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@@ -89,86 +106,227 @@ 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
- - Cuts and Sequence Edits don't properly relocate sequence features
+ -
+ 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)
-
- 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)
+
-
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+