X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=b58cb31ab448eecead8fdb9f141e490fb3aae856;hb=4992ecae64d0c987c217e8c584161706188f9d52;hp=bf8dc304888f15cb9ec8f54f4e5d1d4d4f9faaa4;hpb=ecdffdf0f1f8aad4f0f5433051a8d82019f9e234;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index bf8dc30..b58cb31 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -51,40 +51,332 @@ li:before {

- + + + + + - - - - + + - + +
  • + 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. +
    • + + +
    -
    - Release -
    +     		ReleaseNew FeaturesIssues Resolved
    + 2.11
    + 14/05/2019 (final due date !)         		-
    - New Features -
    +     		+
      +
    • + Optional automatic backups when saving + Jalview project or alignment files
      • +
    • + Principal Components Analysis and + Viewer state is saved in Jalview Project
      The 'Change + parameters' option has also been removed from the PCA viewer
      • +
    • + New 'Colour by Sequence ID' (subgroup) option
      • +
    • + Alternative genetic code tables supported for + 'Translate as cDNA'
      • +
    • + Finder panel remembers last position in each view
      • +
    • + More efficient creation of selections and + multiple groups when working with large alignments
      • +
    • + Speedier import of annotation rows when + parsing stockholm files
      • +
    • + Update of Ensembl Rest Client to API v10.0
      • +
    • + Sequence features can be filtered and + shaded according to any associated attributes (e.g. variant + attributes from VCF file, or key-value pairs imported from + column 9 of GFF file)
      • +
    • + Show synonymous codon variants on peptide sequences
      • +
    • + Popup report of a selected sequence feature's details
      • +
    • + More efficient sequence feature render + algorithm (Z-sort/transparency and filter aware)
      • +
    • + Alignment Overview now by default shows + only visible region of alignment (this can be changed in + user preferences)
      • +
    • + File Chooser stays open after Cancel overwrite
      • +
    • + Better popup menu behaviour when + all sequences are hidden
      • +
    • + Status bar shows bounds when dragging a selection + region, and gap count when inserting or deleting gaps
      • +
    • + Status bar updates over sequence and annotation labels
      • +
    • + Show annotation tooltips and popup menus in wrapped mode
      • +
    • + Can select columns by dragging left/right in annotations
      • +
    • + Improved tooltips in Feature Settings dialog
      • +
    • + Help button on Uniprot and PDB search panels
      • +
    • + Cursor changes over draggable box in Overview panel
      • +
    • + Overview panel default changed to not show hidden regions
      • +
    • + Consistent ordering of links in sequence id popup menu
      • +
    • + Sequence Details report opens positioned to top of report
      • +
    • + Scale panel popup menu allows Hide selected columns adjacent + to a hidden column marker
      • +
    • + Can use shift + arrow keys to rotate PCA image incrementally
      • +
    • + PCA depth queuing with graduated colours
      • +
    + Deprecations +
      +
    • + DAS sequence retrieval and annotation + capabilities removed from the Jalview Desktop +
      • +
    + Release Processes +
      +
    • + Atlassian Bamboo continuous integration server for + unattended Test Suite execution
      • +
    • + Memory test suite to detect leaks in common + operations
      • +
    • + IntervalStoreJ (new updatable NCList + implementation) used for Sequence Feature collections
      • +
    • + Castor library for XML marshalling and + unmarshalling has been replaced by JAXB for Jalview projects + and XML based data retrieval clients
      • +
    		-
    - Issues Resolved -
    +     		+
      +
    • + Timeouts when retrieving data from Ensembl
      • +
    • + Warning of 'Duplicate entry' when saving + Jalview project involving multiple views
      • +
    • + Overview for complementary view in a linked + CDS/Protein alignment is not updated when Hide Columns by + Annotation dialog hides columns
      • +
    • + Selection highlighting in the complement of + a CDS/Protein alignment stops working after making a + selection in one view, then making another selection in the + other view
      • +
    • + Annotations tooltip changes beyond visible columns
      • +
    • + Table Columns could be re-ordered in + Feature Settings and Jalview Preferences panels
      • +
    • + Jalview hangs when closing windows + or the overview updates with large alignments
      • +
    • + Tree and PCA calculation fails for selected + region if columns were selected by dragging right-to-left + and the mouse moved to the left of the first column
      • +
    • + Error message for trying to load in invalid + URLs doesn't tell users the invalid URL
      • +
    • + Nonpositional features lose feature group + on export as Jalview features file
      • +
    • + Blank extra columns drawn or + printed when columns are hidden
      • +
    • + Regular expression error for '(' in Select Columns by Annotation description
      • +
    • + Scroll doesn't stop on mouse up after + dragging out of Scale or Annotation Panel
      • +
    • + Column selection incorrect after scrolling out of scale panel
      • +
    • + Left/right drag in annotation can scroll alignment down
      • +
    • + Error if mouse moved before clicking Reveal in scale panel
      • +
    • + Column display is out by one after Page Down, Page Up in wrapped mode
      • +
    • + Finder doesn't skip hidden regions
      • +
    • + Finder searches in minimised alignments
      • +
    • + 'Apply Colour to All Groups' not always selected on + opening an alignment
      • +
    • + 'Colour by Annotation' not marked selected in Colour menu
      • +
    • + Per-group Clustal colour scheme changes when + different groups in the alignment are selected
      • +
    • + Internationalised colour scheme names not shown correctly in menu
      • +
    • + Colour by Annotation can go black at min/max threshold limit
      • +
    • + Value input for graduated feature colour threshold gets 'unrounded'
      • +
    • + PCA image export doesn't respect background colour
      • +
    • + PCA points don't dim when rotated about y axis
      • +
    • + PCA Print dialog continues after Cancel
      • +
    • + Cancel in Tree Font dialog resets alignment, not Tree font
      • +
    • + Associate Tree with All Views not restored from project file
      • +
    • + Scrolling of split frame is sluggish if Overview shown in complementary view
      • +
    • + stop_gained variants not shown correctly on peptide sequence
      • +
    • + Help page can be opened twice
      • +
    + Editing +
      +
    • + Start and End should be updated when + sequence data at beginning or end of alignment added/removed + via 'Edit' sequence
      • +
    • + Delete/Cut selection doesn't relocate + sequence features correctly when start of sequence is + removed (Known defect since 2.10)
      • +
    + New Known Defects +
      +
    • + Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
      • +
    • + Alignment panel height can be too small after 'New View'
      • +
    -
    - 2.10.5
    - 4/09/2018     -
    -
    - +
    +
    + 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
      -
    -
    -
    @@ -130,7 +422,8 @@ li:before { annotation added to view (Windows)
  • - Jalview Desktop is slow to start up when network connectivity is poor + Jalview Desktop is slow to start up when + network connectivity is poor
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