X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=38a18ec2a9af1f8f869eff109d73ce857b56a583;hb=c4a72d18f6a7b2cf3de4a46b7a35cbfd0d76438f;hp=7d34557d2435413c19801b6f7d226d6183816871;hpb=6f936a369fb1cbf5dc2327d6e3f5bcfe5a953827;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 7d34557..38a18ec 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -21,6 +21,29 @@ --> Release History +

@@ -47,60 +70,933 @@

- 2.10.0b1
- 25/10/2016 + 2.10.3
+ 10/10/2017
- Application - - -
+
+ + + +
+ +
    +
  • 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 +
    • +
+ + + + +
+ 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 +
    • + +
  • + 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 +
+ +
General
    -
  • Colour by conservation always enabled and no tick - shown in menu when BLOSUM or PID shading applied
    • +
  • + 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 + for 2016-2017
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
    • +
  • + 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 +
- Build and deployment +
+ +
+ General
    -
  • URL link checker now copes with multi-line anchor - tags
    • +
  • + 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 +
    • +
- New Known Issues + Application
    -
  • Drag and drop from URL links in browsers do not - work on Windows
    • +
  • + 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 +
    • +
  • + 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 +
    +
  • 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
    • +
+
+ +
@@ -110,8 +1006,8 @@ General
  • - Updated Spanish translations. -
    • + Updated Spanish translations. +
  • Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and @@ -400,6 +1296,10 @@ Quality and Conservation are now shown on load even when Consensus calculation is disabled
    • +
  • + Remove right on penultimate column of + alignment does nothing +
Application
    @@ -485,7 +1385,8 @@
  • 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 @@ -546,6 +1447,15 @@ 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. +
@@ -614,6 +1524,12 @@ Applet
  • Split frame example added to applet examples page
    • +
Build and Deployment +
    +
  • + New ant target for running Jalview's test + suite +
@@ -1001,10 +1917,10 @@ Deployment and Documentation +
    +
General +
    +
--> Deployment and Documentation
  • 2G and 1G options in launchApp have no effect on memory allocation
    • @@ -1212,8 +2128,7 @@ 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
  • Export/import group and sequence associated line @@ -1842,11 +2757,6 @@
    • 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
      • @@ -1874,8 +2784,8 @@
    • 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 @@ -2299,11 +3209,6 @@
    • 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'
    @@ -2318,11 +3223,6 @@
  • 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 @@ -2334,11 +3234,6 @@
  • WsDbFetch query/result association resolved
  • Tree leaf to sequence mapping improved
  • Smooth fonts switch moved to FontChooser dialog box. - - - - -