+ |
+
|
General
- - 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
-
+ -
+ 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
- - 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
+ -
+ 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.
+
+ |
+
+
+ General
+
-
- Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
+ reinstate CTRL-click for opening pop-up
+ menu on OSX
-
- Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10
+ Export features in Jalview format (again)
+ includes graduated colourschemes
-
- Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API
+ More responsive when
+ working with big alignments and lots of hidden columns
-
- Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)
+ Hidden column markers not always rendered
+ at right of alignment window
- - ENA CDS 'show cross references' for Uniprot sequences
-
-
+ 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
-
-
- Applet
- |
-
-
- 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
- - 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
@@ -151,96 +359,185 @@
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)
+ 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
-
- 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
- - Quality and Conservation are now shown on load even when Consensus calculation is disabled
+
+ Application
+
-
-
+ 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
-
- 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
- - 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
- - 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
+ Export complete shown after destination
+ file chooser is cancelled during an image export
-
- amino acid physicochemical conservation is case dependent
+ Error when querying PDB Service with
+ sequence name containing special characters
-
- RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
+ Manual PDB structure querying should be
+ case insensitive
- - 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
+ Large tooltips with broken HTML
+ formatting don't wrap
-
- Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
+ Figures exported from wrapped view are
+ truncated so L looks like I in consensus annotation
-
- Structures not always superimposed after multiple structures are shown for one or more sequences.
+ Export features should only export the
+ currently displayed features for the current selection or
+ view
-
- Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
+ Enable 'Get Cross-References' in menu
+ after fetching cross-references, and restoring from project
-
- Cannot specify chain code when entering specific PDB id for sequence
+ Mouseover of a copy of a sequence is not
+ followed in the structure viewer
-
- File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
+ Titles for individual alignments in
+ splitframe not restored from project
- - 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
+ 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
+ Incorrect columns are selected when
+ hidden columns present before start of sequence
- - Updated instructions for applet deployment on examples pages.
+
-
+ 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.
+
- Signed OSX InstallAnywhere installer
- Support for per-sequence based annotations in BioJSON
@@ -1518,6 +1815,10 @@
- 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
@@ -1561,7 +1862,8 @@
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
@@ -1970,6 +2272,10 @@
- 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'
@@ -1985,6 +2291,10 @@
of alignment)
- Slowed DAS Feature Fetching for increased robustness.
+
+
+
+
- Made angle brackets in ASCII feature descriptions
display correctly
@@ -1997,6 +2307,10 @@
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
+
+
+
+
|