X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_10_4.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_10_4.md;h=ad0c592b667b4eaba0e70721191d1cc9bb380c49;hp=0000000000000000000000000000000000000000;hb=07727bb7e06eb681af51a95e941cb035ac637d10;hpb=ce916cd46bbe1ec0446d8672b7341f5af7471b6e diff --git a/help/markdown/releases/release-2_10_4.md b/help/markdown/releases/release-2_10_4.md new file mode 100644 index 0000000..ad0c592 --- /dev/null +++ b/help/markdown/releases/release-2_10_4.md @@ -0,0 +1,57 @@ +--- +channel: release +version: 2.10.4 +date: 2018-05-10 +--- + +## New Features + + + +### + - New Structure Chooser control for disabling automatic superposition of multiple structures and open structures in existing views + - Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them. + - Jalview uses HTTPS for Uniprot, Xfam and Ensembl services + - Improved performance for large alignments and lots of hidden columns + - Improved performance when rendering lots of features (particularly when transparency is disabled) + - Experimental features in 2.10.2 for exchange of Jalview features and Chimera attributes made generally available + + +## Issues Resolved + + + - Structure and Overview aren't updated when Colour By Annotation threshold slider is adjusted + - Slow redraw when Overview panel shown overlapping alignment panel + - Overview doesn't show end of unpadded sequence as gaps + - Cross-reference handling improved: CDS not handled correctly if transcript has no UTR + - Secondary structure and temperature factor annotation not added to sequence when local PDB file associated with it by drag'n'drop or structure chooser + - Answering 'No' to PDB Autoassociate dialog doesn't import PDB files dropped on an alignment + - Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views + - Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+. + - Tooltip shouldn't be displayed for empty columns in annotation row + - Preferences panel's ID Width control is not honored in batch mode + - Linked sequence highlighting doesn't work for structures added to existing Jmol view + - 'View Mappings' includes duplicate entries after importing project with multiple views + - Viewing or annotating Uniprot protein sequences via SIFTS from associated PDB entries with negative residue numbers or missing residues fails + - Exception when shading sequence with negative Temperature Factor values from annotated PDB files (e.g. as generated by CONSURF) + - Uniprot 'sequence variant' features tooltip doesn't include a text description of mutation + - Invert displayed features very slow when structure and/or overview windows are also shown + - Selecting columns from highlighted regions very slow for alignments with large numbers of sequences + - Copy Consensus fails for group consensus with 'StringIndexOutOfBounds' + - VAqua(4) provided as fallback Look and Feel for OSX platforms running Java 10 + - Adding a structure to existing structure view appears to do nothing because the view is hidden behind the alignment view + + +### Applet + - Copy consensus sequence option in applet should copy the group consensus when popup is opened on it + + +### Batch Mode + - Fixed ID width preference is not respected + + +### New Known Defects + - Exceptions occasionally raised when editing a large alignment and overview is displayed + - 'Overview updating' progress bar is shown repeatedly after a series of edits even when the overview is no longer reflecting updates + - 'SIFTS Mapping Error' when viewing structures for protein subsequence (if 'Trim Retrieved Sequences' enabled) or Ensembl isoforms (Workaround in 2.10.4 is to fail back to N&W mapping) + - Export Annotations from File Menu with CSV option gives blank output