X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=ef55b8a96525fac4fc754125da3f2abd0455d394;hb=9e372eb592af4849237e3387a7f6becb33034c1b;hp=f35494d30d43c3f90304a6a557c6342beefdd72f;hpb=71a996fbcf51882725dd0e22a8fd986e1c5cd97a;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index f35494d..ef55b8a 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -21,6 +21,29 @@ --> Release History +

@@ -39,100 +62,1468 @@ -

- Issues Resolved +
+ Issues Resolved +
+ + + + +
+ 2.10.4
27/02/2018 +
+ +
+ + +
+ +
+ +
+ + + + +
+ 2.10.3b1
24/1/2018 +
+ +
+
+
+ Desktop
+ + + + +
+ 2.10.3
17/11/2017 +
+ +
+ + + Scripting + + Testing and Deployment + +
+
+ General + + Desktop + + Applet
+ + BioJSON
+ + New Known Issues + + Known Java 9 Issues + +
+ + + +
+ 2.10.2b2
+ 2/10/2017 +
+ +
+ New features in Jalview Desktop + +
+
+
+ + + +
+ 2.10.2b1
+ 7/9/2017 +
+ +
+ + +
+
+ + +
+ + + +
+ 2.10.2
17/8/2017 +
+ +
+ Calculations + + Rendering + + Overview + + + Data import/export + + User Interface + + 3D Structure + + Web Services + + + Scripting + + Example files + + Documentation + + Test Suite + +
+
+ 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 + + Application + +
+ +
+ General + + Application + +
+ +
+ 2.10.0b1
+ 25/10/2016 +
+ + Application + + +
+ General + + Application + + Build and deployment + + New Known Issues + +
+ +
- 2.10.0
04/10/2016 + 2.10.0
06/10/2016
General Application + +
+ General + Applet - - -
- General -
    -
  • reinstate CTRL-click for opening pop-up menu on OSX
    • -
  • Export features in Jalview format (again) includes graduated colourschemes
    • -
  • More responsive when working with big alignments and lots of hidden columns
    • -
  • Hidden column markers not always rendered at right of alignment window
    • -
  • Tidied up links in help file table of contents
    • -
  • Feature based tree calculation not shown for DNA alignments
    • -
  • Hidden columns ignored during feature based tree calculation
    • -
  • Alignment view stops updating when show unconserved enabled for group on alignment
    • -
  • Cannot insert gaps into sequence when set as reference
    • -
  • Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation
    • -
  • Incorrect column numbers in ruler when hidden columns present
    • -
  • Colour by RNA Helices not enabled when user created annotation added to alignment
    • -
  • RNA Structure consensus only computed for '()' base pair annotation
    • -
  • Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus
    • -
  • Extend selection with columns containing feature not working
    • -
  • Pfam format writer puts extra space at beginning of sequence
    • -
  • Incomplete sequence extracted from pdb entry 3a6s
    • -
  • Cannot create groups on an alignment from from a tree when t-coffee scores are shown
    • -
  • Cannot import and view PDB structures with chains containing negative resnums (4q4h)
    • -
  • ArithmeticExceptions raised when parsing some structures
    • -
  • 'Empty' alignment blocks added to Clustal, PIR and PileUp output
    • -
  • Reordering sequence features that are not visible causes alignment window to repaint
  • Threshold sliders don't work in graduated colour and colour by annotation row for e-value @@ -147,95 +1538,203 @@ columns
  • - FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar) + FER1_ARATH and FER2_ARATH mislabelled in + example file (uniref50.fa, feredoxin.fa, unaligned.fa, + exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
  • - Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled + Null pointer exceptions and redraw + problems when reference sequence defined and 'show + non-conserved' enabled
  • - + Quality and Conservation are now shown on + load even when Consensus calculation is disabled
  • - -
    • -
  • - + Remove right on penultimate column of + alignment does nothing
Application
    -
    • -
  • Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
    • -
  • URLs and links can imported by drag'n'drop on OSX webstart
    • -
  • InstallAnywhere distribution fails when launching Chimera
    • -
  • Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
    • -
  • Cannot save project when view has a reference sequence defined
    • -
  • Columns are suddenly selected in other alignments and views when revealing hidden columns
    • -
  • Hide columns not mirrored in complement view in a cDNA/Protein splitframe
    • -
  • Cannot save/restore representative sequence from project when only one sequence is represented
    • -
  • Disabled 'Best Uniprot Coverage' option in Structure Chooser
    • -
  • Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
    • -
  • View mapping in structure view shows mappings between sequence and all chains in a PDB file
    • -
  • PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type
    • -
  • Export complete shown after destination file chooser is cancelled during an image export
    • -
  • Error when querying PDB Service with sequence name containing special characters
    • -
  • Manual PDB structure querying should be case insensitive
    • -
  • Large tooltips with broken HTML formatting don't wrap
    • -
  • Figures exported from wrapped view are truncated so L looks like I in consensus annotation
    • -
  • Export features should only export the currently displayed features for the current selection or view
    • -
  • Enable 'Get Cross-References' in menu after fetching cross-references
    • -
  • Mouseover of a copy of a sequence is not followed in the structure viewer
    • -
  • Titles for individual alignments in splitframe not restored from project
  • - missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default + 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
  • - amino acid physicochemical conservation is case dependent + Error thrown when exporting a view with + hidden sequences as flat-file alignment
  • - RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems) + InstallAnywhere distribution fails when + launching Chimera
    • -
  • 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 + Jalview very slow to launch via webstart + (also hotfix for 2.9.0b2)
  • - Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records. + Cannot save project when view has a + reference sequence defined
  • - Structures not always superimposed after multiple structures are shown for one or more sequences. + Columns are suddenly selected in other + alignments and views when revealing hidden columns
  • - Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled. + Hide columns not mirrored in complement + view in a cDNA/Protein splitframe
  • - Cannot specify chain code when entering specific PDB id for sequence + Cannot save/restore representative + sequence from project when only one sequence is + represented
  • - File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled. + Disabled 'Best Uniprot Coverage' option + in Structure Chooser
    • -
  • 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 + 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 + 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. +
  • + Updated instructions for applet + deployment on examples pages.
@@ -277,13 +1776,19 @@
  • Updated Spanish translations of localized text for 2.9
    • Application - Deployment and Documentation + General + --> Deployment and Documentation