X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=d436b34d0a15ccb7e90807cc2e904eb7379fc92b;hb=5ba9b9ce2c9b6e887430d4ac80efde577ca434d4;hp=b67b69b63b47898af4dd5c052b4a34919ce9a44b;hpb=c78133920a45e1b5b0b1bea5807f3ae880425914;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index b67b69b..d436b34 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1,20 +1,21 @@
Release History
@@ -33,201 +34,457 @@
Issues Resolved
-
- |
- |
- 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
- |
-
-
+
+ |
+ |
+
+
+ - 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
+
+ |
+
+
+ |
+ 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
@@ -244,7 +501,7 @@
- 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
@@ -291,11 +548,11 @@
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
|
@@ -439,7 +696,7 @@
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
| |