|
+ |
+ Application
+
+ - 3D Structure chooser opens with 'Cached structures'
+ view if structures already loaded
+ - Progress bar reports models as they are loaded to
+ structure views
+ |
+
+
+ General
+
+ - Colour by conservation always enabled and no tick
+ shown in menu when BLOSUM or PID shading applied
+ - FER1_ARATH and FER2_ARATH labels were switched in
+ example sequences/projects/trees
+
+ Application
+
+ - Jalview projects with views of local PDB structure
+ files saved on Windows cannot be opened on OSX
+ - Multiple structure views can be opened and
+ superposed without timeout for structures with multiple
+ models or multiple sequences in alignment
+ - Cannot import or associated local PDB files without
+ a PDB ID HEADER line
+ - RMSD is not output in Jmol console when
+ superposition is performed
+ - Drag and drop of URL from Browser fails for Linux
+ and OSX versions earlier than El Capitan
+ - ENA client ignores invalid content from ENA server
+ - Exceptions are not raised in console when ENA
+ client attempts to fetch non-existent IDs via Fetch DB
+ Refs UI option
+ - Exceptions are not raised in console when a new
+ view is created on the alignment
+ - OSX right-click fixed for group selections:
+ CMD-click to insert/remove gaps in groups and CTRL-click
+ to open group pop-up menu
+
+ Build and deployment
+
+ - URL link checker now copes with multi-line anchor
+ tags
+
+ New Known Issues
+
+ - Drag and drop from URL links in browsers do not
+ work on Windows
+
+ |
+
+
+ |
+
|
General
-
- - Alignment ruler shows positions relative to reference sequence
+ -
+ Updated Spanish translations.
+
+ -
+ Jmol now primary parser
+ for importing structure data to Jalview. Enables mmCIF and
+ better PDB parsing.
+
+ -
+ Alignment ruler shows positions relative to
+ reference sequence
+
+ -
+ Position/residue shown in status bar when
+ mousing over sequence associated annotation
+
+ -
+ Default RNA SS symbol to 'matching bracket'
+ for manual entry
+
+ -
+ RNA Structure consensus indicates wc-only
+ '()', canonical '[]' and invalid '{}' base pair populations
+ for each column
+
+ -
+ Feature settings popup menu options for
+ showing or hiding columns containing a feature
+
+ -
+ Edit selected group by double clicking on
+ group and sequence associated annotation labels
+
+ -
+ Sequence name added to annotation label in
+ select/hide columns by annotation and colour by annotation
+ dialogs
+
+
Application
-
- - Support for reverse-complement coding regions in ENA and EMBL
- - Upgrade to EMBL XML 1.2 for ENA record retrieval
- - New 'execute Groovy script' option in an alignment window's Calculate menu
- - Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
- - Store/restore reference sequence in Jalview projects
-
- Applet
+
+ Automatically hide introns when opening a
+ gene/transcript view
+
+
+ Uniprot Sequence fetcher Free Text Search
+ dialog
+
+
+ UniProt - PDB protein
+ structure mappings with the EMBL-EBI PDBe SIFTS database
+
+
+ Updated download sites used for Rfam and
+ Pfam sources to xfam.org
+
+
+ Disabled Rfam(Full) in the sequence fetcher
+
+
+ Show residue labels in Chimera when mousing
+ over sequences in Jalview
+
+
+ Support for reverse-complement coding
+ regions in ENA and EMBL
+
+
+ Upgrade to EMBL XML 1.2
+ for record retrieval via ENA rest API
+
+
+ Support for ENA CDS records with reverse
+ complement operator
+
+
+ Update to groovy-2.4.6-indy - for faster
+ groovy script execution
+
+
+ New 'execute Groovy script' option in an
+ alignment window's Calculate menu
+
+
+ Allow groovy scripts that call
+ Jalview.getAlignFrames() to run in headless mode
+
+
+ Support for creating new alignment
+ calculation workers from groovy scripts
+
+
+ Store/restore reference sequence in
+ Jalview projects
+
+
+ Chain codes for a sequence's PDB
+ associations are now saved/restored from project
+
+
+ Database selection dialog always shown
+ before sequence fetcher is opened
+
+
+ Double click on an entry in Jalview's
+ database chooser opens a sequence fetcher
+
+
+ Free-text search client for UniProt using
+ the UniProt REST API
+
+
+ -nonews command line parameter to prevent
+ the news reader opening
+
+
+ Displayed columns for PDBe and Uniprot
+ querying stored in preferences
+
+
+ Pagination for displaying PDBe and Uniprot
+ search results
+
+
+ Tooltips shown on database chooser
+
+
+ Reverse complement function in calculate
+ menu for nucleotide sequences
+
+
+ Alignment sort by feature scores
+ and feature counts preserves alignment ordering (and
+ debugged for complex feature sets).
+
+
+ Chimera 1.11.1 minimum requirement for
+ viewing structures with Jalview 2.10
+
+
+ Retrieve
+ genome, transcript CCDS and gene ids via the Ensembl and
+ Ensembl Genomes REST API
+
+
+ Protein sequence variant annotation
+ computed for 'sequence_variant' annotation on CDS regions
+ (Ensembl)
+
+
+ ENA CDS 'show cross references' for Uniprot
+ sequences
+
+
+ Improved warning messages when DB
+ Ref Fetcher fails to match, or otherwise updates sequence
+ data from external database records.
+
+
+ Revised Jalview Project format for
+ efficient recovery of sequence coding and alignment
+ annotation relationships.
+
+
- |
+
+ -- JAL---
+
+ -->
General
- - reinstate CTRL-click for opening pop-up menu on OSX
- - Export features in Jalview format (again) includes graduated colourschemes
- - More responsive when working with big alignments and lots of hidden columns
- - hidden column markers not always rendered at right of alignment window
- - Tidied up links in help file table of contents
- - Feature based tree calculation not shown for DNA alignments
- - Hidden columns ignored during feature based tree calculation
- - Alignment view stops updating when show unconserved enabled for group on alignment
- - Cannot insert gaps into sequence when set as reference
-
+ -
+ reinstate CTRL-click for opening pop-up
+ menu on OSX
+
+ -
+ Export features in Jalview format (again)
+ includes graduated colourschemes
+
+ -
+ More responsive when
+ working with big alignments and lots of hidden columns
+
+ -
+ Hidden column markers not always rendered
+ at right of alignment window
+
+ -
+ Tidied up links in help file table of
+ contents
+
+ -
+ Feature based tree calculation not shown
+ for DNA alignments
+
+ -
+ Hidden columns ignored during feature
+ based tree calculation
+
+ -
+ Alignment view stops updating when show
+ unconserved enabled for group on alignment
+
+ -
+ Cannot insert gaps into sequence when
+ set as reference
+
+ -
+ Alignment column in status incorrectly
+ shown as "Sequence position" when mousing over
+ annotation
+
+ -
+ Incorrect column numbers in ruler when
+ hidden columns present
+
+ -
+ Colour by RNA Helices not enabled when
+ user created annotation added to alignment
+
+ -
+ RNA Structure consensus only computed for
+ '()' base pair annotation
+
+ -
+ Enabling 'Ignore Gaps' results
+ in zero scores for all base pairs in RNA Structure
+ Consensus
+
+ -
+ Extend selection with columns containing
+ feature not working
+
+ -
+ Pfam format writer puts extra space at
+ beginning of sequence
+
+ -
+ Incomplete sequence extracted from pdb
+ entry 3a6s
+
+ -
+ Cannot create groups on an alignment from
+ from a tree when t-coffee scores are shown
+
+ -
+ Cannot import and view PDB
+ structures with chains containing negative resnums (4q4h)
+
+ -
+ ArithmeticExceptions raised when parsing
+ some structures
+
+ -
+ 'Empty' alignment blocks added
+ to Clustal, PIR and PileUp output
+
+ -
+ Reordering sequence features that are
+ not visible causes alignment window to repaint
+
+ -
+ Threshold sliders don't work in
+ graduated colour and colour by annotation row for e-value
+ scores associated with features and annotation rows
+
+ -
+ amino acid physicochemical conservation
+ calculation should be case independent
+
+ -
+ Remove annotation also updates hidden
+ columns
+
+ -
+ FER1_ARATH and FER2_ARATH mislabelled in
+ example file (uniref50.fa, feredoxin.fa, unaligned.fa,
+ exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
+
+ -
+ Null pointer exceptions and redraw
+ problems when reference sequence defined and 'show
+ non-conserved' enabled
+
+ -
+ Quality and Conservation are now shown on
+ load even when Consensus calculation is disabled
+
Application
-
- - Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
- - URLs and links can imported by drag'n'drop on OSX webstart
- - InstallAnywhere distribution fails when launching Chimera
- - Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
- - Cannot save project when view has a reference sequence defined
- - Columns are suddenly selected in other alignments and views when revealing hidden columns
- - Hide columns not mirrored in complement view in a cDNA/Protein splitframe
- - Cannot save/restore representative sequence from project when only one sequence is represented
-
+ -
+ URLs and links can't be imported by
+ drag'n'drop on OSX when launched via webstart (note - not
+ yet fixed for El Capitan)
+
+ -
+ Corrupt preferences for SVG, EPS & HTML
+ output when running on non-gb/us i18n platforms
+
+ -
+ Error thrown when exporting a view with
+ hidden sequences as flat-file alignment
+
+ -
+ InstallAnywhere distribution fails when
+ launching Chimera
+
+ -
+ Jalview very slow to launch via webstart
+ (also hotfix for 2.9.0b2)
+
+ -
+ Cannot save project when view has a
+ reference sequence defined
+
+ -
+ Columns are suddenly selected in other
+ alignments and views when revealing hidden columns
+
+ -
+ Hide columns not mirrored in complement
+ view in a cDNA/Protein splitframe
+
+ -
+ Cannot save/restore representative
+ sequence from project when only one sequence is
+ represented
+
+ -
+ Disabled 'Best Uniprot Coverage' option
+ in Structure Chooser
+
+ -
+ Modifying 'Ignore Gaps' on consensus or
+ structure consensus didn't refresh annotation panel
+
+ -
+ View mapping in structure view shows
+ mappings between sequence and all chains in a PDB file
+
+ -
+ PDB and Uniprot FTS
+ dialogs format columns correctly, don't display array
+ data, sort columns according to type
+
+ -
+ Export complete shown after destination
+ file chooser is cancelled during an image export
+
+ -
+ Error when querying PDB Service with
+ sequence name containing special characters
+
+ -
+ Manual PDB structure querying should be
+ case insensitive
+
+ -
+ Large tooltips with broken HTML
+ formatting don't wrap
+
+ -
+ Figures exported from wrapped view are
+ truncated so L looks like I in consensus annotation
+
+ -
+ Export features should only export the
+ currently displayed features for the current selection or
+ view
+
+ -
+ Enable 'Get Cross-References' in menu
+ after fetching cross-references, and restoring from project
+
+ -
+ Mouseover of a copy of a sequence is not
+ followed in the structure viewer
+
+ -
+ Titles for individual alignments in
+ splitframe not restored from project
+
+ -
+ missing autocalculated annotation at
+ trailing end of protein alignment in transcript/product
+ splitview when pad-gaps not enabled by default
+
+ -
+ amino acid physicochemical conservation
+ is case dependent
+
+ -
+ RSS reader doesn't stay hidden after last
+ article has been read (reopened issue due to
+ internationalisation problems)
+
+ -
+ Only offer PDB structures in structure
+ viewer based on sequence name, PDB and UniProt
+ cross-references
+
+
+ -
+ No progress bar shown during export of
+ alignment as HTML
+
+ -
+ Structures not always superimposed after
+ multiple structures are shown for one or more sequences.
+
+ -
+ Reference sequence characters should not
+ be replaced with '.' when 'Show unconserved' format option
+ is enabled.
+
+ -
+ Cannot specify chain code when entering
+ specific PDB id for sequence
+
+ -
+ File->Export->.. as doesn't work when
+ 'Export hidden sequences' is enabled, but 'export hidden
+ columns' is disabled.
+
+ -
+ Best Quality option in structure chooser
+ selects lowest rather than highest resolution structures
+ for each sequence
+
+ -
+ Incorrect start and end reported for PDB
+ to sequence mapping in 'View Mappings' report
+
+
Applet
-
+ -
+ Incorrect columns are selected when
+ hidden columns present before start of sequence
+
+ -
+ Missing dependencies on applet pages
+ (JSON jars)
+
+ -
+ Overview pixel size changes when
+ sequences are hidden in applet
+
+ -
+ Updated instructions for applet
+ deployment on examples pages.
+
|
@@ -138,7 +609,7 @@
Updated Spanish translations of localized text for
2.9
Application
-
+
- Signed OSX InstallAnywhere installer
- Support for per-sequence based annotations in BioJSON
@@ -743,7 +1214,7 @@
Certum to the Jalview
open source project).
- - Jalview SRS links replaced by Uniprot and EBI-search
+
- Jalview SRS links replaced by UniProt and EBI-search
- Output in Stockholm format
- Allow import of data from gzipped files
@@ -1098,8 +1569,8 @@
current built in colourscheme is saved as new scheme
- AlignFrame->Save in application pops up save
dialog for valid filename/format
- - Cannot view associated structure for Uniprot sequence
- - PDB file association breaks for Uniprot sequence
+
- Cannot view associated structure for UniProt sequence
+ - PDB file association breaks for UniProt sequence
P37173
- Associate PDB from file dialog does not tell you
which sequence is to be associated with the file
@@ -1374,6 +1845,10 @@
- URL links generated from description line for
regular-expression based URL links (applet and application)
+
+
+
+
- Non-positional feature URL links are shown in link
menu
@@ -1417,7 +1892,8 @@
between different screens.
- New preference items for sequence ID tooltip and
consensus annotation
- - Client to submit sequences and IDs to Envision2 Workflows
+ - Client to submit sequences and IDs to Envision2
+ Workflows
- Vamsas Capabilities
- Improved VAMSAS synchronization (Jalview archive
@@ -1674,7 +2150,7 @@
- Save works when Jalview project is default format
- Save as dialog opened if current alignment format is
not a valid output format
- - Uniprot canonical names introduced for both das and
+
- UniProt canonical names introduced for both das and
vamsas
- Histidine should be midblue (not pink!) in Zappo
- error messages passed up and output when data read
@@ -1703,7 +2179,7 @@
due to null pointer exceptions
- Secondary structure lines are drawn starting from
first column of alignment
- - Uniprot XML import updated for new schema release in
+
- UniProt XML import updated for new schema release in
July 2008
- Sequence feature to sequence ID match for Features
file is case-insensitive
@@ -1826,6 +2302,10 @@
- PCA and PDB Viewers zoom via mouse roller
- User-defined sub-tree colours and sub-tree selection
+
+
+
+
- 'New Window' button on the 'Output to Text box'
@@ -1841,18 +2321,26 @@
of alignment)
- Slowed DAS Feature Fetching for increased robustness.
+
+
+
+
- Made angle brackets in ASCII feature descriptions
display correctly
- Re-instated Zoom function for PCA
- Sequence descriptions conserved in web service
analysis results
-
- Uniprot ID discoverer uses any word separated by
+
- UniProt ID discoverer uses any word separated by
∣
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
+
+
+
+