@@ -89,87 +111,227 @@ li:before { 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 +

+ 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

- -

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.
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
+ Test to catch memory leaks in Jalview UI +

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
+ 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 only aligns selected regions of each selected sequence
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

- Applet
-

Concurrent modification exception when closing alignment panel
+ 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 +

- BioJSON
+ Applet

- BioJSON export does not preserve non-positional features -
+ Concurrent modification exception when + closing alignment panel +

+ BioJSON
+

+ BioJSON export does not preserve + non-positional features +

- Known Java 9 Issues + New Known Issues

Groovy Console very slow to open and is - not responsive when entering characters (Webstart, Java 9.01, - OSX 10.10) +
+ 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

- New Known Issues + Known Java 9 Issues

+ Groovy Console very slow to open and is + not responsive when entering characters (Webstart, Java + 9.01, OSX 10.10) +

- Version 2.10.3 was released in November 2017. The full list of - bug fixes and new features can be found in the 2.10.3 Release Notes, but - the highlights are below. + This is the January 2018 patch release, which addresses critical bugs including trackpad function in OSX, and display of multiple 3D structures. + The full list bugs fixed in this release can be found in the 2.10.3b1 + Release Notes. In addition, Jalview 2.10.3 provides:

- This release of Jalview introduces an Experimental Features - option in the Jalview Desktop's Tools menu that allows you - to try out features that are still in development. To access the - experimental features below - first enable the Tools→Enable - Experimental Features option, and then restart Jalview. + Remember, please enable the Experimental Features option in + the Jalview Desktop's Tools menu, and then restart Jalview + if you want to try out features below: