X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=25fc04bd396a1db701d3b2de658acb538b6cfe85;hb=181cd6607ecd631aa5972582ff1d99c5bea75b23;hp=aa589e9e7a2de0c06048ac0ef0b44c730146c4c5;hpb=d8bf5506216e7a0726a1fa5baa6b4d244f035741;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index aa589e9..3eaf234 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -25,53 +25,1350 @@ ul { /* remove bullets, narrower indent */ list-style-type: none; - margin:0; + margin: 0; padding-left: 10px; padding-bottom: 4px; } li { /* separate the items from eachother */ - margin-left: -3px; - padding-bottom: 3px; - padding-left: 6px; + margin-left: -3px; + padding-bottom: 3px; + padding-left: 6px; } + li:before { /* doesnt get processed in javahelp */ content: '\00b7 '; padding: 3px; margin-left: -14px; } + + + +

+ Release History +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ Release +
+ 		+
+ New Features +
+ 		+
+ Issues Resolved +
+
+
+ 2.11.0
+ 8/09/2018 +
+
+ +
    +
  • + +
    • +
+
+ +
    +
  • + DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop +
    • +
+
+
+ 2.10.5
10/09/2018 +
+
+ +
    +
  • + Default memory for Jalview webstart and + InstallAnywhere increased to 1G. +
    • +
  • + Hidden sequence markers and representative + sequence bolding included when exporting alignment as EPS, + SVG, PNG or HTML. Display is configured via the + Format menu, or for command-line use via a jalview + properties file. +
    • +
  • + Ensembl client updated to Version 7 REST + API and sequence data now imported as JSON. +
    • +
  • + Change in recommended way of starting + Jalview via a Java command line: add jars in lib directory + to CLASSPATH, rather than via the deprecated java.ext.dirs + property. +
    • +
+ Development +
    +
  • + Support added to execute test suite + instrumented with Open + Clover +
    • +
+
+ +
    +
  • + Poorly scaled bar in quality annotation + row shown in Feredoxin Structure alignment view of example + alignment. +
    • +
  • + Annotation obscures sequences if lots of + annotation displayed. +
    • +
  • + Group conservation/consensus not shown + for newly created group when 'Apply to all groups' + selected +
    • +
  • + Corrupted display when switching to + wrapped mode when sequence panel's vertical scrollbar is + visible. +
    • +
  • + Alignment is black in exported EPS file + when sequences are selected in exported view. +
    • +
  • + Groups with different coloured borders + aren't rendered with correct colour. +
    • +
  • + Jalview could hang when importing certain + types of knotted RNA secondary structure. +
    • +
  • + Sequence highlight and selection in + trimmed VARNA 2D structure is incorrect for sequences that + do not start at 1. +
    • +
  • + '.' inserted into RNA secondary structure + annotation when columns are inserted into an alignment, + and when exporting as Stockholm flatfile. +
    • +
  • + Jalview annotation rows containing upper + and lower-case 'E' and 'H' do not automatically get + treated as RNA secondary structure. +
    • +
  • + .jvp should be used as default extension + (not .jar) when saving a jalview project file. +
    • +
  • + Mac Users: closing a window correctly + transfers focus to previous window on OSX +
    • +
+ Java 10 Issues Resolved +
    +
  • + OSX - Can't save new files via the File + or export menus by typing in a name into the Save dialog + box. +
    • +
  • + Jalview now uses patched version + of the VAqua5 + 'look and feel' which has improved compatibility with the + latest version of OSX. +
    • +
+
+
+
+ 2.10.4b1
+ 7/06/2018 +
+
+ +
    +
  • + Use HGVS nomenclature for variant + annotation retrieved from Uniprot +
    • +
  • + Windows File Shortcuts can be dragged + onto the Jalview Desktop +
    • +
+
+ +
    +
  • + Cannot import features with multiple + variant elements (blocks import of some Uniprot records) +
    • +
  • + Clustal files with sequence positions in + right-hand column parsed correctly +
    • +
  • + Wrap view - export to SVG - IDs shown but + not alignment area in exported graphic +
    • +
  • + F2/Keyboard mode edits work when Overview + window has input focus +
    • +
  • + Annotation panel set too high when + annotation added to view (Windows) +
    • +
  • + Jalview Desktop is slow to start up when + network connectivity is poor +
    • +
  • + Drag URL from chrome, firefox, IE to + Jalview desktop on Windows doesn't open file
    Dragging + the currently open URL and links from a page viewed in + Firefox or Chrome on Windows is now fully supported. If + you are using Edge, only links in the page can be + dragged, and with Internet Explorer, only the currently + open URL in the browser can be dropped onto Jalview. +
    • +
+
+
+ 2.10.4
10/05/2018 +
+
+ +
    +
  • + New Structure Chooser control + for disabling automatic superposition of multiple + structures and open structures in existing views +
    • +
  • + Mouse cursor changes to indicate Sequence + ID and annotation area margins can be click-dragged to + adjust them. +
    • +
  • + Jalview uses HTTPS for Uniprot, Xfam and + Ensembl services +
    • +
  • + Improved performance for large alignments + and lots of hidden columns +
    • +
  • + Improved performance when rendering lots + of features (particularly when transparency is disabled) +
    • +
+
+
+
    +
  • + Structure and Overview aren't updated + when Colour By Annotation threshold slider is adjusted +
    • +
  • + Slow redraw when Overview panel shown + overlapping alignment panel +
    • +
  • + Overview doesn't show end of unpadded + sequence as gaps +
    • +
  • + Cross-reference handling + improved: CDS not handled correctly if transcript has no + UTR +
    • +
  • + Secondary structure and temperature + factor annotation not added to sequence when local PDB + file associated with it by drag'n'drop or structure + chooser +
    • +
  • + Answering 'No' to PDB Autoassociate + dialog doesn't import PDB files dropped on an alignment +
    • +
  • + Linked scrolling via protein horizontal + scroll bar doesn't work for some CDS/Protein views +
    • +
  • + Trackpad scrolling is broken on OSX on + Java 1.8u153 onwards and Java 1.9u4+. +
    • +
  • + Tooltip shouldn't be displayed for empty + columns in annotation row +
    • +
  • + Preferences panel's ID Width control is not + honored in batch mode +
    • +
  • + Linked sequence highlighting doesn't work + for structures added to existing Jmol view +
    • +
  • + 'View Mappings' includes duplicate + entries after importing project with multiple views +
    • +
  • + Viewing or annotating Uniprot + protein sequences via SIFTS from associated PDB entries + with negative residue numbers or missing residues fails +
    • +
  • + Exception when shading sequence with negative + Temperature Factor values from annotated PDB files (e.g. + as generated by CONSURF) +
    • +
  • + Uniprot 'sequence variant' features + tooltip doesn't include a text description of mutation +
    • +
  • + Invert displayed features very slow when + structure and/or overview windows are also shown +
    • +
  • + Selecting columns from highlighted regions + very slow for alignments with large numbers of sequences +
    • +
  • + Copy Consensus fails for group consensus + with 'StringIndexOutOfBounds' +
    • +
  • + VAqua(4) provided as fallback Look and Feel for OSX + platforms running Java 10 +
    • +
  • + Adding a structure to existing structure + view appears to do nothing because the view is hidden behind the alignment view +
    • +
+ Applet +
    +
  • + Copy consensus sequence option in applet + should copy the group consensus when popup is opened on it +
    • +
+ Batch Mode +
    +
  • + Fixed ID width preference is not respected +
    • +
+ New Known Defects +
    +
  • + Exceptions occasionally raised when + editing a large alignment and overview is displayed +
    • +
  • + 'Overview updating' progress bar is shown + repeatedly after a series of edits even when the overview + is no longer reflecting updates +
    • +
  • + 'SIFTS Mapping Error' when viewing + structures for protein subsequence (if 'Trim Retrieved + Sequences' enabled) or Ensembl isoforms (Workaround in + 2.10.4 is to fail back to N&W mapping) +
    • +
+
+
+
+ 2.10.3b1
24/1/2018 +
+
+
  • Updated Certum Codesigning Certificate + (Valid till 30th November 2018)
+ Desktop
    +
      +
    • Only one structure is loaded when several sequences and structures are selected for viewing/superposing
      • +
    • Alignment doesn't appear to scroll vertically via trackpad and scrollwheel
      • +
    • Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment
      • +
    • Helix annotation has 'notches' when scrolled into view if columns are hidden
      • +
    • Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns
      • +
    • User preference for disabling inclusion of sequence limits when exporting as flat file has no effect
      • +
    • Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes
      • +
    +
+
+
+ 2.10.3
17/11/2017 +
+
+ +
    +
  • + Faster and more efficient management and + rendering of sequence features +
    • +
  • + More reliable Ensembl fetching with HTTP + 429 rate limit request hander +
    • +
  • + 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 +
    • +
  • + 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.
    • +
+ Testing and Deployment +
    +
  • + 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 +
    • +
  • + 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 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 +
    • +
+ Applet
+
    +
  • + Concurrent modification exception when + closing alignment panel +
    • +
+ BioJSON
+
    +
  • + BioJSON export does not preserve + non-positional features +
    • +
+ New Known Issues +
    +
  • + 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 +
    • +
+ Known Java 9 Issues +
    +
  • + Groovy Console very slow to open and is + not responsive when entering characters (Webstart, Java + 9.01, OSX 10.10) +
    • +
+
+
+ 2.10.2b2
+ 2/10/2017 +
+
+ New features in Jalview Desktop +
    +
  • + Uniprot Sequence Fetcher now uses web API at uniprot.org +
    • +
  • HTTPS used for all connections to ebi.ac.uk +
    • +
+
+
+
+ 2.10.2b1
+ 7/9/2017 +
+
+ +
    +
  • + Show gaps in overview window by colouring + in grey (sequences used to be coloured grey, and gaps were + white) +
    • +
  • + Overview tab in Jalview Desktop + Preferences +
    • +
  • + Overview updates immediately on increase + in size and progress bar shown as higher resolution + overview is recalculated +
    • + +
+
+ +
    +
  • + Overview window redraws every hidden + column region row by row +
    • +
  • + duplicate protein sequences shown after + retrieving Ensembl crossrefs for sequences from Uniprot +
    • +
  • + Overview window throws NPE if show boxes + format setting is unticked +
    • +
  • + Groups are coloured wrongly in overview + if group has show boxes format setting unticked +
    • +
  • + Redraw problems when + autoscrolling whilst dragging current selection group to + include sequences and columns not currently displayed +
    • +
  • + Not all chains are mapped when multimeric + assemblies are imported via CIF file +
    • +
  • + Gap colour in custom colourscheme is not + displayed when threshold or conservation colouring is also + enabled. +
    • +
  • + JABAWS 2.2 services report wrong JABAWS + server version +
    • +
  • + Jalview continues to scroll after + dragging a selected region off the visible region of the + alignment +
    • +
  • + Cannot apply annotation based + colourscheme to all groups in a view +
    • +
  • + IDs don't line up with sequences + initially after font size change using the Font chooser or + middle-mouse zoom +
    • +
+
+
+ 2.10.2
17/8/2017 +
+
+ Calculations +
    + +
  • + Occupancy annotation row shows number of + ungapped positions in each column of the alignment. +
    • +
  • + Tree/PCA calculation menu items merged to + a calculation dialog box +
    • +
  • + Revised implementation of PCA for speed + and memory efficiency (~30x faster) +
    • +
  • + Revised implementation of sequence + similarity scores as used by Tree, PCA, Shading Consensus + and other calculations +
    • +
  • + Score matrices are stored as resource + files within the Jalview codebase +
    • +
  • + Trees computed on Sequence Feature + Similarity may have different topology due to increased + precision +
    • +
+ Rendering +
    +
  • + More robust colours and shader + model for alignments and groups +
    • +
  • + Custom shading schemes created via groovy + scripts +
    • +
+ Overview +
    +
  • + Efficiency improvements for interacting + with alignment and overview windows +
    • +
  • + Scrolling of wrapped alignment views via + overview +
    • +
  • + Hidden columns and sequences can be + omitted in Overview +
    • +
  • + Click-drag in visible area allows fine + adjustment of visible position +
    • +
+ + Data import/export +
    +
  • + Posterior probability annotation from + Stockholm files imported as sequence associated annotation +
    • +
  • + More robust per-sequence positional + annotation input/output via stockholm flatfile +
    • +
  • + Sequence names don't include file + extension when importing structure files without embedded + names or PDB accessions +
    • +
  • + Drag and drop load of AAIndex and NCBI + format sequence substitution matrices +
    • +
+ User Interface +
    +
  • + Experimental Features Checkbox in + Desktop's Tools menu to hide or show untested features in + the application. +
    • +
  • + Linked scrolling of CDS/Protein views + via Overview or sequence motif search operations +
    • +
  • + Amend sequence features dialog box can be + opened by double clicking gaps within sequence feature + extent +
    • +
  • + Status bar message shown when not enough + aligned positions were available to create a 3D structure + superposition. +
    • +
+ 3D Structure +
    +
  • + Hidden regions in alignment views are not + coloured in linked structure views +
    • +
  • + Faster Chimera/Jalview communication by + file-based command exchange +
    • +
  • + Structure chooser automatically shows + Cached Structures rather than querying the PDBe if + structures are already available for sequences +
    • +
  • + Structures imported via URL are cached in + the Jalview project rather than downloaded again when the + project is reopened. +
    • +
  • + New entries in the Chimera menu + to transfer Chimera's structure attributes as Jalview + features, and vice-versa (Experimental + Feature) +
    • +
+ Web Services +
    +
  • + Updated JABAWS client to v2.2 +
    • +
  • + Filter non-standard amino acids and + nucleotides when submitting to AACon and other MSA + Analysis services +
    • +
  • + URLs for viewing database + cross-references provided by identifiers.org and the + EMBL-EBI's MIRIAM DB +
    • +
+ + Scripting +
    +
  • + FileFormatI interface for describing and + identifying file formats (instead of String constants) +
    • +
  • + FeatureCounter script refactored for + efficiency when counting all displayed features (not + backwards compatible with 2.10.1) +
    • +
+ Example files +
    +
  • + Graduated feature colour style example + included in the example feature file +
    • +
+ Documentation +
    +
  • + Release notes reformatted for readability + with the built-in Java help viewer +
    • +
  • + Find documentation updated with 'search + sequence description' option +
    • +
+ Test Suite +
    +
  • + External service integration tests for + Uniprot REST Free Text Search Client +
    • +
  • + Added PrivilegedAccessor to test suite +
    • +
  • + Prevent or clear modal dialogs raised + during tests +
    • +
+
+ Calculations + + User Interface +
    +
  • + Reopening Colour by annotation dialog + doesn't reselect a specific sequence's associated + annotation after it was used for colouring a view +
    • +
  • + Current selection lost if popup menu + opened on a region of alignment without groups +
    • +
  • + Popup menu not always shown for regions + of an alignment with overlapping groups +
    • +
  • + Finder double counts if both a sequence's + name and description match +
    • +
  • + Hiding column selection containing two + hidden regions results in incorrect hidden regions +
    • +
  • + 'Apply to all groups' setting when + changing colour does not apply Conservation slider value + to all groups +
    • +
  • + Percentage identity and conservation menu + items do not show a tick or allow shading to be disabled +
    • +
  • + Conservation shading or PID threshold + lost when base colourscheme changed if slider not visible +
    • +
  • + Sequence features shown in tooltip for + gaps before start of features +
    • +
  • + Graduated feature colour threshold not + restored to UI when feature colour is edited +
    • +
  • + Vertical scrollbar jumps one page-width at + a time when scrolling vertically in wrapped mode. +
    • +
  • + Structure and alignment overview update + as graduate feature colour settings are modified via the + dialog box +
    • +
  • + Overview window doesn't always update + when a group defined on the alignment is resized +
    • +
  • + Mouseovers on left/right scale region in + wrapped view result in positional status updates +
    • - - - -

    - Release History -

    - - - - - - - - + + - +
  • 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
      • +
    + +
    -
    - Release -
    -     		-
    - New Features -
    -     		-
    - Issues Resolved +
  • + Status bar doesn't show position for + ambiguous amino acid and nucleotide symbols +
    • +
  • + Copy consensus sequence failed if + alignment included gapped columns +
    • +
  • + Minimum size set for Jalview windows so + widgets don't permanently disappear +
    • +
  • + Cannot select or filter quantitative + annotation that are shown only as column labels (e.g. + T-Coffee column reliability scores) +
    • +
  • + Exception thrown if trying to create a + sequence feature on gaps only +
    • +
  • + Features created with 'New feature' + button from a Find inherit previously defined feature type + rather than the Find query string +
    • +
  • + incorrect title in output window when + exporting tree calculated in Jalview +
    • +
  • + Hiding sequences at bottom of alignment + and then revealing them reorders sequences on the + alignment +
    • +
  • + Group panel in sequence feature settings + doesn't update to reflect available set of groups after + interactively adding or modifying features +
    • +
  • + Sequence Database chooser unusable on + Linux +
    • +
  • + Hide insertions in PopUp->Selection menu + only excluded gaps in current sequence and ignored + selection. +
    • + + Rendering +
      +
    • + Overview window visible region moves + erratically when hidden rows or columns are present +
      • +
    • + Per-residue colourschemes applied via the + Structure Viewer's colour menu don't correspond to + sequence colouring +
      • +
    • + Protein specific colours only offered in + colour and group colour menu for protein alignments +
      • +
    • + Colour threshold slider doesn't update to + reflect currently selected view or group's shading + thresholds +
      • +
    • + Feature colour thresholds not respected + when rendered on overview and structures when opacity at + 100% +
      • +
    • + User defined gap colour not shown in + overview when features overlaid on alignment +
      • +
    + Data import/export +
      +
    • + Very large alignments take a long time to + load +
      • +
    • + Per-sequence RNA secondary structures + added after a sequence was imported are not written to + Stockholm File +
      • +
    • + WUSS notation for simple pseudoknots lost + when importing RNA secondary structure via Stockholm +
      • +
    • + Secondary structure arrows for [] and {} + not shown in correct direction for simple pseudoknots +
      • +
    • + Cannot configure feature colours + with lightGray or darkGray via features file (but can + specify lightgray) +
      • +
    • + Above PID colour threshold not recovered + when alignment view imported from project +
      • +
    • + No mappings generated between + structure and sequences extracted from structure files + imported via URL and viewed in Jmol +
      • +
    • + Structures loaded via URL are saved in + Jalview Projects rather than fetched via URL again when + the project is loaded and the structure viewed +
      • +
    + Web Services +
      +
    • + EnsemblGenomes example failing after + release of Ensembl v.88 +
      • +
    • + Proxy server address and port always + appear enabled in Preferences->Connections +
      • +
    • + DAS registry not found exceptions + removed from console output +
      • +
    • + Cannot retrieve protein products from + Ensembl by Peptide ID +
      • +
    • + Incorrect PDB-Uniprot mappings + created from SIFTs, and spurious 'Couldn't open structure + in Chimera' errors raised after April 2017 update (problem + due to 'null' string rather than empty string used for + residues with no corresponding PDB mapping). +
      • +
    + Application UI +
      +
    • + User Defined Colours not added to Colour + menu +
      • +
    • + Easier creation of colours for all 'Lower + case' residues (button in colourscheme editor debugged and + new documentation and tooltips added) +
      • +
    • + Text colour threshold's 'Cancel' button + doesn't restore group-specific text colour thresholds +
      • +
    • + Feature settings panel does not update as + new features are added to alignment +
      • +
    • + Cancel in feature settings reverts + changes to feature colours via the Amend features dialog +
      • +
    • + Null pointer exception when attempting to + edit graduated feature colour via amend features dialog + box +
      • +
    • + Structure viewer's View -> Colour By view + selection menu changes colours of alignment views +
      • +
    • + Spurious exceptions in console raised + from alignment calculation workers after alignment has + been closed +
      • +
    • + Typo in selection popup menu - Create + groups now 'Create Group' +
      • +
    • + CMD/CTRL and G or Shift G for + Create/Undefine group doesn't always work +
      • +
    • + Tree Viewer's Print Dialog doesn't get + shown again after pressing 'Cancel' +
      • +
    • + Trackpad horizontal scroll gesture + adjusts start position in wrap mode +
      • +
    • + Status bar doesn't show positions for + ambiguous amino acids +
      • +
    • + cDNA Consensus annotation not shown in + CDS/Protein view after CDS sequences added for aligned + proteins +
      • +
    • + User defined colourschemes called 'User + Defined' don't appear in Colours menu +
      • +
    + Applet +
      +
    • + Switching between Nucleotide and Protein + score models doesn't always result in an updated PCA plot +
      • +
    • + Features not rendered as transparent on + overview or linked structure view +
      • +
    • + Colour group by conservation doesn't + work (since 2.8) +
      • +
    • + Hitting Cancel after applying + user-defined colourscheme doesn't restore original + colourscheme +
      • +
    + Test Suite +
      +
    • + Unit test failure: + jalview.ws.jabaws.RNAStructExportImport setup fails +
      • +
    • + Unit test failure: + jalview.ws.sifts.SiftsClientTest due to compatibility + problems with deep array comparison equality asserts in + successive versions of TestNG +
      • +
    • + Relocated StructureChooserTest and + ParameterUtilsTest Unit tests to Network suite +
      • +
    + New Known Issues +
      +
    • + Protein/CDS view scrolling not always in + phase after a sequence motif find operation +
      • +
    • + Importing annotation file with rows + containing just upper and lower case letters are + interpreted as WUSS RNA secondary structure symbols +
      • +
    • + Cannot load and display Newick trees + reliably from eggnog Ortholog database +
      • +
    • + Status bar shows 'Marked x columns + containing features of type Highlight' when 'B' is pressed + to mark columns containing highlighted regions. +
      • +
    • + Dropping a PDB file onto a sequence + doesn't always add secondary structure annotation. +
      • +
    -
    - 2.10.1
    - 29/11/2016     + 2.10.1
    29/11/2016
    @@ -82,7 +1379,8 @@ li:before { for all consensus calculations
  • - Jmol updated to version 14.6.4 (released 3rd Oct 2016) + Jmol updated to version 14.6.4 (released + 3rd Oct 2016)
  • Updated Jalview's Certum code signing certificate for 2016-2017
    • @@ -110,9 +1408,9 @@ li:before {
  • 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) + 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 @@ -211,71 +1509,79 @@ li:before { Attempting to view structure for Hen lysozyme results in a PDB Client error dialog box
    • +
  • + Structure View's mapping report switched + ranges for PDB and sequence for SIFTS +
    • + + SIFTS 'Not_Observed' residues mapped to non-existant + coordindate data + -
    -
    - 2.10.0b1
    - 25/10/2016     -
    -     		Application + +
    + 2.10.0b1
    + 25/10/2016     +
    +     		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
      -
    • 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
      • -
    -
    -
    @@ -286,8 +1592,8 @@ li:before { General
    • - Updated Spanish translations. -
      • + Updated Spanish translations. +
    • Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and @@ -577,7 +1883,7 @@ li:before { load even when Consensus calculation is disabled
    • - Remove right on penultimate column of + Remove right on penultimate column of alignment does nothing
    @@ -665,7 +1971,8 @@ li:before {
  • Enable 'Get Cross-References' in menu - after fetching cross-references, and restoring from project + after fetching cross-references, and restoring from + project
  • Mouseover of a copy of a sequence is not @@ -730,10 +2037,15 @@ li:before { 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.
    • +
  • + Null Pointer Exception raised when + pressing Add on an orphaned cut'n'paste window. +
    • @@ -802,9 +2114,12 @@ li:before { Applet
    • Split frame example added to applet examples page
      • -
    Build and Deployment + Build and Deployment
      -
    • New ant target for running Jalview's test suite
      • +
    • + New ant target for running Jalview's test + suite +
    @@ -1192,10 +2507,10 @@ li:before { Deployment and Documentation +
      +
    General +
      +
    --> Deployment and Documentation
    • 2G and 1G options in launchApp have no effect on memory allocation
      • @@ -1403,8 +2718,7 @@ li:before { 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
    • Export/import group and sequence associated line @@ -2033,11 +3347,6 @@ li:before {
      • 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
        • @@ -2065,8 +3374,8 @@ li:before {
      • Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
        • - +
      • Group-associated consensus, sequence logos and conservation plots
      • Symbol distributions for each column can be exported @@ -2490,11 +3799,6 @@ li:before {
      • Cancel button for DAS Feature Fetching
      • 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'
      @@ -2509,11 +3813,6 @@ li:before {
    • Fixed Remove Empty Columns Bug (empty columns at end of alignment)
    • Slowed DAS Feature Fetching for increased robustness. - - - - -
    • Made angle brackets in ASCII feature descriptions display correctly @@ -2525,11 +3824,6 @@ li:before {
    • WsDbFetch query/result association resolved
    • Tree leaf to sequence mapping improved
    • Smooth fonts switch moved to FontChooser dialog box. - - - - -