From 17863d983fe946ec642e3d6d86cabd2e01be3b19 Mon Sep 17 00:00:00 2001 From: James Procter Date: Wed, 15 Feb 2023 13:59:29 +0000 Subject: [PATCH] JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version --- help/markdown/releases/release-2_11_3.md | 24 ------------- help/markdown/releases/release-2_11_3_0.md | 52 +++++++++++++++++++++++----- 2 files changed, 44 insertions(+), 32 deletions(-) delete mode 100644 help/markdown/releases/release-2_11_3.md diff --git a/help/markdown/releases/release-2_11_3.md b/help/markdown/releases/release-2_11_3.md deleted file mode 100644 index 18b15ea..0000000 --- a/help/markdown/releases/release-2_11_3.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -version: 2.11.3 -date: 2022-12-12 -channel: "release" ---- - -## New Features - -- Find can search sequence features' type and description -- Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences -JAL-4089 use selected columns for superposition -JAL-4086 Highlight aligned positions on all associated structures when mousing over a column -JAL-4083 Exceptions for multiple residue highlights in Jmol -JAL-4075 Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows -JAL-4033 selections with visual feedback via contact matrix annotation -JAL-4027 contact matrix datatype in Jalview -JAL-3895 Alphafold red/orange/yellow/green colourscheme for structures -JAL-3855 Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/ -JAL-3416 FlatLAF default look and feel on Linux, OSX and everywhere else ? -JAL-2961 Jmol view not always centred on structures when multiple structures are viewed -JAL-2382 Import and display sequence-associated contact predictions in CASP-RR format -JAL-2349 Contact prediction visualisation -JAL-2348 modularise annotation renderer -JAL-1551 Standard source code formatting and editing settings diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md index 7776081..46de783 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -5,13 +5,49 @@ channel: "release" --- ## New Features -JAL-4064 Native M1 build for macOS using Adoptium JRE 11 macos-aarch64 -JAL-4054 Installers built with install4j10 -JAL-3676 Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button -JAL-3416 FlatLAF default look and feel on Linux, OSX and everywhere else ? +- Native M1 build for macOS using Adoptium JRE 11 macos-aarch64 +- Installers built with install4j10 +- Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button +- FlatLAF default look and feel on Linux, OSX and everywhere else ? -## Issues Resolved -JAL-3776 Cancelling interactive calculation leaves empty progress bar. -JAL-3772 Unsaved Alignment windows close without prompting to save, individually or at application quit. -JAL-1988 Can quit Jalview while 'save project' is in progress +- Ambiguous Base Colourscheme +- Find can search sequence features' type and description +- Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences +- Use selected columns for superposition +- Highlight aligned positions on all associated structures when mousing over a column + +- Alphafold red/orange/yellow/green colourscheme for structures +- Interactive picking of low pAE score regions +- contact matrix datatype in Jalview +- Selections with visual feedback via contact matrix annotation + +- Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows +- Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/ + +- Jmol view not always centred on structures when multiple structures are viewed + +- Overview window is saved in project file, and state of 'show hidden regions' is preserved. + +- Name of alignment and view included in overview window's title + +- Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows +- Shift+Click+Drag to adjust height of all annotation tracks of same type + +## Still in progress (delete on release) + +- Import and display sequence-associated contact predictions in CASP-RR format +- Contact prediction visualisation +- modularise annotation renderer + + + +## Issues Resolved +- Cancelling interactive calculation leaves empty progress bar. +- Unsaved Alignment windows close without prompting to save, individually or at application quit. +- Can quit Jalview while 'save project' is in progress +- 'Use original colours' option of colour by annotation not honoured when restoring view from project +- PDB structures slow to view when Jalview Java Console is open (2.11.2.7 patch) +- Multiple overview windows can be opened for a particular alignment view when multiple views are present +- Overview windows opened automatically (due to preferences settings) lack title +- Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession \ No newline at end of file -- 1.7.10.2