X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=5b6180d084faa935e8dbaf10b05ea428020844f5;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=973e867e7108d6b8ec7a7230339e94e83fa1b6e4;hpb=61ff8fb4efa315c35149c9d11850d99e3d00c441;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
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-
-
- Development
-
- - Updated building instructions
-
-
-
- -
- Occupancy calculation is incorrect for
- alignment columns with over -1+2^32 gaps (breaking filtering
- and display)
-
- -
- Caps on Hi-DPI scaling to prevent crazy
- scale factors being set with buggy window-managers (linux
- only)
-
- -
- Removed RNAview checkbox and logic from Structure Preferences
-
- Development
-
- - Fixed non-fatal gradle errors during build
-
- |
-
-
- 2.11.1.4
- 09/03/2021 |
- Improved control of
- Jalview's use of network services via jalview_properties
-
- -
- New .jalview_properties token controlling
- launch of the news browser (like -nonews argument)
-
- -
- New .jalview_properties token controlling
- download of linkout URLs from
- www.jalview.org/services/identifiers
-
- -
- New .jalview_properties token controlling
- download of BIOJSHTML templates
-
- -
- New 'Discover Web Services' option to
- trigger a one off JABAWS discovery if autodiscovery was
- disabled
-
- |
-
-
- -
- Intermittent deadlock opening structure in
- Jmol
-
- New Known defects
-
- -
- Protein Cross-Refs for Gene Sequence not
- always restored from project (since 2.10.3)
-
- -
- Selections from tree built from CDS aren't
- propagated to Protein alignment (since 2.11.1.3)
-
-
- |
-
-
- 2.11.1.3
- 29/10/2020 |
-
-
- |
-
-
- -
- Find doesn't always highlight all matching
- positions in a sequence (bug introduced in 2.11.1.2)
-
- -
- Alignments containing one or more protein
- sequences can be classed as nucleotide
-
- -
- CDS alignment doesn't match original CDS
- sequences after alignment of protein products (known defect
- first reported for 2.11.1.0)
-
- -
- No tooltip or popup menu for genomic
- features outwith CDS shown overlaid on protein
-
- -
- Overlapping CDS in ENA accessions are not
- correctly mapped by Jalview (e.g. affects viral CDS with
- ribosomal slippage, since 2.9.0)
-
- -
- Spliced transcript CDS sequences don't show
- CDS features
-
- -
- Selections in CDS sequence panel don't
- always select corresponding protein sequences
-
- -
- Make groups from selection for a
- column selection doesn't always ignore hidden columns
-
- Installer
-
- -
- Space character in Jalview install path on
- Windows prevents install4j launching getdown
-
- Development
-
- -
- Fixed typos and specified compatible gradle
- version numbers in doc/building.md
-
-
- |
-
-
- 2.11.1.2
- 25/09/2020 |
-
-
- |
-
-
- -
- Fresh install of Jalview 2.11.1.1 reports
- "Encountered problems opening
- https://www.jalview.org/examples/exampleFile_2_7.jvp"
-
-
- |
-
-
- 2.11.1.1
- 17/09/2020 |
-
-
- -
- Shift+arrow keys navigate to next gap or
- residue in cursor mode
-
- -
- Support import of VCF 4.3 by updating
- HTSJDK from 2.12 to 2.23
-
- -
- IntervalStore library updated to v.1.1:
- optimisations and improvements suggested by Bob Hanson and
- improved compatibility with JalviewJS
-
- -
- Retrieve GZipped stockholm formatted
- alignments from Pfam and Rfam
-
- -
- Recognise GZipped content for URLs and File
- import (no longer based on .gz extension)
-
- -
- Updated Spanish Translation for 2.11.1
-
- -
- Migrate EMBL record retrieval to use latest
- ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
- EMBL flat file
-
- -
- Improved warning messages, debug logging
- and fixed Retry action when Jalview encounters errors when
- saving or making backup files.
-
- -
- Enhanced Jalview Java Console:
-
- - Jalview's logging level can be configured
- - Copy to Clipboard Buttion
-
-
- -
- Improved support for Hi-DPI (4K) screens
- when running on Linux (Requires Java 11+)
-
- Launching Jalview
-
- -
- Configure Jalview Desktop's look and feel
- through a system property
-
- -
- Improved built-in documentation and command
- line help for configuring Jalview's memory
-
-
- |
-
-
- -
- Conservation and Quality tracks are shown
- but not calculated and no protein or DNA score models are
- available for tree/PCA calculation when launched with
- Turkish language locale
-
- -
- Escape does not clear highlights on the
- alignment (Since Jalview 2.10.3)
-
- -
- Alt+Left or Right arrow in cursor mode
- doesn't slide selected sequences, just sequence under cursor
-
- -
- Alt+Up/Down in cursor mode doesn't move
- sequence under the cursor
-
- -
- Peptide-to-CDS tracking broken when
- multiple EMBL gene products shown for a single contig
-
- -
- Errors encountered when processing variants
- from VCF files yield "Error processing VCF: Format specifier
- '%s'" on the console
-
- -
- Count of features not shown can be wrong
- when there are both local and complementary features mapped
- to the position under the cursor
-
- -
- Sequence ID for reference sequence is
- clipped when Right align Sequence IDs enabled
-
- -
- Slider with negative range values not
- rendered correctly in VAqua4 (Since 2.10.4)
-
- -
- Single quotes not displayed correctly in
- internationalised text for some messages and log output
-
- -
- Find doesn't report matches that span
- hidden gapped columns
-
- -
- Resolved memory leaks in Tree and PCA
- panels, Alignment viewport and annotation renderer.
-
- -
- Jalview ignores file format parameter
- specifying output format when exporting an alignment via the
- command line
-
- -
- Windows 10: For a minority of users, if
- backups are not enabled, Jalview sometimes fails to
- overwrite an existing file and raises a warning dialog. (in
- 2.11.0, and 2.11.1.0, the workaround is to try to save the
- file again, and if that fails, delete the original file and
- save in place.)
-
- -
- Cannot process alignments from HTTPS urls
- via command line
-
- -
- References to http://www.jalview.org in
- program and documentation
-
- Launching Jalview
-
- -
- Jalview application fails when launched the
- first time for a version that has different jars to the
- previous launched version.
-
- Developing Jalview
-
- -
- Fixed issue with cleaning up old coverage
- data, causing cloverReport gradle task to fail with an
- OutOfMemory error.
-
- -
- Migrated the Jalview Version Checker to
- monitor the release channel
-
- New Known defects
-
- -
- CDS shown in result of submitting proteins
- in a CDS/Protein alignment to a web service is wrong when
- proteins share a common transcript sequence (e.g.
- genome of RNA viruses)
-
- -
- Co-located features exported and re-imported
- are ordered differently when shown on alignment and in
- tooltips. (Also affects v2.11.1.0)
-
- -
- Drag and drop of alignment file onto
- alignment window when in a HiDPI scaled mode in Linux only
- works for the top left quadrant of the alignment window
-
- -
- Stale build data in jalview standalone jar
- builds (only affects 2.11.1.1 branch)
-
- -
- Sequence ID colourscheme not re-applied
- when alignment view restored from project (since Jalview 2.11.0)
-
- -
- Duplicate CDS sequences are generated when
- protein products for certain ENA records are repeatedly
- shown via Calculate->Show Cross Refs
-
-
- |
-
-
- 2.11.1.0
22/04/2020 |
|