X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=6b92a2c6b40295f16922c73be927b6e2b4fd15f9;hb=d711cefe41664274ff4c9c39c13a10c5d889284e;hp=b8ad47c9e50f7687953205823fe9086d6eb8103a;hpb=136ceaaa8e6d5fe32255dda01f15d3d0024c066b;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index b8ad47c..6b92a2c 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1,21 +1,24 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Release History
@@ -33,369 +36,576 @@
Issues Resolved
-
- |
-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 GUISupport fetching and database reference look up against multiple DAS sources
-
-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
-
-
-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
-
-
-
- |
- |
- |
+ |
+ |
+
+
+ - Trusted certificates for JalviewLite applet and
+ Jalview Desktop application
Certificate was donated by
+ Certum to the Jalview
+ open source project).
+
+ - Jalview SRS links replaced by Uniprot and EBI-search
+
+ - Output in Stockholm format
+ - Allow import of data from gzipped files
+ - Export/import group and sequence associated line
+ graph thresholds
+ - Nucleotide substitution matrix that supports RNA and
+ ambiguity codes
+ - 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
+ Other improvements
+
+ - Upgrade desktop installer to InstallAnywhere 2013
+ - COMBINE statement uses current SEQUENCE_REF and
+ GROUP_REF scope to group annotation rows
+ - Support '' style escaping of quotes in Newick
+ files
+ - Group options for JABAWS service by command line name
+ - Empty tooltip shown for JABA service options with a
+ link but no description
+ - Select primary source when selecting authority in
+ database fetcher GUI
+ - Add .mfa to FASTA file extensions recognised by
+ Jalview
+ - Annotation label tooltip text wrap
+
+ |
+
+
+ - Slow scrolling when lots of annotation rows are
+ displayed
+ - Lots of NPE (and slowness) after creating RNA
+ secondary structure annotation line
+ - Sequence database accessions not imported when
+ fetching alignments from Rfam
+ - Incorrect SHMR submission for sequences with
+ identical IDs
+ - View all structures does not always superpose
+ structures
+ - Option widgets in service parameters not updated to
+ reflect user or preset settings
+ - Null pointer exceptions for some services without
+ presets or adjustable parameters
+ - Discover PDB IDs entry in structure menu doesn't
+ discover PDB xRefs
+ - Exception encountered while trying to retrieve
+ features with DAS
+ - Lowest value in annotation row isn't coloured
+ when colour by annotation (per sequence) is coloured
+ - Keyboard mode P jumps to start of gapped region when
+ residue follows a gap
+ - Jalview appears to hang importing an alignment with
+ Wrap as default or after enabling Wrap
+ - 'Right click to add annotations' message
+ shown in wrap mode when no annotations present
+ - Disorder predictions fail with NPE if no automatic
+ annotation already exists on alignment
+ - oninit javascript function should be called after
+ initialisation completes
+ - Remove redundancy after disorder prediction corrupts
+ alignment window display
+ - Example annotation file in documentation is invalid
+ - Grouped line graph annotation rows are not exported
+ to annotation file
+ - Multi-harmony analysis cannot be run when only two
+ groups created
+ - Cannot create multiple groups of line graphs with
+ several 'combine' statements in annotation file
+ - Pressing return several times causes Number Format
+ exceptions in keyboard mode
+ - Multi-harmony (SHMMR) method doesn't submit
+ correct partitions for input data
+ - Translation from DNA to Amino Acids fails
+ - Jalview fail to load newick tree with quoted label
+ - --headless flag isn't understood
+ - 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
+
+ |
+
+
+ |
+ 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
+
+
+
+ - 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
+
+ |
+
+ |
+
+ |
+ 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
@@ -412,7 +622,7 @@
- Modeller PIR IO broken - cannot correctly import a pir
- file emitted by jalview
+ 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
@@ -459,11 +669,11 @@
1.5
- Allow Jalview feature colour specification for GFF sequence
annotation files
- - New 'colour by label' keword in jalview feature file type
+
- 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
+ operation from the Jalview command line
|
@@ -607,7 +817,7 @@
href="webServices/index.html#envision2">Envision2 Workflows
Vamsas Capabilities
- - Improved VAMSAS synchronization (jalview archive used to
+
- 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
| |