X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=65ef80aa1ce965f846a29b5c3fdf2453f04158bc;hb=9155298ec531aa1af53e00509d29c235572373d8;hp=e6f23b2f3956175edf9019ae87ba83d5d806b1a3;hpb=a84a61e465c49e5e279ff78884004815dcd18367;p=jalview.git diff --git a/help/help/html/releases.html b/help/help/html/releases.html index e6f23b2..65ef80a 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -24,25 +24,25 @@ Release History @@ -59,27 +59,235 @@ li:before { 2.11.2.0
- 01/02/2022 + 3/03/2022 Uniprot and PDBe autosearch option is + disabled by default + +
  • + -nowebservicediscovery command line + argument to prevent automatic discovery of analysis + webservices on launch +
    • +
  • + Allow 'App' directories to be opened when + locating Chimera, ChimeraX or Pymol binaries via filechooser + opened by double clicking the Structure Preferences' path + textbox +
    • + + Jalview Native App JalviewJS + Development + --> +
  • + Improved JalviewJS/Jalview build + process, added support for system package provided eclipse + installs on linux +
    • +
  • Install4j 9.0.x used for installer packaging
    • +
  • Notarized MacOS installer for compatibility with Big + Sur and Monterey
    • +
  • + Uninstaller application for old + (InstallAnywhere based) Jalview installations removed from + the DMG +
    • +
  • + Improved use of installers for unattended + installation with a customizedId of "JALVIEW" in install4j's + Jalview Launcher +
    • +
  • + Improved compatibility of Jalview build + with Java 17 (next LTS target) +
    • + + JalviewJS + Development @@ -88,18 +296,20 @@ li:before { id="Jalview.2.11.1">2.11.1.7
    18/01/2022 - Security + + Security + Security - - + Improved built-in documentation and command line help for configuring Jalview's memory - + @@ -431,13 +641,13 @@ li:before {
  • CDS shown in result of submitting proteins in a CDS/Protein alignment to a web service is wrong when - proteins share a common transcript sequence (e.g. - genome of RNA viruses) + proteins share a common transcript sequence (e.g. genome of + RNA viruses)
  • - Co-located features exported and re-imported - are ordered differently when shown on alignment and in - tooltips. (Also affects v2.11.1.0) + Co-located features exported and + re-imported are ordered differently when shown on alignment + and in tooltips. (Also affects v2.11.1.0)
  • Drag and drop of alignment file onto @@ -450,7 +660,8 @@ li:before {
  • Sequence ID colourscheme not re-applied - when alignment view restored from project (since Jalview 2.11.0) + when alignment view restored from project (since Jalview + 2.11.0)
  • Duplicate CDS sequences are generated when @@ -506,32 +717,42 @@ li:before { with no feature types visible
  • - Improved support for filtering feature attributes with large integer values + Improved support for filtering feature + attributes with large integer values +
    • + + Jalview Installer +
      +
    • + Versions for install4j and getdown and + installer template version reported in console (may be null + when Jalview launched as executable jar or via conda) +
      • +
    • + Layout improvements for OSX .dmg Finder and + higher quality background images
      • -
    Jalview Installer -
    • - Versions for install4j and getdown and installer template version reported - in console (may be null when Jalview launched as executable jar or via conda) + New installer/application launcher + generated with install4j 8.0.4
    • - Layout improvements for OSX .dmg Finder and higher quality background images + Jalview File Associations shown for Unix + Platforms
    • - New installer/application launcher generated with install4j 8.0.4 + Improved defaults for maximum memory + setting when running on large memory machines
      • -
    • - Jalview File Associations shown for Unix Platforms
      • -
    • - Improved defaults for maximum memory setting when running on large memory machines
    Release processes
    • New point release version scheme - 2.11.1.0
    • - 'Jalview Test' installers/apps for easier access to test-release channel builds -
      • + 'Jalview Test' installers/apps for easier + access to test-release channel builds +
    Build System
    • @@ -541,9 +762,8 @@ li:before { Test code included in Clover coverage report
      • -
    - Groovy Scripts -
      +
    Groovy Scripts +
    • exportconsensus.groovy prints a FASTA file to stdout containing the consensus sequence for each @@ -665,57 +885,69 @@ li:before { 'Source' in console output
    • - Test Suite: Certain Functional tests fail on jalview's - bamboo server but run fine locally. + Test Suite: Certain Functional tests fail + on jalview's bamboo server but run fine locally.
    - -     2.11.0
    - 04/07/2019     - + 2.11.0
    04/07/2019
  • - Symmetric score matrices for faster - tree and PCA calculations + Symmetric score matrices for faster tree + and PCA calculations
  • Principal Components Analysis Viewer
    • - Principal Components Analysis results - and Viewer state saved in Jalview Project + Principal Components Analysis + results and Viewer state saved in Jalview Project
      • -
    • 'Change parameters' option removed from viewer's - drop-down menus
    • - Can use shift + arrow keys to rotate PCA image - incrementally + 'Change parameters' option removed from + viewer's drop-down menus +
      • +
    • + Can use shift + arrow keys to rotate + PCA image incrementally
    • PCA plot is depth cued
      • -
    -
    • +
  • New 'Colour by Sequence ID' option
  • Speed and Efficiency -
      +
      • - More efficient creation of selections and - multiple groups when working with large alignments + More efficient creation of + selections and multiple groups when working with large + alignments
      • - Speedier import of annotation rows when parsing - Stockholm files + Speedier import of annotation rows when + parsing Stockholm files
    • User Interface -
        +
        • - Finder panel remembers last position in each - view + Finder panel remembers last position in + each view
        • - Alignment Overview now WYSIWIS (What you see is - what is shown)
          Only visible regions of alignment are shown by - default (can be changed in user preferences) + Alignment Overview now WYSIWIS + (What you see is what is shown)
          Only visible + regions of alignment are shown by default (can be + changed in user preferences)
        • - File Chooser stays open after responding Cancel - to the Overwrite Dialog + File Chooser stays open after + responding Cancel to the Overwrite Dialog
        • - Better popup menu behaviour when all - sequences are hidden + 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 + selection region, and gap count when inserting or + deleting gaps
        • - Status bar updates over sequence and annotation - labels + Status bar updates over sequence and + annotation labels
        • - Annotation tooltips and popup menus are shown - when in wrapped mode + Annotation tooltips and popup menus are + shown when in wrapped mode
        • - Can select columns by dragging left/right in a graph or histogram - annotation + Can select columns by dragging + left/right in a graph or histogram annotation
        • - Help button on Uniprot and PDB search panels + Help button on Uniprot and PDB + search panels
        • - Cursor changes over draggable box in Overview - panel + Cursor changes over draggable box in + Overview panel
        • - Consistent ordering of links in sequence id - popup menu + Consistent ordering of links in + sequence id popup menu
        • - Red line indicating tree-cut position not shown if no subgroups are created
          • + Red line indicating tree-cut position + not shown if no subgroups are created +
        • - Removed ability to configure length of search history by right-clicking search box
          • - - + Removed ability to configure length of + search history by right-clicking search box + + +
        -
      • Jalview Groovy Scripting Console updated to Groovy v2.5
        • -
      • Java 11 Support (not yet on general release) +
      • + Jalview Groovy Scripting Console updated to + Groovy v2.5 +
        • +
      • Java 11 Support (not yet on general + release)
        • - OSX GUI integrations for App menu's 'About' entry and - trapping CMD-Q + OSX GUI integrations for App menu's 'About' + entry and trapping CMD-Q
        • -
      - Deprecations +
    Deprecations
      -
    • DAS sequence retrieval and annotation +
    • + DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop
      • -
    • Castor library for XML marshalling and - unmarshalling has been replaced by JAXB for Jalview projects - and XML based data retrieval clients
      • -
    • Disable VAMSAS menu in preparation for removal
      • -
    • Jalview Desktop no longer distributed via Java Web Start
      • +
    • + Castor library for XML marshalling + and unmarshalling has been replaced by JAXB for Jalview + projects and XML based data retrieval clients +
      • +
    • + Disable VAMSAS menu in preparation for + removal +
      • +
    • + Jalview Desktop no longer distributed via Java Web + Start +
    Documentation
      -
    • Added remarks about transparent rendering effects - not supported in EPS figure export +
    • + Added remarks about transparent rendering + effects not supported in EPS figure export +
      • +
    • + Typos in documentation for Preferences + dialog
      • -
    • Typos in documentation for Preferences dialog
    Development and Release Processes
    • - Build system migrated from Ant to Gradle + Build system migrated + from Ant to Gradle +
      • +
    • + Enhanced checks for missing and duplicated + keys in Message bundles
      • -
    • - Enhanced checks for missing and duplicated keys in Message bundles
    • - Eclipse project configuration managed with + Eclipse project configuration managed with gradle-eclipse
    • - Atlassian - Bamboo continuous integration for unattended Test Suite - execution + Atlassian Bamboo + continuous integration for unattended Test Suite execution
    • - Memory test suite to detect leaks in common + Memory test suite to detect leaks in common operations
    • - More unit test coverage, and minor + More unit test coverage, and minor issues resolved
    • - Developer documentation migrated to + Developer documentation migrated to markdown (with HTML rendering)
    • - HelpLinksChecker runs on Windows + HelpLinksChecker runs on Windows
    • - New URLs for publishing development + New URLs for publishing development versions of Jalview
    @@ -908,16 +1167,17 @@ li:before { superposition in Jmol fail on Windows
  • - Blank error dialog is displayed when discovering - structures for sequences with lots of PDB structures + Blank error dialog is displayed when + discovering structures for sequences with lots of PDB + structures
  • - Text misaligned in EPS or SVG image export with - monospaced font + Text misaligned in EPS or SVG image export + with monospaced font
  • - Warning of 'Duplicate entry' when saving Jalview - project involving multiple views + Warning of 'Duplicate entry' when saving + Jalview project involving multiple views
  • Overview for complementary view in a linked @@ -925,79 +1185,81 @@ li:before { 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 + 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 + Table Columns could be re-ordered in + Feature Settings and Jalview Preferences panels
  • - Jalview hangs when closing windows, or redrawing the - overview with large alignments + Jalview hangs when closing windows, or + redrawing the overview 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 + region if columns were selected by dragging right-to-left + and the mouse moved to the left of the first column
  • - Couldn't hide selected columns adjacent to a - hidden column marker via scale popup menu + Couldn't hide selected columns adjacent to + a hidden column marker via scale popup menu
  • - Error message for trying to load in invalid URLs - doesn't tell users the invalid URL + Error message for trying to load in invalid + URLs doesn't tell users the invalid URL
  • Tooltips displayed for features filtered by score from view
  • - Sequence Variants retrieved from Ensembl during - show cross references or Fetch Database References are shown in - red in original view + Sequence Variants retrieved from Ensembl + during show cross references or Fetch Database References + are shown in red in original view
  • - stop_gained variants not shown correctly on - peptide sequence (computed variant shown as p.Res.null) + stop_gained variants not shown + correctly on peptide sequence (computed variant shown as + p.Res.null)
  • 'Graduated colour' option not offered for manually created features (where feature score is Float.NaN)
  • - Blank extra columns drawn or printed - when columns are hidden + 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 + Scroll doesn't stop on mouse up after + dragging out of Scale or Annotation Panel
  • - Column selection incorrect after scrolling out of - scale 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 + Error if mouse moved before clicking Reveal + in scale panel
  • - Column display is out by one after Page Down, - Page Up in wrapped mode + Column display is out by one after Page + Down, Page Up in wrapped mode
  • Finder doesn't skip hidden regions @@ -1006,24 +1268,24 @@ li:before { Finder searches in minimised alignments
  • - 'Apply Colour to All Groups' not always selected - on opening an alignment + 'Apply Colour to All Groups' not always + selected on opening an alignment
  • - 'Colour by Annotation' not marked selected in - Colour menu + 'Colour by Annotation' not marked selected + in Colour menu
  • - Per-group Clustal colour scheme changes when - different groups in the alignment are selected + Per-group Clustal colour scheme changes + when different groups in the alignment are selected
  • - Internationalised colour scheme names not shown - correctly in menu + Internationalised colour scheme names not + shown correctly in menu
  • - Colour by Annotation can go black at min/max - threshold limit + Colour by Annotation can go black at + min/max threshold limit
  • Value input for graduated feature colour @@ -1034,56 +1296,59 @@ li:before { colour
  • - PCA points don't dim when rotated about y axis + 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 + Cancel in Tree Font dialog resets + alignment, not Tree font
  • - Associate Tree with All Views not restored from - project file + Associate Tree with All Views not restored + from project file
  • - Scrolling of split frame is sluggish if Overview - shown in complementary view + Scrolling of split frame is sluggish if + Overview shown in complementary view
  • - Codon consensus incorrectly scaled when shown - without normalisation + Codon consensus incorrectly scaled when + shown without normalisation
  • - Sequence Details report should open positioned at top - of report + Sequence Details report should open + positioned at top of report
  • Help page can be opened twice
  • - Fuzzy text in web service status menu on OSX Mojave + Fuzzy text in web service status menu on + OSX Mojave
    • Editing Datamodel Bugs fixed for Java 11 Support (not yet on - general release) + Bugs fixed for Java 11 Support (not yet on general + release) New Known Defects - Java 11 Specific defects - Java 11 Specific defects + - -
    - 2.10.5
    10/09/2018     -
    - -
    - -
      + +
      + 2.10.5
      10/09/2018       +
      + +
      + +
      • Default memory for Jalview webstart and InstallAnywhere increased to 1G. @@ -1188,9 +1456,9 @@ li:before {
      -
      - -
        +
        + +
        • Poorly scaled bar in quality annotation row shown in Feredoxin Structure alignment view of example @@ -1260,8 +1528,7 @@ li:before { latest version of OSX.
        -
        - +
      @@ -1322,7 +1589,10 @@ li:before {
    New Known Defects
      -
    • Cancel option doesn't reset Colour by Annotation
      • +
    • + Cancel option doesn't reset Colour by + Annotation +
    @@ -1358,13 +1628,12 @@ li:before { of features (particularly when transparency is disabled)
  • - Experimental features in 2.10.2 for - exchange of Jalview features and Chimera attributes made - generally available + Experimental features in 2.10.2 + for exchange of Jalview features and Chimera attributes + made generally available
    • - - +
    • @@ -1407,8 +1676,8 @@ li:before { columns in annotation row
    • - Preferences panel's ID Width control is not - honored in batch mode + Preferences panel's ID Width control is + not honored in batch mode
    • Linked sequence highlighting doesn't work @@ -1424,9 +1693,9 @@ li:before { 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) + Exception when shading sequence with + negative Temperature Factor values from annotated PDB + files (e.g. as generated by CONSURF)
    • Uniprot 'sequence variant' features @@ -1437,20 +1706,22 @@ li:before { structure and/or overview windows are also shown
    • - Selecting columns from highlighted regions - very slow for alignments with large numbers of sequences + 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 + 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 + view appears to do nothing because the view is hidden + behind the alignment view
    Applet @@ -1462,9 +1733,10 @@ li:before { Batch Mode
      -
    • - Fixed ID width preference is not respected -
      • +
    • + Fixed ID width preference is not + respected +
    New Known Defects
      @@ -1484,35 +1756,64 @@ li:before { 2.10.4 is to fail back to N&W mapping)
    • - Export Annotations from File Menu with CSV - option gives blank output + Export Annotations from File Menu with + CSV option gives blank output
    -
    - +
    - 2.10.3b1
    24/1/2018     + 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
        • +
      • 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 +
        • +
      +
    @@ -1768,14 +2069,16 @@ li:before { New features in Jalview Desktop -
    -
    +
    @@ -2244,9 +2547,9 @@ li:before { recovered correctly from Jalview project file
  • - Feature colours in overview when first opened - (automatically via preferences) are different to the main - alignment panel + Feature colours in overview when first + opened (automatically via preferences) are different to + the main alignment panel
    • Data import/export @@ -3122,7 +3425,7 @@ li:before { column.
  • - Null Pointer Exception raised when + Null Pointer Exception raised when pressing Add on an orphaned cut'n'paste window.