Issues Resolved

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 after clicking on it to create new annotation for a column.
• Null Pointer Exception raised when pressing Add on an orphaned cut’n’paste window.

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.