X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=b58cb31ab448eecead8fdb9f141e490fb3aae856;hb=4992ecae64d0c987c217e8c584161706188f9d52;hp=639631391f48e9250b710b7a614fdc8b7df8ad1c;hpb=f8b17a9e7363b8a9e7cd12d61bc6d611c7c97d7d;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 6396313..b58cb31 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -51,27 +51,575 @@ li:before {

+ + + + + + + + + + + + + + + - + + + + - + + + + + + + + +
ReleaseNew FeaturesIssues Resolved
+ 2.11
+ 14/05/2019 (final due date !) + 		+
    +
  • + 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
    • +
+ 		+
    +
  • + 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
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. +
    • +
+
+
- Release + 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. +
    • +
+
- New Features + 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) +
    • +
+
+
- Issues Resolved + 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
- 14/11/2017 + 2.10.3
17/11/2017
@@ -89,83 +637,227 @@ li:before { 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 +
  • + 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
    • - -
  • 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
    • - Scripting
      -
    • Groovy interpreter updated to 2.4.12
      • -
    • Example groovy script for generating a matrix of percent identity scores for current alignment.
      • +
    • 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
      • +
    • + 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 only aligns selected regions of each selected sequence
      • -
    • 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)
      • -
    - Applet
    -
      -
    • Concurrent modification exception when closing alignment panel
      • +
    • + 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 +
    - BioJSON
    + Applet
      -
    • - BioJSON export does not preserve non-positional features -
      • +
    • + Concurrent modification exception when + closing alignment panel +
    - Known Java 9 Issues + BioJSON
      -
    • Groovy Console very slow to open and is - not responsive when entering characters (Webstart, Java 9.01, - OSX 10.10) +
    • + 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
    - New Known Issues + Known Java 9 Issues
      -
      • +
    • + Groovy Console very slow to open and is + not responsive when entering characters (Webstart, Java + 9.01, OSX 10.10) +
    -
    -