X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=475a8da04c862bc642fe85654cbf1ff5ea7a68b7;hb=ac93424cd4c19aa35f7831e4f3da7bbcaf6baf15;hp=e8e6ee7c772610ae2d5650a8e559266fbd0b363e;hpb=2bd067a769d1e781c3547f5685a04b400fdd8f0e;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index e8e6ee7..475a8da 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,7 +1,7 @@ Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing. +

Alignment ruler shows positions relative to reference sequence

Position/residue shown in status bar when mousing over sequence associated annotation

Default RNA SS symbol to 'matching bracket' for manual entry

RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column

+ Application +

Updated download sites used for Rfam and Pfam sources to xfam.org
Disabled Rfam(Full) in the sequence fetcher
Show residue labels in Chimera when mousing over sequences in Jalview
Support for reverse-complement coding regions in ENA and EMBL
Upgrade to EMBL XML 1.2 for ENA record retrieval
Support for ENA CDS records with reverse complement operator
New 'execute Groovy script' option in an alignment window's Calculate menu
Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
Support for creating new alignment calculation workers from groovy scripts
Store/restore reference sequence in Jalview projects
Chain codes for a sequence's PDB associations are now saved/restored from project
Double click on an entry in Jalview's database chooser opens a sequence fetcher
Free-text search client for UniProt using the UniProt REST API

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

+ 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

+ Applet +

+ + + + +

+ 2.9.0b2
+ 16/10/2015 +

+ + General +

Time stamps for signed Jalview application and applet + jars

+ +

+ Application +

Duplicate group consensus and conservation rows + shown when tree is partitioned
Erratic behaviour when tree partitions made with + multiple cDNA/Protein split views

+ + + + +

+ 2.9.0b1
+ 8/10/2015 +

+ + General +

Updated Spanish translations of localized text for + 2.9

Application +

Signed OSX InstallAnywhere installer
Support for per-sequence based annotations in BioJSON

Applet +

Split frame example added to applet examples page

+ +

+ General +

Mapping of cDNA to protein in split frames + incorrect when sequence start > 1
Broken images in filter column by annotation dialog + documentation
Feature colours not parsed from features file
Exceptions and incomplete link URLs recovered when + loading a features file containing HTML tags in feature + description

+ Application +

Annotations corrupted after BioJS export and + reimport
Incorrect sequence limits after Fetch DB References + with 'trim retrieved sequences'
Incorrect warning about deleting all data when + deleting selected columns
Patch to build system for shipping properly signed + JNLP templates for webstart launch
EMBL-PDBe fetcher/viewer dialogs do not offer + unreleased structures for download or viewing
Tab/space/return keystroke operation of EMBL-PDBe + fetcher/viewer dialogs works correctly
Disabled 'minimise' button on Jalview windows + running on OSX to workaround redraw hang bug
Split cDNA/Protein view position and geometry not + recovered from jalview project
Initial enabled/disabled state of annotation menu + sorter 'show autocalculated first/last' corresponds to + alignment view
Restoring of Clustal, RNA Helices and T-Coffee + color schemes from BioJSON

+ Applet +

Reorder sequences mirrored in cDNA/Protein split + frame
Applet with Jmol examples not loading correctly

+ + + +

+ 2.9
10/9/2015 +

+ General +

Linked visualisation and analysis of DNA and Protein + alignments: +
- Translated cDNA alignments shown as split protein + and DNA alignment views
- Codon consensus annotation for linked protein and + cDNA alignment views
- Link cDNA or Protein product sequences by loading + them onto Protein or cDNA alignments
- Reconstruct linked cDNA alignment from aligned + protein sequences
+
Jmol integration updated to Jmol v14.2.14
Import and export of Jalview alignment views as BioJSON
New alignment annotation file statements for + reference sequences and marking hidden columns
Reference sequence based alignment shading to + highlight variation
Select or hide columns according to alignment + annotation
Find option for locating sequences by description
Conserved physicochemical properties shown in amino + acid conservation row
Alignments can be sorted by number of RNA helices

Application +

New cDNA/Protein analysis capabilities +
- Get Cross-References should open a Split Frame + view with cDNA/Protein
- Detect when nucleotide sequences and protein + sequences are placed in the same alignment
- Split cDNA/Protein views are saved in Jalview + projects
+
Sequence database accessions imported when fetching - alignments from Rfam
update VARNA version to 3.91
Use REST API to talk to Chimera
Selected regions in Chimera are highlighted in linked + Jalview windows
VARNA RNA viewer updated to v3.93
VARNA views are saved in Jalview Projects
Pseudoknots displayed as Jalview RNA annotation can + be shown in VARNA
Make groups for selection uses marked columns as well + as the active selected region
Calculate UPGMA and NJ trees using sequence feature + similarity
New Export options +
- New Export Settings dialog to control hidden + region export in flat file generation
- Export alignment views for display with the BioJS MSAViewer
- Export scrollable SVG in HTML page
- Optional embedding of BioJSON data when exporting + alignment figures to HTML
- 3D structure retrieval and display +
  - Free text and structured queries with the PDBe + Search API
  - PDBe Search API based discovery and selection of + PDB structures for a sequence set
  +
- JPred4 employed for protein secondary structure + predictions
- Hide Insertions menu option to hide unaligned columns + for one or a group of sequences
- Automatically hide insertions in alignments imported + from the JPred4 web server
- (Nearly) Native 'Quaqua' dialogs for browsing file + system on OSX
  LGPL libraries courtesy of http://www.randelshofer.ch/quaqua/ +
- changed 'View nucleotide structure' submenu to 'View + VARNA 2D Structure'
- change "View protein structure" menu option to "3D + Structure ..."
Applet +
- New layout for applet example pages
- New parameters to enable SplitFrame view + (file2,enableSplitFrame, scaleProteinAsCdna)
- New example demonstrating linked viewing of cDNA and + Protein alignments
Development and deployment +
- Java 1.7 minimum requirement for Jalview 2.9
- Include installation type and git revision in build + properties and console log output
- Jalview Github organisation, and new github site for + storing BioJsMSA Templates
- Jalview's unit tests now managed with TestNG
+ + Application +
- Escape should close any open find dialogs
- Typo in select-by-features status report
- Consensus RNA secondary secondary structure + predictions are not highlighted in amber
- Missing gap character in v2.7 example file means + alignment appears unaligned when pad-gaps is not enabled
- First switch to RNA Helices colouring doesn't colour + associated structure views
- ID width preference option is greyed out when auto + width checkbox not enabled
- Stopped a warning dialog from being shown when + creating user defined colours
- 'View Mapping' in structure viewer shows sequence + mappings for just that viewer's sequences
- Workaround for superposing PDB files containing + multiple models in Chimera
- Report sequence position in status bar when hovering + over Jmol structure
- Cannot output gaps as '.' symbols with Selection -> + output to text box
- Flat file exports of alignments with hidden columns + have incorrect sequence start/end
- 'Aligning' a second chain to a Chimera structure from + Jalview fails
- Colour schemes applied to structure viewers don't + work for nucleotide
- Loading/cut'n'pasting an empty or invalid file leads + to a grey/invisible alignment window
- Exported Jpred annotation from a sequence region + imports to different position
- Space at beginning of sequence feature tooltips shown + on some platforms
- Chimera viewer 'View | Show Chain' menu is not + populated
- 'New View' fails with a Null Pointer Exception in + console if Chimera has been opened
- Mouseover to Chimera not working
- Miscellaneous ENA XML feature qualifiers not + retrieved
- NPE in annotation renderer after 'Extract Scores'
- If two structures in one Chimera window, mouseover of + either sequence shows on first structure
- 'Show annotations' options should not make + non-positional annotations visible
- Subsequence secondary structure annotation not shown + in right place after 'view flanking regions'
- File Save As type unset when current file format is + unknown
- Save as '.jar' option removed for saving Jalview + projects
- Colour by Sequence colouring in Chimera more + responsive
- Cannot 'add reference annotation' for a sequence in + several views on same alignment
- Cannot show linked products for EMBL / ENA records
- Jalview's tooltip wraps long texts containing no + spaces
Applet +
- Jmol to JalviewLite mouseover/link not working
- JalviewLite can't import sequences with ID + descriptions containing angle brackets
General +
- Cannot export and reimport RNA secondary structure + via jalview annotation file
- Random helix colour palette for colour by annotation + with RNA secondary structure
- Mouseover to cDNA from STOP residue in protein + translation doesn't work.
- hints when using the select by annotation dialog box
- Jmol alignment incorrect if PDB file has alternate CA + positions
- FontChooser message dialog appears to hang after + choosing 1pt font
- Peptide secondary structure incorrectly imported from + annotation file when annotation display text includes 'e' or + 'h'
- Cannot set colour of new feature type whilst creating + new feature
- cDNA translation alignment should not be sequence + order dependent
- 'Show unconserved' doesn't work for lower case + sequences
- Nucleotide ambiguity codes involving R not recognised
Deployment and Documentation +
- Applet example pages appear different to the rest of + www.jalview.org
Application Known issues +
- Incomplete sequence extracted from PDB entry 3a6s
- Misleading message appears after trying to delete + solid column.
- Jalview icon not shown in dock after InstallAnywhere + version launches
- Fetching EMBL reference for an RNA sequence results + fails with a sequence mismatch
- Corrupted or unreadable alignment display when + scrolling alignment to right
- ArrayIndexOutOfBoundsException thrown when remove + empty columns called on alignment with ragged gapped ends
- auto calculated alignment annotation rows do not get + placed above or below non-autocalculated rows
- Jalview dekstop becomes sluggish at full screen in + ultra-high resolution
- Cannot disable consensus calculation independently of + quality and conservation
- Mouseover highlighting between cDNA and protein can + become sluggish with more than one splitframe shown
Applet Known Issues +
- Core PDB parsing code requires Jmol
- Sequence canvas panel goes white when alignment + window is being resized
+ + + +
+ 2.8.2
3/12/2014 +
+ General +
- Updated Java code signing certificate donated by + Certum.PL.
- Features and annotation preserved when performing + pairwise alignment
- RNA pseudoknot annotation can be + imported/exported/displayed
- 'colour by annotation' can colour by RNA and + protein secondary structure
- Warn user if 'Find' regular expression is invalid (mentioned + post-hoc with 2.9 release) +
Application +
- Extract and display secondary structure for sequences + with 3D structures
- Support for parsing RNAML
- Annotations menu for layout +
  - sort sequence annotation rows by alignment
  - place sequence annotation above/below alignment + annotation
  +
- Output in Stockholm format
- Internationalisation: improved Spanish (es) + translation
- Structure viewer preferences tab
- Disorder and Secondary Structure annotation tracks + shared between alignments
- UCSF Chimera launch and linked highlighting from + Jalview
- Show/hide all sequence associated annotation rows for + all or current selection
- disorder and secondary structure predictions + available as dataset annotation
- Per-sequence rna helices colouring
- New groovy scripts for exporting aligned positions, - conservation values, and calculating sum of pairs scores.
- Command line argument to set default JABAWS server
- include installation type in build properties and console - log output
- Updated Jalview project format to preserve dataset annotation
- - Application -
- Distinguish alignment and sequence associated RNA - structure in structure->view->VARNA
- Raise dialog box if user deletes all sequences in an - alignment
- Pressing F1 results in documentation opening twice
- Sequence feature tooltip is wrapped
- Double click on sequence associated annotation selects - only first column
- Redundancy removal doesn't result in unlinked leaves - shown in tree
- Undos after several redundancy removals don't undo - properly
- Hide sequence doesn't hide associated annotation
- User defined colours dialog box too big to fit on screen - and buttons not visible
- author list isn't updated if already written to jalview - properties
- Popup menu won't open after retrieving sequence from - database
- File open window for associate PDB doesn't open
- Left-then-right click on a sequence id opens a browser - search window
- Cannot open sequence feature shading/sort popup menu in - feature settings dialog
- better tooltip placement for some areas of Jalview desktop
- Unable to add JABAWS Server which doesn't pass - validation
- Web services parameters dialog box is too large to fit on - screen
- Muscle nucleotide alignment preset obscured by tooltip
- JABAWS preset submenus don't contain newly defined - user preset
- MSA web services warns user if they were launched with - invalid input
- Jalview cannot contact DAS Registy when running on Java 8
- - - 'Superpose with' submenu not shown when new view created -
Application +
- Distinguish alignment and sequence associated RNA + structure in structure->view->VARNA
- Raise dialog box if user deletes all sequences in an + alignment
- Pressing F1 results in documentation opening twice
- Sequence feature tooltip is wrapped
- Double click on sequence associated annotation + selects only first column
- Redundancy removal doesn't result in unlinked + leaves shown in tree
- Undos after several redundancy removals don't undo + properly
- Hide sequence doesn't hide associated annotation
- User defined colours dialog box too big to fit on + screen and buttons not visible
- author list isn't updated if already written to + Jalview properties
- Popup menu won't open after retrieving sequence + from database
- File open window for associate PDB doesn't open
- Left-then-right click on a sequence id opens a + browser search window
- Cannot open sequence feature shading/sort popup menu + in feature settings dialog
- better tooltip placement for some areas of Jalview + desktop
- Allow addition of JABAWS Server which doesn't + pass validation
- Web services parameters dialog box is too large to + fit on screen
- Muscle nucleotide alignment preset obscured by + tooltip
- JABAWS preset submenus don't contain newly + defined user preset
- MSA web services warns user if they were launched + with invalid input
- Jalview cannot contact DAS Registy when running on + Java 8
- + + 'Superpose with' submenu not shown when new view + created +
Deployment and Documentation -
- 2G and 1G options in launchApp have no effect on memory - allocation
- launchApp service doesn't automatically open - www.jalview.org/examples/exampleFile.jar if no file is given
- - - InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is - available -
Application Known issues -
- - - corrupted or unreadable alignment display when scrolling alignment - to right -
- - - retrieval fails but progress bar continues for DAS retrieval with - large number of ID -
- - - flatfile output of visible region has incorrect sequence start/end -
- - - rna structure consensus doesn't update when secondary - structure tracks are rearranged -
- - - invalid rna structure positional highlighting does not highlight - position of invalid base pairs -
- - - out of memory errors are not raised when saving jalview project - from alignment window file menu -
- - - Switching to RNA Helices colouring doesn't propagate to - structures -
- - - colour by RNA Helices not enabled when user created annotation - added to alignment -
- - - Jalview icon not shown on dock in Mountain Lion/Webstart -
Applet Known Issues -
- - - JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies -
- - - Jalview and Jmol example not compatible with IE9 -
Applet +
- Remove group option is shown even when selection is + not a group
- Apply to all groups ticked but colourscheme changes + don't affect groups
- Documented RNA Helices and T-Coffee Scores as valid + colourscheme name
- Annotation labels drawn on sequence IDs when + Annotation panel is not displayed
- Increased font size for dropdown menus on OSX and + embedded windows
Other +
- Consensus sequence for alignments/groups with a + single sequence were not calculated
- annotation files that contain only groups imported as + annotation and junk sequences
- Fasta files with sequences containing '*' incorrectly + recognised as PFAM or BLC
- conservation/PID slider apply all groups option + doesn't affect background (2.8.0b1) +
- redundancy highlighting is erratic at 0% and 100%
- Remove gapped columns fails for sequences with ragged + trailing gaps
- AMSA annotation row with leading spaces is not + registered correctly on import
- Jalview crashes when selecting PCA analysis for + certain alignments
- Opening the colour by annotation dialog for an + existing annotation based 'use original colours' + colourscheme loses original colours setting
+ + + +
+ 2.8.0b1
+ 30/1/2014 +
- Trusted certificates for JalviewLite applet and @@ -338,7 +767,7 @@ 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
- Allow disorder predictions to be made on the current selection (or visible selection) in the same way that JPred works
- Groovy scripting for headless jalview operation
- Groovy scripting for headless Jalview operation
Other improvements
- Upgrade desktop installer to InstallAnywhere 2013
- ClassCastException when generating EPS in headless mode
- Adjusting sequence-associated shading threshold only - changes one row's threshold
- Preferences and Feature settings panel panel doesn't open
- hide consensus histogram also hides conservation and - quality histograms
+
hide consensus histogram also hides conservation and + quality histograms

- -

- 2.8
12/11/2012 -

- Application -

Support for JABAWS 2.0 Services (AACon alignment - conservation, protein disorder and Clustal Omega)
JABAWS server status indicator in Web Services preferences -
VARNA (http://varna.lri.fr) viewer for RNA structures in - Jalview alignment window
Updated Jalview build and deploy framework for OSX mountain - lion, windows 7, and 8
Nucleotide substitution matrix for PCA that supports RNA - and ambiguity codes

+ 2.8
12/11/2012 +

Application

Support for JABAWS 2.0 Services (AACon alignment + conservation, protein disorder and Clustal Omega)
JABAWS server status indicator in Web Services + preferences
VARNA (http://varna.lri.fr) viewer for RNA structures + in Jalview alignment window
Updated Jalview build and deploy framework for OSX + mountain lion, windows 7, and 8
Nucleotide substitution matrix for PCA that supports + RNA and ambiguity codes
Improved sequence database retrieval GUI
Support fetching and database reference look up against - multiple DAS sources (Fetch all from in 'fetch db refs')
Jalview project improvements -
- Store and retrieve the 'belowAlignment' flag for - annotation
- calcId attribute to group annotation rows on the - alignment
- Store AACon calculation settings for a view in Jalview - project
- Improved sequence database retrieval GUI
- Support fetching and database reference look up + against multiple DAS sources (Fetch all from in 'fetch db + refs')
- Jalview project improvements +
  - Store and retrieve the 'belowAlignment' + flag for annotation
  - calcId attribute to group annotation rows on the + alignment
  - Store AACon calculation settings for a view in + Jalview project
  -
- horizontal scrolling gesture support
- Visual progress indicator when PCA calculation is running
- Simpler JABA web services menus
- visual indication that web service results are still being - retrieved from server
- Serialise the dialogs that are shown when Jalview starts up - for first time
- Jalview user agent string for interacting with HTTP - services
- DAS 1.6 and DAS 2.0 source support using new JDAS client - library
- Examples directory and Groovy library included in - InstallAnywhere distribution
Applet -
- RNA alignment and secondary structure annotation - visualization applet example
General -
- Normalise option for consensus sequence logo
- Reset button in PCA window to return dimensions to - defaults
- Allow seqspace or Jalview variant of alignment PCA - calculation
- PCA with either nucleic acid and protein substitution - matrices -
- Allow windows containing HTML reports to be exported in - HTML
- Interactive display and editing of RNA secondary structure - contacts
- RNA Helix Alignment Colouring
- RNA base pair logo consensus
- Parse sequence associated secondary structure information - in Stockholm files
- HTML Export database accessions and annotation information - presented in tooltip for sequences
- Import secondary structure from LOCARNA clustalw style RNA - alignment files
- import and visualise T-COFFEE quality scores for an - alignment
- 'colour by annotation' per sequence option to - shade each sequence according to its associated alignment - annotation
- New Jalview Logo
Documentation and Development -
- documentation for score matrices used in Jalview
- New Website!
- Application -
- PDB, Unprot and EMBL (ENA) databases retrieved via - wsdbfetch REST service
- Stop windows being moved outside desktop on OSX
- Filetype associations not installed for webstart launch
- Jalview does not always retrieve progress of a JABAWS job - execution in full once it is complete
- revise SHMR RSBS definition to ensure alignment is - uploaded via ali_file parameter
- Jalview 2.7 is incompatible with Jmol-12.2.2
- View all structures superposed fails with exception
- Jnet job queues forever if a very short sequence is - submitted for prediction
- Cut and paste menu not opened when mouse clicked on - desktop window
- Putting fractional value into integer text box in - alignment parameter dialog causes Jalview to hang
- Structure view highlighting doesn't work on windows 7 -
- View all structures fails with exception shown in - structure view
- Characters in filename associated with PDBEntry not - escaped in a platform independent way
- Jalview desktop fails to launch with exception when using - proxy
- Tree calculation reports 'you must have 2 or more - sequences selected' when selection is empty
- Jalview desktop fails to launch with jar signature failure - when java web start temporary file caching is disabled
- DAS Sequence retrieval with range qualification results in - sequence xref which includes range qualification
- Errors during processing of command line arguments cause - progress bar (JAL-898) to be removed
- Replace comma for semi-colon option not disabled for DAS - sources in sequence fetcher
- Cannot close news reader when JABAWS server warning dialog - is shown
- Option widgets not updated to reflect user settings
- Edited sequence not submitted to web service
- Jalview 2.7 Webstart does not launch on mountain lion
- InstallAnywhere installer doesn't unpack and run on - OSX Mountain Lion
- Annotation panel not given a scroll bar when sequences - with alignment annotation are pasted into the alignment
- Sequence associated annotation rows not associated when - loaded from Jalview project
- Browser launch fails with NPE on java 1.7
- JABAWS alignment marked as finished when job was cancelled - or job failed due to invalid input
- NPE with v2.7 example when clicking on Tree associated - with all views
- Exceptions when copy/paste sequences with grouped - annotation rows to new window
Applet -
- Sequence features are momentarily displayed before they - are hidden using hidefeaturegroups applet parameter
- loading features via javascript API automatically enables - feature display
- scrollToColumnIn javascript API method doesn't work
General -
- Redundancy removal fails for rna alignment
- PCA calculation fails when sequence has been selected and - then deselected
- PCA window shows grey box when first opened on OSX
- Letters coloured pink in sequence logo when alignment - coloured with clustalx
- Choosing fonts without letter symbols defined causes - exceptions and redraw errors
- Initial PCA plot view is not same as manually reconfigured - view
- Grouped annotation graph label has incorrect line colour
- Grouped annotation graph label display is corrupted for - lots of labels
- - - -
- 2.7
27/09/2011 -
- - Application -
- Jalview Desktop News Reader
- Tweaked default layout of web services menu
- View/alignment association menu to enable user to easily - specify which alignment a multi-structure view takes its - colours/correspondences from
- Allow properties file location to be specified as URL
- Extend Jalview project to preserve associations between - many alignment views and a single Jmol display
- Store annotation row height in Jalview project file
- Annotation row column label formatting attributes stored - in project file
- Annotation row order for auto-calculated annotation rows - preserved in Jalview project file
- Visual progress indication when Jalview state is saved - using Desktop window menu
- Visual indication that command line arguments are still - being processed
- Groovy script execution from URL
- Colour by annotation default min and max colours in - preferences
- Automatically associate PDB files dragged onto an - alignment with sequences that have high similarity and matching - IDs
- Update JGoogleAnalytics to latest release (0.3)
- 'view structures' option to open many structures - in same window
- Sort associated views menu option for tree panel
- Group all JABA and non-JABA services for a particular - analysis function in its own submenu
Applet -
- Userdefined and autogenerated annotation rows for groups
- Adjustment of alignment annotation pane height
- Annotation scrollbar for annotation panel
- Drag to reorder annotation rows in annotation panel
- 'automaticScrolling' parameter
- Allow sequences with partial ID string matches to be - annotated from GFF/Jalview features files
- Sequence logo annotation row in applet
- Absolute paths relative to host server in applet - parameters are treated as such
- New in the JalviewLite javascript API: -
  - JalviewLite.js javascript library
  - Javascript callbacks for +
  +
- horizontal scrolling gesture support
- Visual progress indicator when PCA calculation is + running
- Simpler JABA web services menus
- visual indication that web service results are still + being retrieved from server
- Serialise the dialogs that are shown when Jalview + starts up for first time
- Jalview user agent string for interacting with HTTP + services
- DAS 1.6 and DAS 2.0 source support using new JDAS + client library
- Examples directory and Groovy library included in + InstallAnywhere distribution
Applet +
- RNA alignment and secondary structure annotation + visualization applet example
General +
- Normalise option for consensus sequence logo
- Reset button in PCA window to return dimensions to + defaults
- Allow seqspace or Jalview variant of alignment PCA + calculation
- PCA with either nucleic acid and protein substitution + matrices +
- Allow windows containing HTML reports to be exported + in HTML
- Interactive display and editing of RNA secondary + structure contacts
- RNA Helix Alignment Colouring
- RNA base pair logo consensus
- Parse sequence associated secondary structure + information in Stockholm files
- HTML Export database accessions and annotation + information presented in tooltip for sequences
- Import secondary structure from LOCARNA clustalw + style RNA alignment files
- import and visualise T-COFFEE quality scores for an + alignment
- 'colour by annotation' per sequence option to + shade each sequence according to its associated alignment + annotation
- New Jalview Logo
Documentation and Development +
- documentation for score matrices used in Jalview
- New Website!
+ Application +
- PDB, Unprot and EMBL (ENA) databases retrieved via + wsdbfetch REST service
- Stop windows being moved outside desktop on OSX
- Filetype associations not installed for webstart + launch
- Jalview does not always retrieve progress of a JABAWS + job execution in full once it is complete
- revise SHMR RSBS definition to ensure alignment is + uploaded via ali_file parameter
- Jalview 2.7 is incompatible with Jmol-12.2.2
- View all structures superposed fails with exception
- Jnet job queues forever if a very short sequence is + submitted for prediction
- Cut and paste menu not opened when mouse clicked on + desktop window
- Putting fractional value into integer text box in + alignment parameter dialog causes Jalview to hang
- Structure view highlighting doesn't work on + windows 7
- View all structures fails with exception shown in + structure view
- Characters in filename associated with PDBEntry not + escaped in a platform independent way
- Jalview desktop fails to launch with exception when + using proxy
- Tree calculation reports 'you must have 2 or more + sequences selected' when selection is empty
- Jalview desktop fails to launch with jar signature + failure when java web start temporary file caching is + disabled
- DAS Sequence retrieval with range qualification + results in sequence xref which includes range qualification
- Errors during processing of command line arguments + cause progress bar (JAL-898) to be removed
- Replace comma for semi-colon option not disabled for + DAS sources in sequence fetcher
- Cannot close news reader when JABAWS server warning + dialog is shown
- Option widgets not updated to reflect user settings
- Edited sequence not submitted to web service
- Jalview 2.7 Webstart does not launch on mountain lion
- InstallAnywhere installer doesn't unpack and run + on OSX Mountain Lion
- Annotation panel not given a scroll bar when + sequences with alignment annotation are pasted into the + alignment
- Sequence associated annotation rows not associated + when loaded from Jalview project
- Browser launch fails with NPE on java 1.7
- JABAWS alignment marked as finished when job was + cancelled or job failed due to invalid input
- NPE with v2.7 example when clicking on Tree + associated with all views
- Exceptions when copy/paste sequences with grouped + annotation rows to new window
Applet
- Applet initialisation
- Sequence/alignment mouse-overs and selections
- Sequence features are momentarily displayed before + they are hidden using hidefeaturegroups applet parameter
- loading features via javascript API automatically + enables feature display
- scrollToColumnIn javascript API method doesn't + work
General +
- Redundancy removal fails for rna alignment
- PCA calculation fails when sequence has been selected + and then deselected
- PCA window shows grey box when first opened on OSX
- Letters coloured pink in sequence logo when alignment + coloured with clustalx
- Choosing fonts without letter symbols defined causes + exceptions and redraw errors
- Initial PCA plot view is not same as manually + reconfigured view
- Grouped annotation graph label has incorrect line + colour
- Grouped annotation graph label display is corrupted + for lots of labels
-
scrollTo row and column alignment scrolling functions
Select sequence/alignment regions from javascript
javascript structure viewer harness to pass messages - between Jmol and Jalview when running as distinct applets
sortBy method
Set of applet and application examples shipped with - documentation
New example to demonstrate JalviewLite and Jmol - javascript message exchange

General -

Enable Jmol displays to be associated with multiple - multiple alignments
Option to automatically sort alignment with new tree
User configurable link to enable redirects to a - www.Jalview.org mirror
Jmol colours option for Jmol displays
Configurable newline string when writing alignment and - other flat files
Allow alignment annotation description lines to contain - html tags

Documentation and Development -

Add groovy test harness for bulk load testing to examples -
Groovy script to load and align a set of sequences using a - web service before displaying the result in the Jalview desktop
Restructured javascript and applet api documentation
Ant target to publish example html files with applet - archive
Netbeans project for building Jalview from source
ant task to create online javadoc for Jalview source

- Application -

User defined colourscheme throws exception when current - built in colourscheme is saved as new scheme
AlignFrame->Save in application pops up save dialog for - valid filename/format
Cannot view associated structure for Uniprot sequence
PDB file association breaks for Uniprot sequence P37173
Associate PDB from file dialog does not tell you which - sequence is to be associated with the file
Find All raises null pointer exception when query only - matches sequence IDs
Pre 2.6 Jalview project cannot be loaded into v2.6
Jalview project with Jmol views created with Jalview 2.4 - cannot be loaded
Filetype associations not installed for webstart launch
Two or more chains in a single PDB file associated with - sequences in different alignments do not get coloured by their - associated sequence
Visibility status of autocalculated annotation row not - preserved when project is loaded
Annotation row height and visibility attributes not stored - in Jalview project
Tree bootstraps are not preserved when saved as a Jalview - project
Envision2 workflow tooltips are corrupted
Enabling show group conservation also enables colour by - conservation
Duplicate group associated conservation or consensus - created on new view
Annotation scrollbar not displayed after 'show all - hidden annotation rows' option selected
Alignment quality not updated after alignment annotation - row is hidden then shown
Preserve colouring of structures coloured by sequences in - pre Jalview 2.7 projects
Web service job parameter dialog is not laid out properly -
Web services menu not refreshed after 'reset - services' button is pressed in preferences
Annotation off by one in Jalview v2_3 example project
Structures imported from file and saved in project get - name like jalview_pdb1234.txt when reloaded
Jalview does not always retrieve progress of a JABAWS job - execution in full once it is complete

Applet -

Alignment height set incorrectly when lots of annotation - rows are displayed
Relative URLs in feature HTML text not resolved to - codebase
View follows highlighting does not work for positions in - sequences
<= shown as = in tooltip
Export features raises exception when no features exist
Separator string used for serialising lists of IDs for - javascript api is modified when separator string provided as - parameter
Null pointer exception when selecting tree leaves for - alignment with no existing selection
Relative URLs for datasources assumed to be relative to - applet's codebase
Status bar not updated after finished searching and search - wraps around to first result
StructureSelectionManager instance shared between several - Jalview applets causes race conditions and memory leaks
Hover tooltip and mouseover of position on structure not - sent from Jmol in applet
Certain sequences of javascript method calls to applet API - fatally hang browser

General -

View follows structure mouseover scrolls beyond position - with wrapped view and hidden regions
Find sequence position moves to wrong residue with/without - hidden columns
Sequence length given in alignment properties window is - off by 1
InvalidNumberFormat exceptions thrown when trying to - import PDB like structure files
Positional search results are only highlighted between - user-supplied sequence start/end bounds
End attribute of sequence is not validated
Find dialog only finds first sequence containing a given - sequence position
Sequence numbering not preserved in MSF alignment output
Jalview PDB file reader does not extract sequence from - nucleotide chains correctly
Structure colours not updated when tree partition changed - in alignment
Sequence associated secondary structure not correctly - parsed in interleaved stockholm
Colour by annotation dialog does not restore current state -
Hiding (nearly) all sequences doesn't work properly
Sequences containing lowercase letters are not properly - associated with their pdb files

Documentation and Development -

schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright - tool

- - - -

- 2.6.1 -
15/11/2010 -

- Application -

New warning dialog when the Jalview Desktop cannot contact - web services
JABA service parameters for a preset are shown in service - job window
JABA Service menu entries reworded

- -

Modeller PIR IO broken - cannot correctly import a pir - file emitted by Jalview
Existing feature settings transferred to new alignment - view created from cut'n'paste
Improved test for mixed amino/nucleotide chains when - parsing PDB files
Consensus and conservation annotation rows occasionally - become blank for all new windows
Exception raised when right clicking above sequences in - wrapped view mode

Application -

multiple multiply aligned structure views cause cpu usage - to hit 100% and computer to hang
Web Service parameter layout breaks for long user - parameter names
Jaba service discovery hangs desktop if Jaba server is - down

- - - -

2.6
- 26/9/2010

- - Application -

Support for Java bioinformatics - analysis web services (JABAWS)
Web Services preference tab
Analysis parameters dialog box and user defined preferences
Improved speed and layout of Envision2 service menu
Superpose structures using associated sequence alignment
Export coordinates and projection as CSV from PCA viewer

- Applet -

enable javascript: execution by the applet via the link out - mechanism

- Other -

Updated the Jmol Jalview interface to work with Jmol series - 12
The Jalview Desktop and JalviewLite applet now require Java - 1.5
Allow Jalview feature colour specification for GFF sequence - annotation files
New 'colour by label' keword in Jalview feature file type - colour specification
New Jalview Desktop Groovy API method that allows a script - to check if it being run in an interactive session or in a batch - operation from the Jalview command line

- - -

clustalx colourscheme colours Ds preferentially when both - D+E are present in over 50% of the column

+ + + +

+ 2.7
27/09/2011 +

+ + Application +

Jalview Desktop News Reader
Tweaked default layout of web services menu
View/alignment association menu to enable user to + easily specify which alignment a multi-structure view takes + its colours/correspondences from
Allow properties file location to be specified as URL
Extend Jalview project to preserve associations + between many alignment views and a single Jmol display
Store annotation row height in Jalview project file
Annotation row column label formatting attributes + stored in project file
Annotation row order for auto-calculated annotation + rows preserved in Jalview project file
Visual progress indication when Jalview state is + saved using Desktop window menu
Visual indication that command line arguments are + still being processed
Groovy script execution from URL
Colour by annotation default min and max colours in + preferences
Automatically associate PDB files dragged onto an + alignment with sequences that have high similarity and + matching IDs
Update JGoogleAnalytics to latest release (0.3)
'view structures' option to open many + structures in same window
Sort associated views menu option for tree panel
Group all JABA and non-JABA services for a particular + analysis function in its own submenu

Applet +

Userdefined and autogenerated annotation rows for + groups
Adjustment of alignment annotation pane height
Annotation scrollbar for annotation panel
Drag to reorder annotation rows in annotation panel
'automaticScrolling' parameter
Allow sequences with partial ID string matches to be + annotated from GFF/Jalview features files
Sequence logo annotation row in applet
Absolute paths relative to host server in applet + parameters are treated as such
New in the JalviewLite javascript API: +
- JalviewLite.js javascript library
- Javascript callbacks for +
  - Applet initialisation
  - Sequence/alignment mouse-overs and selections
  +
- scrollTo row and column alignment scrolling + functions
- Select sequence/alignment regions from javascript
- javascript structure viewer harness to pass + messages between Jmol and Jalview when running as + distinct applets
- sortBy method
- Set of applet and application examples shipped + with documentation
- New example to demonstrate JalviewLite and Jmol + javascript message exchange
+

General +

Enable Jmol displays to be associated with multiple + multiple alignments
Option to automatically sort alignment with new tree
User configurable link to enable redirects to a + www.Jalview.org mirror
Jmol colours option for Jmol displays
Configurable newline string when writing alignment + and other flat files
Allow alignment annotation description lines to + contain html tags

Documentation and Development +

Add groovy test harness for bulk load testing to + examples
Groovy script to load and align a set of sequences + using a web service before displaying the result in the + Jalview desktop
Restructured javascript and applet api documentation
Ant target to publish example html files with applet + archive
Netbeans project for building Jalview from source
ant task to create online javadoc for Jalview source

+ Application +

User defined colourscheme throws exception when + current built in colourscheme is saved as new scheme
AlignFrame->Save in application pops up save + dialog for valid filename/format
Cannot view associated structure for UniProt sequence
PDB file association breaks for UniProt sequence + P37173
Associate PDB from file dialog does not tell you + which sequence is to be associated with the file
Find All raises null pointer exception when query + only matches sequence IDs
Pre 2.6 Jalview project cannot be loaded into v2.6
Jalview project with Jmol views created with Jalview + 2.4 cannot be loaded
Filetype associations not installed for webstart + launch
Two or more chains in a single PDB file associated + with sequences in different alignments do not get coloured + by their associated sequence
Visibility status of autocalculated annotation row + not preserved when project is loaded
Annotation row height and visibility attributes not + stored in Jalview project
Tree bootstraps are not preserved when saved as a + Jalview project
Envision2 workflow tooltips are corrupted
Enabling show group conservation also enables colour + by conservation
Duplicate group associated conservation or consensus + created on new view
Annotation scrollbar not displayed after 'show + all hidden annotation rows' option selected
Alignment quality not updated after alignment + annotation row is hidden then shown
Preserve colouring of structures coloured by + sequences in pre Jalview 2.7 projects
Web service job parameter dialog is not laid out + properly
Web services menu not refreshed after 'reset + services' button is pressed in preferences
Annotation off by one in Jalview v2_3 example project
Structures imported from file and saved in project + get name like jalview_pdb1234.txt when reloaded
Jalview does not always retrieve progress of a JABAWS + job execution in full once it is complete

Applet +

Alignment height set incorrectly when lots of + annotation rows are displayed
Relative URLs in feature HTML text not resolved to + codebase
View follows highlighting does not work for positions + in sequences
<= shown as = in tooltip
Export features raises exception when no features + exist
Separator string used for serialising lists of IDs + for javascript api is modified when separator string + provided as parameter
Null pointer exception when selecting tree leaves for + alignment with no existing selection
Relative URLs for datasources assumed to be relative + to applet's codebase
Status bar not updated after finished searching and + search wraps around to first result
StructureSelectionManager instance shared between + several Jalview applets causes race conditions and memory + leaks
Hover tooltip and mouseover of position on structure + not sent from Jmol in applet
Certain sequences of javascript method calls to + applet API fatally hang browser

General +

View follows structure mouseover scrolls beyond + position with wrapped view and hidden regions
Find sequence position moves to wrong residue + with/without hidden columns
Sequence length given in alignment properties window + is off by 1
InvalidNumberFormat exceptions thrown when trying to + import PDB like structure files
Positional search results are only highlighted + between user-supplied sequence start/end bounds
End attribute of sequence is not validated
Find dialog only finds first sequence containing a + given sequence position
Sequence numbering not preserved in MSF alignment + output
Jalview PDB file reader does not extract sequence + from nucleotide chains correctly
Structure colours not updated when tree partition + changed in alignment
Sequence associated secondary structure not correctly + parsed in interleaved stockholm
Colour by annotation dialog does not restore current + state
Hiding (nearly) all sequences doesn't work + properly
Sequences containing lowercase letters are not + properly associated with their pdb files

Documentation and Development +

schemas/JalviewWsParamSet.xsd corrupted by + ApplyCopyright tool

+ + + +

+ 2.6.1
15/11/2010 +

+ + Application +

New warning dialog when the Jalview Desktop cannot + contact web services
JABA service parameters for a preset are shown in + service job window
JABA Service menu entries reworded

+ +

Modeller PIR IO broken - cannot correctly import a + pir file emitted by Jalview
Existing feature settings transferred to new + alignment view created from cut'n'paste
Improved test for mixed amino/nucleotide chains when + parsing PDB files
Consensus and conservation annotation rows + occasionally become blank for all new windows
Exception raised when right clicking above sequences + in wrapped view mode

Application +

multiple multiply aligned structure views cause cpu + usage to hit 100% and computer to hang
Web Service parameter layout breaks for long user + parameter names
Jaba service discovery hangs desktop if Jaba server + is down

+ + + + +

+ 2.6
26/9/2010 +

+ + Application +

Support for Java bioinformatics + analysis web services + (JABAWS) +
Web Services preference tab
Analysis parameters dialog box and user defined + preferences
Improved speed and layout of Envision2 service menu
Superpose structures using associated sequence + alignment
Export coordinates and projection as CSV from PCA + viewer

Applet +

enable javascript: execution by the applet via the + link out mechanism

Other +

Updated the Jmol Jalview interface to work with Jmol + series 12
The Jalview Desktop and JalviewLite applet now + require Java 1.5
Allow Jalview feature colour specification for GFF + sequence annotation files
New 'colour by label' keword in Jalview feature file + type colour specification
New Jalview Desktop Groovy API method that allows a + script to check if it being run in an interactive session or + in a batch operation from the Jalview command line

+ +

clustalx colourscheme colours Ds preferentially when + both D+E are present in over 50% of the column

Application +

typo in AlignmentFrame->View->Hide->all but + selected Regions menu item
sequence fetcher replaces ',' for ';' when the ',' is + part of a valid accession ID
fatal OOM if object retrieved by sequence fetcher + runs out of memory
unhandled Out of Memory Error when viewing pca + analysis results
InstallAnywhere builds fail to launch on OS X java + 10.5 update 4 (due to apple Java 1.6 update)
Installanywhere Jalview silently fails to launch

Applet +

Jalview.getFeatureGroups() raises an + ArrayIndexOutOfBoundsException if no feature groups are + defined.

+ + + + +

+ 2.5.1
14/6/2010 +

+ + + +

Alignment prettyprinter doesn't cope with long + sequence IDs
clustalx colourscheme colours Ds preferentially when + both D+E are present in over 50% of the column
nucleic acid structures retrieved from PDB do not + import correctly
More columns get selected than were clicked on when a + number of columns are hidden
annotation label popup menu not providing correct + add/hide/show options when rows are hidden or none are + present
Stockholm format shown in list of readable formats, + and parser copes better with alignments from RFAM.
CSV output of consensus only includes the percentage + of all symbols if sequence logo display is enabled

Application

typo in AlignmentFrame->View->Hide->all but - selected Regions menu item
sequence fetcher replaces ',' for ';' when the ',' is part - of a valid accession ID
fatal OOM if object retrieved by sequence fetcher runs out - of memory
unhandled Out of Memory Error when viewing pca analysis - results
InstallAnywhere builds fail to launch on OS X java 10.5 - update 4 (due to apple Java 1.6 update)
Installanywhere Jalview silently fails to launch

Applet

Jalview.getFeatureGroups() raises an - ArrayIndexOutOfBoundsException if no feature groups are defined.

2.5.1
- 14/6/2010

Alignment prettyprinter doesn't cope with long sequence IDs -
clustalx colourscheme colours Ds preferentially when both - D+E are present in over 50% of the column
nucleic acid structures retrieved from PDB do not import - correctly
More columns get selected than were clicked on when a number - of columns are hidden
annotation label popup menu not providing correct - add/hide/show options when rows are hidden or none are present
Stockholm format shown in list of readable formats, and - parser copes better with alignments from RFAM.
CSV output of consensus only includes the percentage of all - symbols if sequence logo display is enabled

Applet

annotation panel disappears when annotation is + hidden/removed

Application

Alignment view not redrawn properly when new + alignment opened where annotation panel is visible but no + annotations are present on alignment
pasted region containing hidden columns is + incorrectly displayed in new alignment window
Jalview slow to complete operations when stdout is + flooded (fix is to close the Jalview console)
typo in AlignmentFrame->View->Hide->all but + selected Rregions menu item.
inconsistent group submenu and Format submenu entry + 'Un' or 'Non'conserved
Sequence feature settings are being shared by + multiple distinct alignments
group annotation not recreated when tree partition is + changed
double click on group annotation to select sequences + does not propagate to associated trees
Mac OSX specific issues: +
- exception raised when mouse clicked on desktop + window background
- Desktop menu placed on menu bar and application + name set correctly
- sequence feature settings not wide enough for the + save feature colourscheme button
+

- Applet -

annotation panel disappears when annotation is - hidden/removed

- Application -

Alignment view not redrawn properly when new alignment - opened where annotation panel is visible but no annotations are - present on alignment
pasted region containing hidden columns is incorrectly - displayed in new alignment window
Jalview slow to complete operations when stdout is flooded - (fix is to close the Jalview console)
typo in AlignmentFrame->View->Hide->all but - selected Rregions menu item.
inconsistent group submenu and Format submenu entry 'Un' or - 'Non'conserved
Sequence feature settings are being shared by multiple - distinct alignments
group annotation not recreated when tree partition is - changed
double click on group annotation to select sequences does - not propagate to associated trees
Mac OSX specific issues: -
- exception raised when mouse clicked on desktop window - background
- Desktop menu placed on menu bar and application name set - correctly
- sequence feature settings not wide enough for the save - feature colourscheme button
-

- - - + +

+ 2.5
30/4/2010 +

+ + New Capabilities +

URL links generated from description line for + regular-expression based URL links (applet and application) - -
2.5
- 30/4/2010
- - New Capabilities -
- 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
- Linked viewing of nucleic acid sequences and structures
- Automatic Scrolling option in View menu to display the - currently highlighted region of an alignment.
- Order an alignment by sequence length, or using the average - score or total feature count for each sequence.
- Shading features by score or associated description
- Subdivide alignment and groups based on identity of selected - subsequence (Make Groups from Selection).
- New hide/show options including Shift+Control+H to hide - everything but the currently selected region.
- Application -
- Fetch DB References capabilities and UI expanded to support - retrieval from DAS sequence sources
- Local DAS Sequence sources can be added via the command line - or via the Add local source dialog box.
- DAS Dbref and DbxRef feature types are parsed as database - references and protein_name is parsed as description line (BioSapiens - terms).
- Enable or disable non-positional feature and database - references in sequence ID tooltip from View menu in application.
Application +
- Fetch DB References capabilities and UI expanded to + support retrieval from DAS sequence sources
- Local DAS Sequence sources can be added via the + command line or via the Add local source dialog box.
- DAS Dbref and DbxRef feature types are parsed as + database references and protein_name is parsed as + description line (BioSapiens terms).
- 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 and - visualized as sequence logos
- Optionally scale multi-character column labels to fit within - each column of annotation row
- Optional automatic sort of associated alignment view when a - new tree is opened.
- Jalview Java Console
- Better placement of desktop window when moving between - different screens.
- New preference items for sequence ID tooltip and consensus - annotation
- Client to submit sequences and IDs to Envision2 Workflows
- Vamsas Capabilities -
  - Improved VAMSAS synchronization (Jalview archive used to - preserve views, structures, and tree display settings)
  - Import of vamsas documents from disk or URL via command - line
  - Sharing of selected regions between views and with other - VAMSAS applications (Experimental feature!)
  - Updated API to VAMSAS version 0.2
  -
- Applet -
- Middle button resizes annotation row height
- New Parameters -
  - sortByTree (true/false) - automatically sort the associated - alignment view by the tree when a new tree is opened.
  - showTreeBootstraps (true/false) - show or hide branch - bootstraps (default is to show them if available)
  - showTreeDistances (true/false) - show or hide branch - lengths (default is to show them if available)
  - showUnlinkedTreeNodes (true/false) - indicate if - unassociated nodes should be highlighted in the tree view
  - heightScale and widthScale (1.0 or more) - increase the - height or width of a cell in the alignment grid relative to the - current font size.
  -
- Non-positional features displayed in sequence ID tooltip
- Other -
- Features format: graduated colour definitions and - specification of feature scores
- Alignment Annotations format: new keywords for group - associated annotation (GROUP_REF) and annotation row display - properties (ROW_PROPERTIES)
- XML formats extended to support graduated feature - colourschemes, group associated annotation, and profile visualization - settings.
- Group-associated consensus, sequence logos and + conservation plots
- Symbol distributions for each column can be exported + and visualized as sequence logos
- Optionally scale multi-character column labels to fit + within each column of annotation row +
- Optional automatic sort of associated alignment view + when a new tree is opened.
- Jalview Java Console
- Better placement of desktop window when moving + between different screens.
- New preference items for sequence ID tooltip and + consensus annotation
- Client to submit sequences and IDs to Envision2 Workflows
- Vamsas Capabilities +
  - Improved VAMSAS synchronization (Jalview archive + used to preserve views, structures, and tree display + settings)
  - Import of vamsas documents from disk or URL via + command line
  - Sharing of selected regions between views and + with other VAMSAS applications (Experimental feature!)
  - Updated API to VAMSAS version 0.2
Applet +
- Middle button resizes annotation row height
- New Parameters +
  - sortByTree (true/false) - automatically sort the + associated alignment view by the tree when a new tree is + opened.
  - showTreeBootstraps (true/false) - show or hide + branch bootstraps (default is to show them if available)
  - showTreeDistances (true/false) - show or hide + branch lengths (default is to show them if available)
  - showUnlinkedTreeNodes (true/false) - indicate if + unassociated nodes should be highlighted in the tree + view
  - heightScale and widthScale (1.0 or more) - + increase the height or width of a cell in the alignment + grid relative to the current font size.
  +
- Non-positional features displayed in sequence ID + tooltip
Other +
- Features format: graduated colour definitions and + specification of feature scores
- Alignment Annotations format: new keywords for group + associated annotation (GROUP_REF) and annotation row display + properties (ROW_PROPERTIES)
- XML formats extended to support graduated feature + colourschemes, group associated annotation, and profile + visualization settings.
- export annotation rows as CSV for spreadsheet import
- Jalview projects record alignment dataset associations, EMBL - products, and cDNA sequence mappings
- Sequence Group colour can be specified in Annotation File
- Ad-hoc colouring of group in Annotation File using RGB - triplet as name of colourscheme
- VAMSAS Client capabilities (Experimental) -
- treenode binding for VAMSAS tree exchange
- local editing and update of sequences in VAMSAS alignments - (experimental)
- Create new or select existing session to join
- load and save of vamsas documents
- Application command line -
- -tree parameter to open trees (introduced for passing from - applet)
- -fetchfrom command line argument to specify nicknames of DAS - servers to query for alignment features
- -dasserver command line argument to add new servers that are - also automatically queried for features
- -groovy command line argument executes a given groovy script - after all input data has been loaded and parsed
- Applet-Application data exchange -
- Trees passed as applet parameters can be passed to - application (when using "View in full application")
- Applet Parameters -
- feature group display control parameter
- debug parameter
- showbutton parameter
- Applet API methods -
- newView public method
- Window (current view) specific get/set public methods
- Feature display control methods
- get list of currently selected sequences
- New Jalview distribution features -
- InstallAnywhere Installer upgraded to IA 2008 VP1
- RELEASE file gives build properties for the latest Jalview - release.
- Java 1.1 Applet build made easier and donotobfuscate - property controls execution of obfuscator
- Build target for generating source distribution
- Debug flag for javacc
- .jalview_properties file is documented (slightly) in - jalview.bin.Cache
- Continuous Build Integration for stable and development - version of Application, Applet and source distribution
+
+ 2.4
27/8/2008 +
+ + User Interface +
- Linked highlighting of codon and amino acid from + translation and protein products
- Linked highlighting of structure associated with + residue mapping to codon position
- Sequence Fetcher provides example accession numbers + and 'clear' button
- MemoryMonitor added as an option under Desktop's + Tools menu
- Extract score function to parse whitespace separated + numeric data in description line
- Column labels in alignment annotation can be centred.
- Tooltip for sequence associated annotation give name + of sequence
Web Services and URL fetching +
- JPred3 web service
- Prototype sequence search client (no public services + available yet)
- Fetch either seed alignment or full alignment from + PFAM
- URL Links created for matching database cross + references as well as sequence ID
- URL Links can be created using regular-expressions
Sequence Database Connectivity +
- Retrieval of cross-referenced sequences from other + databases
- Generalised database reference retrieval and + validation to all fetchable databases
- Fetch sequences from DAS sources supporting the + sequence command
Import and Export +
export annotation rows as CSV for spreadsheet import
Jalview projects record alignment dataset associations, + EMBL products, and cDNA sequence mappings
Sequence Group colour can be specified in Annotation + File
Ad-hoc colouring of group in Annotation File using RGB + triplet as name of colourscheme

VAMSAS Client capabilities (Experimental) +

treenode binding for VAMSAS tree exchange
local editing and update of sequences in VAMSAS + alignments (experimental)
Create new or select existing session to join
load and save of vamsas documents

Application command line +

-tree parameter to open trees (introduced for passing + from applet)
-fetchfrom command line argument to specify nicknames + of DAS servers to query for alignment features
-dasserver command line argument to add new servers + that are also automatically queried for features
-groovy command line argument executes a given groovy + script after all input data has been loaded and parsed

Applet-Application data exchange +

Trees passed as applet parameters can be passed to + application (when using "View in full + application")

Applet Parameters +

feature group display control parameter
debug parameter
showbutton parameter

Applet API methods +

newView public method
Window (current view) specific get/set public methods
Feature display control methods
get list of currently selected sequences

New Jalview distribution features +

InstallAnywhere Installer upgraded to IA 2008 VP1
RELEASE file gives build properties for the latest + Jalview release.
Java 1.1 Applet build made easier and donotobfuscate + property controls execution of obfuscator
Build target for generating source distribution
Debug flag for javacc
.jalview_properties file is documented (slightly) in + jalview.bin.Cache
Continuous Build Integration for stable and + development version of Application, Applet and source + distribution

+ +

selected region output includes visible annotations + (for certain formats)
edit label/displaychar contains existing label/char + for editing
update PDBEntries when DBRefEntries change (vamsas)
shorter peptide product names from EMBL records
Newick string generator makes compact representations
bootstrap values parsed correctly for tree files with + comments
pathological filechooser bug avoided by not allowing + filenames containing a ':'
Fixed exception when parsing GFF files containing + global sequence features
Alignment datasets are finalized only when number of + references from alignment sequences goes to zero
Close of tree branch colour box without colour + selection causes cascading exceptions
occasional negative imgwidth exceptions
better reporting of non-fatal warnings to user when + file parsing fails.
Save works when Jalview project is default format
Save as dialog opened if current alignment format is + not a valid output format
UniProt canonical names introduced for both das and + vamsas
Histidine should be midblue (not pink!) in Zappo
error messages passed up and output when data read + fails
edit undo recovers previous dataset sequence when + sequence is edited
allow PDB files without pdb ID HEADER lines (like + those generated by MODELLER) to be read in properly
allow reading of JPred concise files as a normal + filetype
Stockholm annotation parsing and alignment properties + import fixed for PFAM records
Structure view windows have correct name in Desktop + window list
annotation consisting of sequence associated scores + can be read and written correctly to annotation file
Aligned cDNA translation to aligned peptide works + correctly
Fixed display of hidden sequence markers and + non-italic font for representatives in Applet
Applet Menus are always embedded in applet window on + Macs.
Newly shown features appear at top of stack (in + Applet)
Annotations added via parameter not drawn properly + due to null pointer exceptions
Secondary structure lines are drawn starting from + first column of alignment
UniProt XML import updated for new schema release in + July 2008
Sequence feature to sequence ID match for Features + file is case-insensitive
Sequence features read from Features file appended to + all sequences with matching IDs
PDB structure coloured correctly for associated views + containing a sub-sequence
PDB files can be retrieved by applet from Jar files
feature and annotation file applet parameters + referring to different directories are retrieved correctly
Fixed application hang whilst waiting for + splash-screen version check to complete
Applet properly URLencodes input parameter values + when passing them to the launchApp service
display name and local features preserved in results + retrieved from web service
Visual delay indication for sequence retrieval and + sequence fetcher initialisation
updated Application to use DAS 1.53e version of + dasobert DAS client
Re-instated Full AMSA support and .amsa file + association
Fixed parsing of JNet Concise annotation sans + sequences +

+ + + + +

+ 2.3
9/5/07 +

+ + +

Jmol 11.0.2 integration
PDB views stored in Jalview XML files
Slide sequences
Edit sequence in place
EMBL CDS features
DAS Feature mapping
Feature ordering
Alignment Properties
Annotation Scores
Sort by scores
Feature/annotation editing in applet

+ + +

Headless state operation in 2.2.1
Incorrect and unstable DNA pairwise alignment
Cut and paste of sequences with annotation
Feature group display state in XML
Feature ordering in XML
blc file iteration selection using filename # suffix
Stockholm alignment properties
Stockhom alignment secondary structure annotation
2.2.1 applet had no feature transparency
Number pad keys can be used in cursor mode
Structure Viewer mirror image resolved

+ - - -

selected region output includes visible annotations (for - certain formats)
edit label/displaychar contains existing label/char for - editing
update PDBEntries when DBRefEntries change (vamsas)
shorter peptide product names from EMBL records
Newick string generator makes compact representations
bootstrap values parsed correctly for tree files with - comments
pathological filechooser bug avoided by not allowing - filenames containing a ':'
Fixed exception when parsing GFF files containing global - sequence features
Alignment datasets are finalized only when number of - references from alignment sequences goes to zero
Close of tree branch colour box without colour selection - causes cascading exceptions
occasional negative imgwidth exceptions
better reporting of non-fatal warnings to user when file - parsing fails.
Save works when Jalview project is default format
Save as dialog opened if current alignment format is not a - valid output format
Uniprot canonical names introduced for both das and vamsas
Histidine should be midblue (not pink!) in Zappo
error messages passed up and output when data read fails
edit undo recovers previous dataset sequence when sequence - is edited
allow PDB files without pdb ID HEADER lines (like those - generated by MODELLER) to be read in properly
allow reading of JPred concise files as a normal filetype
Stockholm annotation parsing and alignment properties import - fixed for PFAM records
Structure view windows have correct name in Desktop window - list
annotation consisting of sequence associated scores can be - read and written correctly to annotation file
Aligned cDNA translation to aligned peptide works correctly
Fixed display of hidden sequence markers and non-italic font - for representatives in Applet
Applet Menus are always embedded in applet window on Macs.
Newly shown features appear at top of stack (in Applet)
Annotations added via parameter not drawn properly due to - null pointer exceptions
Secondary structure lines are drawn starting from first - column of alignment
Uniprot XML import updated for new schema release in July - 2008
Sequence feature to sequence ID match for Features file is - case-insensitive
Sequence features read from Features file appended to all - sequences with matching IDs
PDB structure coloured correctly for associated views - containing a sub-sequence
PDB files can be retrieved by applet from Jar files
feature and annotation file applet parameters referring to - different directories are retrieved correctly
Fixed application hang whilst waiting for splash-screen - version check to complete
Applet properly URLencodes input parameter values when - passing them to the launchApp service
display name and local features preserved in results - retrieved from web service
Visual delay indication for sequence retrieval and sequence - fetcher initialisation
updated Application to use DAS 1.53e version of dasobert DAS - client
Re-instated Full AMSA support and .amsa file association
Fixed parsing of JNet Concise annotation sans - sequences

- - - - -

2.3
- 9/5/07

- - -

Jmol 11.0.2 integration
PDB views stored in Jalview XML files
Slide sequences
Edit sequence in place
EMBL CDS features
DAS Feature mapping
Feature ordering
Alignment Properties
Annotation Scores
Sort by scores
Feature/annotation editing in applet

- - -

Headless state operation in 2.2.1
Incorrect and unstable DNA pairwise alignment
Cut and paste of sequences with annotation
Feature group display state in XML
Feature ordering in XML
blc file iteration selection using filename # suffix
Stockholm alignment properties
Stockhom alignment secondary structure annotation
2.2.1 applet had no feature transparency
Number pad keys can be used in cursor mode
Structure Viewer mirror image resolved

- + + + +

+ 2.2.1
12/2/07 +

+ + +

Non standard characters can be read and displayed +
Annotations/Features can be imported/exported to the + applet via textbox +
Applet allows editing of sequence/annotation/group + name & description +
Preference setting to display sequence name in + italics +
Annotation file format extended to allow + Sequence_groups to be defined +
Default opening of alignment overview panel can be + specified in preferences +
PDB residue numbering annotation added to associated + sequences +

+ + +

Applet crash under certain Linux OS with Java 1.6 + installed +
Annotation file export / import bugs fixed +
PNG / EPS image output bugs fixed +

+ + + + +

+ 2.2
27/11/06 +

+ + +

Multiple views on alignment +
Sequence feature editing +
"Reload" alignment +
"Save" to current filename +
Background dependent text colour +
Right align sequence ids +
User-defined lower case residue colours +
Format Menu +
Select Menu +
Menu item accelerator keys +
Control-V pastes to current alignment +
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' +

+ + +

New memory efficient Undo/Redo System +
Optimised symbol lookups and conservation/consensus + calculations +
Region Conservation/Consensus recalculated after + edits +
Fixed Remove Empty Columns Bug (empty columns at end + of alignment) +
Slowed DAS Feature Fetching for increased robustness. - - - -
2.2.1
- 12/2/07
- - -
- Non standard characters can be read and displayed -
- Annotations/Features can be imported/exported to the applet - via textbox -
- Applet allows editing of sequence/annotation/group name - & description -
- Preference setting to display sequence name in italics -
- Annotation file format extended to allow Sequence_groups to - be defined -
- Default opening of alignment overview panel can be specified - in preferences -
- PDB residue numbering annotation added to associated - sequences -
- - -
- Applet crash under certain Linux OS with Java 1.6 installed -
- Annotation file export / import bugs fixed -
- PNG / EPS image output bugs fixed -
- - - - -
2.2
- 27/11/06
- - -
- Multiple views on alignment -
- Sequence feature editing -
- "Reload" alignment -
- "Save" to current filename -
- Background dependent text colour -
- Right align sequence ids -
- User-defined lower case residue colours -
- Format Menu -
- Select Menu -
- Menu item accelerator keys -
- Control-V pastes to current alignment -
- 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' -
- - -
- New memory efficient Undo/Redo System -
- Optimised symbol lookups and conservation/consensus - calculations -
- Region Conservation/Consensus recalculated after edits -
- 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 -
- Re-instated Zoom function for PCA -
- Sequence descriptions conserved in web service analysis - results -
- Uniprot ID discoverer uses any word separated by ∣ -
- WsDbFetch query/result association resolved -
- Tree leaf to sequence mapping improved -
- Smooth fonts switch moved to FontChooser dialog box. -
- - - - -
2.1.1
- 12/9/06
- - -
- Copy consensus sequence to clipboard
- - -
- Image output - rightmost residues are rendered if sequence - id panel has been resized
- Image output - all offscreen group boundaries are rendered
- Annotation files with sequence references - all elements in - file are relative to sequence position
- Mac Applet users can use Alt key for group editing
- - - - -
2.1
- 22/8/06
- - -
- MAFFT Multiple Alignment in default Web Service list
- DAS Feature fetching
- Hide sequences and columns
- Export Annotations and Features
- GFF file reading / writing
- Associate structures with sequences from local PDB files
- Add sequences to exisiting alignment
- Recently opened files / URL lists
- Applet can launch the full application
- Applet has transparency for features (Java 1.2 required)
- Applet has user defined colours parameter
- Applet can load sequences from parameter "sequencex"
- - -
- Redundancy Panel reinstalled in the Applet
- Monospaced font - EPS / rescaling bug fixed
- Annotation files with sequence references bug fixed
- - - - -
2.08.1
- 2/5/06
- - -
- Change case of selected region from Popup menu
- Choose to match case when searching
- Middle mouse button and mouse movement can compress / expand - the visible width and height of the alignment
- - -
- Annotation Panel displays complete JNet results
- - - - -
2.08b
- 18/4/06
- - - -
- Java 1.5 bug - InternalMessageDialog fix for threads
- Righthand label on wrapped alignments shows correct value
- - - - -
2.08
- 10/4/06
- - -
- Editing can be locked to the selection area
- Keyboard editing
- Create sequence features from searches
- Precalculated annotations can be loaded onto alignments
- Features file allows grouping of features
- Annotation Colouring scheme added
- Smooth fonts off by default - Faster rendering
- Choose to toggle Autocalculate Consensus On/Off
- - -
- Drag & Drop fixed on Linux
- Jalview Archive file faster to load/save, sequence - descriptions saved.
- - - - -
2.07
- 12/12/05
- - -
- PDB Structure Viewer enhanced
- Sequence Feature retrieval and display enhanced
- Choose to output sequence start-end after sequence name for - file output
- Sequence Fetcher WSDBFetch@EBI
- Applet can read feature files, PDB files and can be used for - HTML form input
- - -
- HTML output writes groups and features
- Group editing is Control and mouse click
- File IO bugs
- - - - -
2.06
- 28/9/05
- - -
- View annotations in wrapped mode
- More options for PCA viewer
- - -
- GUI bugs resolved
- Runs with -nodisplay from command line
- - - - -
2.05b
- 15/9/05
- - -
- Choose EPS export as lineart or text
- Jar files are executable
- Can read in Uracil - maps to unknown residue
- - -
- Known OutOfMemory errors give warning message
- Overview window calculated more efficiently
- Several GUI bugs resolved
- - - - -
2.05
- 30/8/05
- - -
- Edit and annotate in "Wrapped" view
- - -
- Several GUI bugs resolved
- - - - -
2.04
- 24/8/05
- - -
- Hold down mouse wheel & scroll to change font size
- - -
- Improved JPred client reliability
- Improved loading of Jalview files
- - - - -
2.03
- 18/8/05
- - -
- Set Proxy server name and port in preferences
- Multiple URL links from sequence ids
- User Defined Colours can have a scheme name and added to - Colour Menu
- Choose to ignore gaps in consensus calculation
- Unix users can set default web browser
- Runs without GUI for batch processing
- Dynamically generated Web Service Menus
- - -
- InstallAnywhere download for Sparc Solaris
- - - - -
2.02
- 18/7/05
- - - -
- Copy & Paste order of sequences maintains alignment - order.
- - - - -
2.01
- 12/7/05
- - -
- Use delete key for deleting selection.
- Use Mouse wheel to scroll sequences.
- Help file updated to describe how to add alignment - annotations.
- Version and build date written to build properties file.
- InstallAnywhere installation will check for updates at - launch of Jalview.
- - -
- Delete gaps bug fixed.
- FileChooser sorts columns.
- Can remove groups one by one.
- Filechooser icons installed.
- Finder ignores return character when searching. Return key - will initiate a search.
  -
- - - - -
2.0
- 20/6/05
- - -
- New codebase
- - - - -

+ +
Made angle brackets in ASCII feature descriptions + display correctly +
Re-instated Zoom function for PCA +
Sequence descriptions conserved in web service + analysis results +
UniProt ID discoverer uses any word separated by + ∣ +
WsDbFetch query/result association resolved +
Tree leaf to sequence mapping improved +
Smooth fonts switch moved to FontChooser dialog box. + + +

+ + + + +

+ 2.1.1
12/9/06 +

+ + +

Copy consensus sequence to clipboard

+ + +

Image output - rightmost residues are rendered if + sequence id panel has been resized
Image output - all offscreen group boundaries are + rendered
Annotation files with sequence references - all + elements in file are relative to sequence position
Mac Applet users can use Alt key for group editing

+ + + + +

+ 2.1
22/8/06 +

+ + +

MAFFT Multiple Alignment in default Web Service list
DAS Feature fetching
Hide sequences and columns
Export Annotations and Features
GFF file reading / writing
Associate structures with sequences from local PDB + files
Add sequences to exisiting alignment
Recently opened files / URL lists
Applet can launch the full application
Applet has transparency for features (Java 1.2 + required)
Applet has user defined colours parameter
Applet can load sequences from parameter + "sequencex" +

+ + +

Redundancy Panel reinstalled in the Applet
Monospaced font - EPS / rescaling bug fixed
Annotation files with sequence references bug fixed

+ + + + +

+ 2.08.1
2/5/06 +

+ + +

Change case of selected region from Popup menu
Choose to match case when searching
Middle mouse button and mouse movement can compress / + expand the visible width and height of the alignment

+ + +

Annotation Panel displays complete JNet results

+ + + + +

+ 2.08b
18/4/06 +

+ + + +

Java 1.5 bug - InternalMessageDialog fix for threads
Righthand label on wrapped alignments shows correct + value

+ + + + +

+ 2.08
10/4/06 +

+ + +

Editing can be locked to the selection area
Keyboard editing
Create sequence features from searches
Precalculated annotations can be loaded onto + alignments
Features file allows grouping of features
Annotation Colouring scheme added
Smooth fonts off by default - Faster rendering
Choose to toggle Autocalculate Consensus On/Off

+ + +

Drag & Drop fixed on Linux
Jalview Archive file faster to load/save, sequence + descriptions saved.

+ + + + +

+ 2.07
12/12/05 +

+ + +

PDB Structure Viewer enhanced
Sequence Feature retrieval and display enhanced
Choose to output sequence start-end after sequence + name for file output
Sequence Fetcher WSDBFetch@EBI
Applet can read feature files, PDB files and can be + used for HTML form input

+ + +

HTML output writes groups and features
Group editing is Control and mouse click
File IO bugs

+ + + + +

+ 2.06
28/9/05 +

+ + +

View annotations in wrapped mode
More options for PCA viewer

+ + +

GUI bugs resolved
Runs with -nodisplay from command line

+ + + + +

+ 2.05b
15/9/05 +

+ + +

Choose EPS export as lineart or text
Jar files are executable
Can read in Uracil - maps to unknown residue

+ + +

Known OutOfMemory errors give warning message
Overview window calculated more efficiently
Several GUI bugs resolved

+ + + + +

+ 2.05
30/8/05 +

+ + +

Edit and annotate in "Wrapped" view

+ + +

Several GUI bugs resolved

+ + + + +

+ 2.04
24/8/05 +

+ + +

Hold down mouse wheel & scroll to change font + size

+ + +

Improved JPred client reliability
Improved loading of Jalview files

+ + + + +

+ 2.03
18/8/05 +

+ + +

Set Proxy server name and port in preferences
Multiple URL links from sequence ids
User Defined Colours can have a scheme name and added + to Colour Menu
Choose to ignore gaps in consensus calculation
Unix users can set default web browser
Runs without GUI for batch processing
Dynamically generated Web Service Menus

+ + +

InstallAnywhere download for Sparc Solaris

+ + + + +

+ 2.02
18/7/05 +

+ + + +

Copy & Paste order of sequences maintains + alignment order.

+ + + + +

+ 2.01
12/7/05 +

+ + +

Use delete key for deleting selection.
Use Mouse wheel to scroll sequences.
Help file updated to describe how to add alignment + annotations.
Version and build date written to build properties + file.
InstallAnywhere installation will check for updates + at launch of Jalview.

+ + +

Delete gaps bug fixed.
FileChooser sorts columns.
Can remove groups one by one.
Filechooser icons installed.
Finder ignores return character when searching. + Return key will initiate a search.
+

+ + + + +

+ 2.0
20/6/05 +

+ + +

New codebase

+ + + + +