X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_10_3.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_10_3.md;h=c3ba109be8262da8a0a2813434f1c603c01124ee;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=0000000000000000000000000000000000000000;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git diff --git a/help/markdown/releases/release-2_10_3.md b/help/markdown/releases/release-2_10_3.md new file mode 100644 index 0000000..c3ba109 --- /dev/null +++ b/help/markdown/releases/release-2_10_3.md @@ -0,0 +1,89 @@ +--- +channel: release +version: 2.10.3 +date: 2017-11-17 +--- + +## New Features + + + + - Faster and more efficient management and rendering of sequence features + - More reliable Ensembl fetching with HTTP 429 rate limit request hander + - Structure views don't get updated unless their colours have changed + - All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera) + - 'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs + - Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references + - Start/End limits are shown in Pairwise Alignment report + - Sequence fetcher's Free text 'autosearch' feature can be disabled + - Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs + - Short names for sequences retrieved from Uniprot + + +### Scripting + - Groovy interpreter updated to 2.4.12 + - Example groovy script for generating a matrix of percent identity scores for current alignment. + + +### Testing and Deployment + - Test to catch memory leaks in Jalview UI + + +## Issues Resolved + + + +### General + - Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view + - Race condition when parsing sequence ID strings in parallel + - Overview windows are also closed when alignment window is closed + - Export of features doesn't always respect group visibility + - Jumping from column 1 to column 100,000 takes a long time in Cursor mode + + +### Desktop + - Structures with whitespace chainCode cannot be viewed in Chimera + - Protein annotation panel too high in CDS/Protein view + - Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs + - Slow EnsemblGenome ID lookup + - Revised Ensembl REST API CDNA query + - Hidden column marker in last column not rendered when switching back from Wrapped to normal view + - Annotation display corrupted when scrolling right in unwapped alignment view + - Existing features on subsequence incorrectly relocated when full sequence retrieved from database + - Last reported memory still shown when Desktop->Show Memory is unticked (OSX only) + - Amend Features dialog doesn't allow features of same type and group to be selected for amending + - Jalview becomes sluggish in wide alignments when hidden columns are present + - Jalview freezes when loading and displaying several structures + - Black outlines left after resizing or moving a window + - Unable to minimise windows within the Jalview desktop on OSX + - Mouse wheel doesn't scroll vertically when in wrapped alignment mode + - Scale mark not shown when close to right hand end of alignment + - Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions + - Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog + - Show cross-references not enabled after restoring project until a new view is created + - Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2) + - Overview redraws whole window when box position is adjusted + - Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10) + - Double residue highlights in cursor mode if new selection moves alignment window + - Alignment vanishes when using arrow key in cursor mode to pass hidden column marker + - Ensembl Genomes example ID changed to one that produces correctly annotated transcripts and products + - Toggling a feature group after first time doesn't update associated structure view + + +### Applet + - Concurrent modification exception when closing alignment panel + + +### BioJSON + - BioJSON export does not preserve non-positional features + + +### New Known Issues + - Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview) + - Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top + - Select columns containing feature ignores graduated colour threshold + - Edit sequence operation doesn't always preserve numbering and sequence features + + +### Known Java 9 Issues + - Groovy Console very slow to open and is not responsive when entering characters (Webstart, Java 9.01, OSX 10.10)