Release History

General

+
• Improved memory usage: sparse arrays used for all consensus calculations
+
• Jmol updated to version 14.6.4 (released 3rd Oct 2016)
Updated Jalview's Certum code signing certificate +
• Updated Jalview's Certum code signing certificate for 2016-2017

Application

+
• Sequence ID tool tip presents abridged set of database cross-references, sorted alphabetically
+
• New replacement token for creating URLs just from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.
+
• Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session
+
• Jalview's Chimera control window closes if the Chimera it is connected to is shut down
+
• New keystroke (B) and Select highlighted columns menu item to mark columns containing highlighted regions (e.g. from structure selections or results of a Find operation)
+
• Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer @@ -102,35 +118,35 @@
General
- +
- • Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2)
- +
- • Threonine incorrectly reported as not hydrophobic
- +
- • Updates to documentation pages (above PID threshold, amino acid properties)
- +
- • Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report
- +
- • Identical features with non-numeric scores could be added multiple times to a sequence
- +
- • Disulphide bond features shown as two highlighted residues rather than a range in linked structure views, and treated correctly when selecting and computing trees from features
- +
- • Custom URL links for database cross-references are matched to database name regardless of case @@ -139,59 +155,59 @@
Application
- +
- • Custom URL links for specific database names without regular expressions also offer links from Sequence ID
- +
- • Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration
- +
- • CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan
- +
- • Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment
- +
- • Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file
- +
- • Certain structures do not get mapped to the structure view when displayed with Chimera
- +
- • No chains shown in the Chimera view panel's View->Show Chains submenu
- +
- • Export as HTML with embedded SVG doesn't work for wrapped alignment views
- +
- • Rename UI components for running JPred predictions from 'JNet' to 'JPred'
- +
- • Export as PNG or SVG is corrupted when annotation panel vertical scroll is not at first annotation row
- +
- • Attempting to view structure for Hen lysozyme results in a PDB Client error dialog box
@@ -204,51 +220,51 @@ Application
- 3D Structure chooser opens with 'Cached structures' +
- • 3D Structure chooser opens with 'Cached structures' view if structures already loaded
- Progress bar reports models as they are loaded to +
- • Progress bar reports models as they are loaded to structure views
General
- Colour by conservation always enabled and no tick +
- • 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 +
- • FER1_ARATH and FER2_ARATH labels were switched in example sequences/projects/trees
Application
- Jalview projects with views of local PDB structure +
- • Jalview projects with views of local PDB structure files saved on Windows cannot be opened on OSX
- Multiple structure views can be opened and +
- • 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 +
- • Cannot import or associated local PDB files without a PDB ID HEADER line
- RMSD is not output in Jmol console when +
- • RMSD is not output in Jmol console when superposition is performed
- Drag and drop of URL from Browser fails for Linux +
- • 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 +
- • 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 +
- • Exceptions are not raised in console when a new view is created on the alignment
- OSX right-click fixed for group selections: +
- • 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 +
- • URL link checker now copes with multi-line anchor tags
New Known Issues
- Drag and drop from URL links in browsers do not +
- • Drag and drop from URL links in browsers do not work on Windows
@@ -262,40 +278,40 @@ General
- +
- • 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 @@ -303,132 +319,132 @@
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
- +
- • 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.
@@ -436,278 +452,278 @@
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 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
- +
- • Remove right on penultimate column of alignment does nothing
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
- +
- • 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
- +
- • Unable to read old Jalview projects that contain non-XML data added after Jalvew wrote project.
- Newly created annotation row reorders +
- • Newly created annotation row reorders after clicking on it to create new annotation for a column.
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.
General
- Linked visualisation and analysis of DNA and Protein +
- • Linked visualisation and analysis of DNA and Protein alignments:
  - Translated cDNA alignments shown as split protein +
  - • Translated cDNA alignments shown as split protein and DNA alignment views
  - Codon consensus annotation for linked protein and +
  - • Codon consensus annotation for linked protein and cDNA alignment views
  - Link cDNA or Protein product sequences by loading +
  - • Link cDNA or Protein product sequences by loading them onto Protein or cDNA alignments
  - Reconstruct linked cDNA alignment from aligned +
  - • Reconstruct linked cDNA alignment from aligned protein sequences
- Jmol integration updated to Jmol v14.2.14
- Import and export of Jalview alignment views as • Jmol integration updated to Jmol v14.2.14
- • Import and export of Jalview alignment views as BioJSON
- New alignment annotation file statements for +
- • New alignment annotation file statements for reference sequences and marking hidden columns
- Reference sequence based alignment shading to +
- • Reference sequence based alignment shading to highlight variation
- Select or hide columns according to alignment +
- • Select or hide columns according to alignment annotation
- Find option for locating sequences by description
- Conserved physicochemical properties shown in amino +
- • Find option for locating sequences by description
- • Conserved physicochemical properties shown in amino acid conservation row
- Alignments can be sorted by number of RNA helices
- • Alignments can be sorted by number of RNA helices
Application
- New cDNA/Protein analysis capabilities +
- • New cDNA/Protein analysis capabilities
  - Get Cross-References should open a Split Frame +
  - • Get Cross-References should open a Split Frame view with cDNA/Protein
  - Detect when nucleotide sequences and protein +
  - • Detect when nucleotide sequences and protein sequences are placed in the same alignment
  - Split cDNA/Protein views are saved in Jalview +
  - • Split cDNA/Protein views are saved in Jalview projects
- Use REST API to talk to Chimera
- Selected regions in Chimera are highlighted in linked +
- • Use REST API to talk to Chimera
- • Selected regions in Chimera are highlighted in linked Jalview windows
- VARNA RNA viewer updated to v3.93
- VARNA views are saved in Jalview Projects
- Pseudoknots displayed as Jalview RNA annotation can +
- • VARNA RNA viewer updated to v3.93
- • VARNA views are saved in Jalview Projects
- • Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA
- Make groups for selection uses marked columns as well +
- • Make groups for selection uses marked columns as well as the active selected region
- Calculate UPGMA and NJ trees using sequence feature +
- • Calculate UPGMA and NJ trees using sequence feature similarity
- New Export options +
- • New Export options
  - New Export Settings dialog to control hidden +
  - • New Export Settings dialog to control hidden region export in flat file generation
  - Export alignment views for display with the • Export alignment views for display with the BioJS MSAViewer
  - Export scrollable SVG in HTML page
  - Optional embedding of BioJSON data when exporting +
  - • Export scrollable SVG in HTML page
  - • Optional embedding of BioJSON data when exporting alignment figures to HTML
  - 3D structure retrieval and display +
  - • 3D structure retrieval and display
    - Free text and structured queries with the PDBe +
    - • Free text and structured queries with the PDBe Search API
    - PDBe Search API based discovery and selection of +
    - • PDBe Search API based discovery and selection of PDB structures for a sequence set
  - JPred4 employed for protein secondary structure +
  - • JPred4 employed for protein secondary structure predictions
  - Hide Insertions menu option to hide unaligned columns +
  - • Hide Insertions menu option to hide unaligned columns for one or a group of sequences
  - Automatically hide insertions in alignments imported +
  - • Automatically hide insertions in alignments imported from the JPred4 web server
  - (Nearly) Native 'Quaqua' dialogs for browsing file +
  - • (Nearly) Native 'Quaqua' dialogs for browsing file system on OSX
    LGPL libraries courtesy of http://www.randelshofer.ch/quaqua/
  - changed 'View nucleotide structure' submenu to 'View +
  - • changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'
  - change "View protein structure" menu option to "3D +
  - • change "View protein structure" menu option to "3D Structure ..."
  Applet
  - New layout for applet example pages
  - New parameters to enable SplitFrame view +
  - • New layout for applet example pages
  - • New parameters to enable SplitFrame view (file2,enableSplitFrame, scaleProteinAsCdna)
  - New example demonstrating linked viewing of cDNA and +
  - • New example demonstrating linked viewing of cDNA and Protein alignments
  Development and deployment
  - Java 1.7 minimum requirement for Jalview 2.9
  - Include installation type and git revision in build +
  - • Java 1.7 minimum requirement for Jalview 2.9
  - • Include installation type and git revision in build properties and console log output
  - Jalview Github organisation, and new github site for +
  - • Jalview Github organisation, and new github site for storing BioJsMSA Templates
  - Jalview's unit tests now managed with TestNG
  - • Jalview's unit tests now managed with TestNG
  Application
  - Escape should close any open find dialogs
  - Typo in select-by-features status report
  - Consensus RNA secondary secondary structure +
  - • Escape should close any open find dialogs
  - • Typo in select-by-features status report
  - • Consensus RNA secondary secondary structure predictions are not highlighted in amber
  - Missing gap character in v2.7 example file means +
  - • Missing gap character in v2.7 example file means alignment appears unaligned when pad-gaps is not enabled
  - First switch to RNA Helices colouring doesn't colour +
  - • First switch to RNA Helices colouring doesn't colour associated structure views
  - ID width preference option is greyed out when auto +
  - • ID width preference option is greyed out when auto width checkbox not enabled
  - Stopped a warning dialog from being shown when +
  - • Stopped a warning dialog from being shown when creating user defined colours
  - 'View Mapping' in structure viewer shows sequence +
  - • 'View Mapping' in structure viewer shows sequence mappings for just that viewer's sequences
  - Workaround for superposing PDB files containing +
  - • Workaround for superposing PDB files containing multiple models in Chimera
  - Report sequence position in status bar when hovering +
  - • Report sequence position in status bar when hovering over Jmol structure
  - Cannot output gaps as '.' symbols with Selection -> +
  - • Cannot output gaps as '.' symbols with Selection -> output to text box
  - Flat file exports of alignments with hidden columns +
  - • Flat file exports of alignments with hidden columns have incorrect sequence start/end
  - 'Aligning' a second chain to a Chimera structure from +
  - • 'Aligning' a second chain to a Chimera structure from Jalview fails
  - Colour schemes applied to structure viewers don't +
  - • Colour schemes applied to structure viewers don't work for nucleotide
  - Loading/cut'n'pasting an empty or invalid file leads +
  - • Loading/cut'n'pasting an empty or invalid file leads to a grey/invisible alignment window
  - Exported Jpred annotation from a sequence region +
  - • Exported Jpred annotation from a sequence region imports to different position
  - Space at beginning of sequence feature tooltips shown +
  - • Space at beginning of sequence feature tooltips shown on some platforms
  - Chimera viewer 'View | Show Chain' menu is not +
  - • Chimera viewer 'View | Show Chain' menu is not populated
  - 'New View' fails with a Null Pointer Exception in +
  - • 'New View' fails with a Null Pointer Exception in console if Chimera has been opened
  - Mouseover to Chimera not working
  - Miscellaneous ENA XML feature qualifiers not +
  - • Mouseover to Chimera not working
  - • Miscellaneous ENA XML feature qualifiers not retrieved
  - NPE in annotation renderer after 'Extract Scores'
  - If two structures in one Chimera window, mouseover of +
  - • NPE in annotation renderer after 'Extract Scores'
  - • If two structures in one Chimera window, mouseover of either sequence shows on first structure
  - 'Show annotations' options should not make +
  - • 'Show annotations' options should not make non-positional annotations visible
  - Subsequence secondary structure annotation not shown +
  - • Subsequence secondary structure annotation not shown in right place after 'view flanking regions'
  - File Save As type unset when current file format is +
  - • File Save As type unset when current file format is unknown
  - Save as '.jar' option removed for saving Jalview +
  - • Save as '.jar' option removed for saving Jalview projects
  - Colour by Sequence colouring in Chimera more +
  - • Colour by Sequence colouring in Chimera more responsive
  - Cannot 'add reference annotation' for a sequence in +
  - • Cannot 'add reference annotation' for a sequence in several views on same alignment
  - Cannot show linked products for EMBL / ENA records
  - Jalview's tooltip wraps long texts containing no +
  - • Cannot show linked products for EMBL / ENA records
  - • Jalview's tooltip wraps long texts containing no spaces
  Applet
  - Jmol to JalviewLite mouseover/link not working
  - JalviewLite can't import sequences with ID +
  - • Jmol to JalviewLite mouseover/link not working
  - • JalviewLite can't import sequences with ID descriptions containing angle brackets
  General
  - Cannot export and reimport RNA secondary structure +
  - • Cannot export and reimport RNA secondary structure via jalview annotation file
  - Random helix colour palette for colour by annotation +
  - • Random helix colour palette for colour by annotation with RNA secondary structure
  - Mouseover to cDNA from STOP residue in protein +
  - • Mouseover to cDNA from STOP residue in protein translation doesn't work.
  - hints when using the select by annotation dialog box
  - Jmol alignment incorrect if PDB file has alternate CA +
  - • hints when using the select by annotation dialog box
  - • Jmol alignment incorrect if PDB file has alternate CA positions
  - FontChooser message dialog appears to hang after +
  - • FontChooser message dialog appears to hang after choosing 1pt font
  - Peptide secondary structure incorrectly imported from +
  - • Peptide secondary structure incorrectly imported from annotation file when annotation display text includes 'e' or 'h'
  - Cannot set colour of new feature type whilst creating +
  - • Cannot set colour of new feature type whilst creating new feature
  - cDNA translation alignment should not be sequence +
  - • cDNA translation alignment should not be sequence order dependent
  - 'Show unconserved' doesn't work for lower case +
  - • 'Show unconserved' doesn't work for lower case sequences
  - Nucleotide ambiguity codes involving R not recognised
  - • Nucleotide ambiguity codes involving R not recognised
  Deployment and Documentation
  - Applet example pages appear different to the rest of +
  - • Applet example pages appear different to the rest of www.jalview.org
  Application Known issues
  - Incomplete sequence extracted from PDB entry 3a6s
  - Misleading message appears after trying to delete +
  - • Incomplete sequence extracted from PDB entry 3a6s
  - • Misleading message appears after trying to delete solid column.
  - Jalview icon not shown in dock after InstallAnywhere +
  - • Jalview icon not shown in dock after InstallAnywhere version launches
  - Fetching EMBL reference for an RNA sequence results +
  - • Fetching EMBL reference for an RNA sequence results fails with a sequence mismatch
  - Corrupted or unreadable alignment display when +
  - • Corrupted or unreadable alignment display when scrolling alignment to right
  - ArrayIndexOutOfBoundsException thrown when remove +
  - • ArrayIndexOutOfBoundsException thrown when remove empty columns called on alignment with ragged gapped ends
  - auto calculated alignment annotation rows do not get +
  - • auto calculated alignment annotation rows do not get placed above or below non-autocalculated rows
  - Jalview dekstop becomes sluggish at full screen in +
  - • Jalview dekstop becomes sluggish at full screen in ultra-high resolution
  - Cannot disable consensus calculation independently of +
  - • Cannot disable consensus calculation independently of quality and conservation
  - Mouseover highlighting between cDNA and protein can +
  - • Mouseover highlighting between cDNA and protein can become sluggish with more than one splitframe shown
  Applet Known Issues
  - Core PDB parsing code requires Jmol
  - Sequence canvas panel goes white when alignment +
  - • Core PDB parsing code requires Jmol
  - • Sequence canvas panel goes white when alignment window is being resized
  @@ -1071,98 +1087,98 @@