--- /dev/null
+---
+channel: release
+version: 2.11.0
+date: 2019-07-04
+---
+
+## New Features
+
+- <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 --> 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
+- <!-- JAL-1929 --> 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))
+- <!-- JAL-1839,JAL-3254,JAL-3260 --> File type associations for formats supported by Jalview (including .jvp project files)
+- <!-- JAL-3260 --> Jalview launch files (.jvl) to pass command line arguments and switch between different getdown channels
+- <!-- JAL-3141 --> Backup files created when saving Jalview project or alignment files
+- <!-- JAL-1793 --> Annotate nucleotide alignments from VCF data files
+- <!-- JAL-2753 --> Version of HTSJDK shipped with Jalview updated to version 2.12.0
+- <!-- JAL-2620 --> Alternative genetic code tables for 'Translate as cDNA'
+- <!-- JAL-3018 --> Update of Ensembl Rest Client to API v10.0
+- **Enhanced visualisation and analysis of Sequence Features**
+ - <!-- JAL-3140 JAL-2446 --> IntervalStoreJ (NCList implementation that allows updates) used for Sequence Feature collections
+ - <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 --> 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)
+ - <!-- JAL-2879 --> Feature Attributes and shading schemes stored and restored from Jalview Projects
+ - <!-- JAL-3334 --> Use full Sequence Ontology (via BioJava) to recognise variant features
+ - <!-- JAL-2897,JAL-3330 --> Show synonymous codon variants on peptide sequences (also coloured red by default)
+ - <!-- JAL-2792 --> Popup window to show full report for a selected sequence feature's details
+ - <!-- JAL-3139,JAL-2816,JAL-1117 --> More efficient sequence feature render algorithm (Z-sort/transparency and filter aware)
+ - <!-- JAL-3049,JAL-3054 --> Improved tooltips in Feature Settings dialog
+- <!-- JAL-3205 --> Symmetric score matrices for faster tree and PCA calculations
+- **Principal Components Analysis Viewer**
+ - <!-- JAL-1767,JAL-2647 --> Principal Components Analysis results and Viewer state saved in Jalview Project
+ - <!-- JAL-2962 --> 'Change parameters' option removed from viewer's drop-down menus
+ - <!-- JAL-2975 --> Can use shift + arrow keys to rotate PCA image incrementally
+ - <!-- JAL-2965, JAL-1285 --> PCA plot is depth cued
+- <!-- JAL-3127 --> New 'Colour by Sequence ID' option
+- **Speed and Efficiency**
+ - <!-- JAL-2185,JAL-3198 --> More efficient creation of selections and multiple groups when working with large alignments
+ - <!-- JAL-3200 --> Speedier import of annotation rows when parsing Stockholm files
+- **User Interface**
+ - <!-- JAL-2933 --> Finder panel remembers last position in each view
+ - <!-- JAL-2527 JAL-3203 --> Alignment Overview now WYSIWIS (What you see is what is shown)<br/>
+Only visible regions of alignment are shown by default (can be changed in user preferences)
+ - <!-- JAL-3169 --> File Chooser stays open after responding Cancel to the Overwrite Dialog
+ - <!-- JAL-2420,JAL-3166 --> Better popup menu behaviour when all sequences are hidden
+ - <!-- JAL-1244 --> Status bar shows bounds when dragging a selection region, and gap count when inserting or deleting gaps
+ - <!-- JAL-3132 --> Status bar updates over sequence and annotation labels
+ - <!-- JAL-3093 --> Annotation tooltips and popup menus are shown when in wrapped mode
+ - <!-- JAL-3073 --> Can select columns by dragging left/right in a graph or histogram annotation
+ - <!-- JAL-2814,JAL-437 --> Help button on Uniprot and PDB search panels
+ - <!-- JAL-2621 --> Cursor changes over draggable box in Overview panel
+ - <!-- JAL-3181 --> Consistent ordering of links in sequence id popup menu
+ - <!-- JAL-3080 --> Red line indicating tree-cut position not shown if no subgroups are created
+ - <!-- JAL-3042 --> Removed ability to configure length of search history by right-clicking search box
+- <!-- JAL-3232 --> 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
+- <!-- JAL-3035 --> DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop
+- <!-- JAL-3063,JAL-3116 --> Castor library for XML marshalling and unmarshalling has been replaced by JAXB for Jalview projects and XML based data retrieval clients
+- <!-- JAL-3311 --> Disable VAMSAS menu in preparation for removal
+- <!-- --> Jalview Desktop no longer distributed via Java Web Start
+
+
+### Documentation
+- <!-- JAL-3003 --> Added remarks about transparent rendering effects not supported in EPS figure export
+- <!-- JAL-2903 --> Typos in documentation for Preferences dialog
+
+
+### Development and Release Processes
+- <!-- JAL-3196,JAL-3179.JAL-2671 --> Build system migrated from Ant to Gradle
+- <!-- JAL-1424 --> Enhanced checks for missing and duplicated keys in Message bundles
+- <!-- JAL-3225 --> Eclipse project configuration managed with gradle-eclipse
+- <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 --> Atlassian Bamboo continuous integration for unattended Test Suite execution
+- <!-- JAL-2864 --> Memory test suite to detect leaks in common operations
+- <!-- JAL-2360,JAL-2416 --> More unit test coverage, and minor issues resolved
+- <!-- JAL-3248 --> Developer documentation migrated to markdown (with HTML rendering)
+- <!-- JAL-3287 --> HelpLinksChecker runs on Windows
+- <!-- JAL-3289 --> New URLs for publishing development versions of Jalview
+
+
+## Issues Resolved
+
+- <!-- JAL-3143 --> Timeouts when retrieving data from Ensembl
+- <!-- JAL-3244 --> 'View [Structure] Mappings' and structure superposition in Jmol fail on Windows
+- <!-- JAL-3286 --> Blank error dialog is displayed when discovering structures for sequences with lots of PDB structures
+- <!-- JAL-3239 --> Text misaligned in EPS or SVG image export with monospaced font
+- <!-- JAL-3171 --> Warning of 'Duplicate entry' when saving Jalview project involving multiple views
+- <!-- JAL-3164 --> Overview for complementary view in a linked CDS/Protein alignment is not updated when Hide Columns by Annotation dialog hides columns
+- <!-- JAL-3158 --> 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
+- <!-- JAL-3161 --> Annotations tooltip changes beyond visible columns
+- <!-- JAL-3154 --> Table Columns could be re-ordered in Feature Settings and Jalview Preferences panels
+- <!-- JAL-2865 --> Jalview hangs when closing windows, or redrawing the overview with large alignments
+- <!-- JAL-2750 --> 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
+- <!-- JAL-3218 --> Couldn't hide selected columns adjacent to a hidden column marker via scale popup menu
+- <!-- JAL-2846 --> Error message for trying to load in invalid URLs doesn't tell users the invalid URL
+- <!-- JAL-2816 --> Tooltips displayed for features filtered by score from view
+- <!-- JAL-3330 --> Sequence Variants retrieved from Ensembl during show cross references or Fetch Database References are shown in red in original view
+- <!-- JAL-2898,JAL-2207 --> stop_gained variants not shown correctly on peptide sequence (computed variant shown as p.Res.null)
+- <!-- JAL-2060 --> 'Graduated colour' option not offered for manually created features (where feature score is Float.NaN)
+- <!-- JAL-3097,JAL-3099 --> Blank extra columns drawn or printed when columns are hidden
+- <!-- JAL-3082 --> Regular expression error for '(' in Select Columns by Annotation description
+- <!-- JAL-3072 --> Scroll doesn't stop on mouse up after dragging out of Scale or Annotation Panel
+- <!-- JAL-3075 --> Column selection incorrect after scrolling out of scale panel
+- <!-- JAL-3074 --> Left/right drag in annotation can scroll alignment down
+- <!-- JAL-3108 --> Error if mouse moved before clicking Reveal in scale panel
+- <!-- JAL-3002 --> Column display is out by one after Page Down, Page Up in wrapped mode
+- <!-- JAL-2839,JAL-781 --> Finder doesn't skip hidden regions
+- <!-- JAL-2932 --> Finder searches in minimised alignments
+- <!-- JAL-2250 --> 'Apply Colour to All Groups' not always selected on opening an alignment
+- <!-- JAL-3180 --> 'Colour by Annotation' not marked selected in Colour menu
+- <!-- JAL-3201 --> Per-group Clustal colour scheme changes when different groups in the alignment are selected
+- <!-- JAL-2717 --> Internationalised colour scheme names not shown correctly in menu
+- <!-- JAL-3206 --> Colour by Annotation can go black at min/max threshold limit
+- <!-- JAL-3125 --> Value input for graduated feature colour threshold gets 'unrounded'
+- <!-- JAL-2982 --> PCA image export doesn't respect background colour
+- <!-- JAL-2963 --> PCA points don't dim when rotated about y axis
+- <!-- JAL-2959 --> PCA Print dialog continues after Cancel
+- <!-- JAL-3078 --> Cancel in Tree Font dialog resets alignment, not Tree font
+- <!-- JAL-2964 --> Associate Tree with All Views not restored from project file
+- <!-- JAL-2915 --> Scrolling of split frame is sluggish if Overview shown in complementary view
+- <!-- JAL-3313 --> Codon consensus incorrectly scaled when shown without normalisation
+- <!-- JAL-3021 --> Sequence Details report should open positioned at top of report
+- <!-- JAL-914 --> Help page can be opened twice
+- <!-- JAL-3333 --> Fuzzy text in web service status menu on OSX Mojave
+
+
+### Editing
+- <!-- JAL-2822 --> Start and End should be updated when sequence data at beginning or end of alignment added/removed via 'Edit' sequence
+- <!-- JAL-2541,JAL-2684 (tests) --> Delete/Cut selection doesn't relocate sequence features correctly when start of sequence is removed (Known defect since 2.10)
+- <!-- JAL-2830 --> Inserting gap sequence via the Edit Sequence dialog corrupts dataset sequence
+- <!-- JAL-868 --> Structure colours not updated when associated tree repartitions the alignment view (Regression in 2.10.5)
+
+
+### Datamodel
+- <!-- JAL-2986 --> 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)
+- <!-- JAL-3288 --> Menus work properly in split-screen
+
+
+### New Known Defects
+- <!-- JAL-3340 --> Select columns containing feature by double clicking ignores bounds of an existing selected region
+- <!-- JAL-3313 --> Codon consensus logo incorrectly scaled in gapped regions of protein alignment.
+- <!-- JAL-2647 --> Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
+- <!-- JAL-3213 --> Alignment panel height can be too small after 'New View'
+- <!-- JAL-3240 --> Display is incorrect after removing gapped columns within hidden columns
+- <!-- JAL-3314 --> Rightmost selection is lost when mouse re-enters window after dragging left to select columns to left of visible region
+- <!-- JAL-2876 --> 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.
+- <!-- JAL-3184 --> Cancel on Feature Settings dialog doesn't reset group visibility
+- <!-- JAL-3338 --> F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
+- <!-- JAL-797 --> Closing tree windows with CMD/CTRL-W for alignments with multiple views can close views unexpectedly
+
+
+### Java 11 Specific defects
+- <!-- JAL-3235 --> Jalview Properties file is not sorted alphabetically when saved
git://source.jalview.org / jalview.git / blobdiff