application and Installers built with [install4j](https://www.ej-technologies.com/products/install4j/overview.html) (licensed to the Jalview open source project) rather than InstallAnywhere +- Jalview Launcher System to auto-configure memory settings, receive over the air updates and launch specific versions via ([Three Rings' GetDown](https://github.com/threerings/getdown)) +- File type associations for formats supported by Jalview (including .jvp project files) +- Jalview launch files (.jvl) to pass command line arguments and switch between different getdown channels +- Backup files created when saving Jalview project or alignment files +- Annotate nucleotide alignments from VCF data files +- Version of HTSJDK shipped with Jalview updated to version 2.12.0 +- Alternative genetic code tables for 'Translate as cDNA' +- Update of Ensembl Rest Client to API v10.0 +- **Enhanced visualisation and analysis of Sequence Features** + - IntervalStoreJ (NCList implementation that allows updates) used for Sequence Feature collections + - Sequence features can be filtered and shaded according to any associated attributes (e.g. variant attributes from VCF file, or key-value pairs imported from column 9 of GFF file) + - Feature Attributes and shading schemes stored and restored from Jalview Projects + - Use full Sequence Ontology (via BioJava) to recognise variant features + - Show synonymous codon variants on peptide sequences (also coloured red by default) + - Popup window to show full report for a selected sequence feature's details + - More efficient sequence feature render algorithm (Z-sort/transparency and filter aware) + - Improved tooltips in Feature Settings dialog +- Symmetric score matrices for faster tree and PCA calculations +- **Principal Components Analysis Viewer** + - Principal Components Analysis results and Viewer state saved in Jalview Project + - 'Change parameters' option removed from viewer's drop-down menus + - Can use shift + arrow keys to rotate PCA image incrementally + - PCA plot is depth cued +- New 'Colour by Sequence ID' option +- **Speed and Efficiency** + - More efficient creation of selections and multiple groups when working with large alignments + - Speedier import of annotation rows when parsing Stockholm files +- **User Interface** + - Finder panel remembers last position in each view + - Alignment Overview now WYSIWIS (What you see is what is shown)
+Only visible regions of alignment are shown by default (can be changed in user preferences) + - File Chooser stays open after responding Cancel to the Overwrite Dialog + - Better popup menu behaviour when all sequences are hidden + - Status bar shows bounds when dragging a selection region, and gap count when inserting or deleting gaps + - Status bar updates over sequence and annotation labels + - Annotation tooltips and popup menus are shown when in wrapped mode + - Can select columns by dragging left/right in a graph or histogram annotation + - Help button on Uniprot and PDB search panels + - Cursor changes over draggable box in Overview panel + - Consistent ordering of links in sequence id popup menu + - Red line indicating tree-cut position not shown if no subgroups are created + - Removed ability to configure length of search history by right-clicking search box +- Jalview Groovy Scripting Console updated to Groovy v2.5 +- **Java 11 Support (not yet on general release)** + - OSX GUI integrations for App menu's 'About' entry and trapping CMD-Q + + +### Deprecations +- DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop +- Castor library for XML marshalling and unmarshalling has been replaced by JAXB for Jalview projects and XML based data retrieval clients +- Disable VAMSAS menu in preparation for removal +- Jalview Desktop no longer distributed via Java Web Start + + +### Documentation +- Added remarks about transparent rendering effects not supported in EPS figure export +- Typos in documentation for Preferences dialog + + +### Development and Release Processes +- Build system migrated from Ant to Gradle +- Enhanced checks for missing and duplicated keys in Message bundles +- Eclipse project configuration managed with gradle-eclipse +- Atlassian Bamboo continuous integration for unattended Test Suite execution +- Memory test suite to detect leaks in common operations +- More unit test coverage, and minor issues resolved +- Developer documentation migrated to markdown (with HTML rendering) +- HelpLinksChecker runs on Windows +- New URLs for publishing development versions of Jalview + + +## Issues Resolved + +- Timeouts when retrieving data from Ensembl +- 'View [Structure] Mappings' and structure superposition in Jmol fail on Windows +- Blank error dialog is displayed when discovering structures for sequences with lots of PDB structures +- Text misaligned in EPS or SVG image export with monospaced font +- Warning of 'Duplicate entry' when saving Jalview project involving multiple views +- Overview for complementary view in a linked CDS/Protein alignment is not updated when Hide Columns by Annotation dialog hides columns +- Selection highlighting in the complement of a CDS/Protein alignment stops working after making a selection in one view, then making another selection in the other view +- Annotations tooltip changes beyond visible columns +- Table Columns could be re-ordered in Feature Settings and Jalview Preferences panels +- Jalview hangs when closing windows, or redrawing the overview with large alignments +- Tree and PCA calculation fails for selected region if columns were selected by dragging right-to-left and the mouse moved to the left of the first column +- Couldn't hide selected columns adjacent to a hidden column marker via scale popup menu +- Error message for trying to load in invalid URLs doesn't tell users the invalid URL +- Tooltips displayed for features filtered by score from view +- Sequence Variants retrieved from Ensembl during show cross references or Fetch Database References are shown in red in original view +- stop_gained variants not shown correctly on peptide sequence (computed variant shown as p.Res.null) +- 'Graduated colour' option not offered for manually created features (where feature score is Float.NaN) +- Blank extra columns drawn or printed when columns are hidden +- Regular expression error for '(' in Select Columns by Annotation description +- Scroll doesn't stop on mouse up after dragging out of Scale or Annotation Panel +- Column selection incorrect after scrolling out of scale panel +- Left/right drag in annotation can scroll alignment down +- Error if mouse moved before clicking Reveal in scale panel +- Column display is out by one after Page Down, Page Up in wrapped mode +- Finder doesn't skip hidden regions +- Finder searches in minimised alignments +- 'Apply Colour to All Groups' not always selected on opening an alignment +- 'Colour by Annotation' not marked selected in Colour menu +- Per-group Clustal colour scheme changes when different groups in the alignment are selected +- Internationalised colour scheme names not shown correctly in menu +- Colour by Annotation can go black at min/max threshold limit +- Value input for graduated feature colour threshold gets 'unrounded' +- PCA image export doesn't respect background colour +- PCA points don't dim when rotated about y axis +- PCA Print dialog continues after Cancel +- Cancel in Tree Font dialog resets alignment, not Tree font +- Associate Tree with All Views not restored from project file +- Scrolling of split frame is sluggish if Overview shown in complementary view +- Codon consensus incorrectly scaled when shown without normalisation +- Sequence Details report should open positioned at top of report +- Help page can be opened twice +- Fuzzy text in web service status menu on OSX Mojave + + +### Editing +- Start and End should be updated when sequence data at beginning or end of alignment added/removed via 'Edit' sequence +- Delete/Cut selection doesn't relocate sequence features correctly when start of sequence is removed (Known defect since 2.10) +- Inserting gap sequence via the Edit Sequence dialog corrupts dataset sequence +- Structure colours not updated when associated tree repartitions the alignment view (Regression in 2.10.5) + + +### Datamodel +- Sequence.findIndex returns wrong value when sequence's End is greater than its length + + +### Bugs fixed for Java 11 Support (not yet on general release) +- Menus work properly in split-screen + + +### New Known Defects +- Select columns containing feature by double clicking ignores bounds of an existing selected region +- Codon consensus logo incorrectly scaled in gapped regions of protein alignment. +- Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project +- Alignment panel height can be too small after 'New View' +- Display is incorrect after removing gapped columns within hidden columns +- Rightmost selection is lost when mouse re-enters window after dragging left to select columns to left of visible region +- Features coloured according to their description string and thresholded by score in earlier versions of Jalview are not shown as thresholded features in 2.11. To workaround please create a Score filter instead. +- Cancel on Feature Settings dialog doesn't reset group visibility +- F2 doesn't enable/disable keyboard mode in linked CDS/Protein view +- Closing tree windows with CMD/CTRL-W for alignments with multiple views can close views unexpectedly + + +### Java 11 Specific defects +- Jalview Properties file is not sorted alphabetically when saved