X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=485cf735ac69f009e0073038fa5444ee7897410e;hb=0865048016e68bb32886129654a5f7f6ae2d675e;hp=cc6e96c08871fd34ffb2c429872739d5d770c384;hpb=543f1be40f86e49b2981dc5b52cafbeb07c5effe;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index cc6e96c..485cf73 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -25,24 +25,24 @@
ul {
/* remove bullets, narrower indent */
list-style-type: none;
- margin:0;
+ margin: 0;
padding-left: 10px;
padding-bottom: 4px;
}
li {
/* separate the items from eachother */
- margin-left: -3px;
- padding-bottom: 3px;
- padding-left: 6px;
+ margin-left: -3px;
+ padding-bottom: 3px;
+ padding-left: 6px;
}
+
li:before {
/* doesnt get processed in javahelp */
content: '\00b7 ';
padding: 3px;
margin-left: -14px;
}
-
@@ -70,126 +70,601 @@ li:before {
|
|
|
+ |
+
+
+ |
+
+ |
+
+ Calculations
+
+
+ -
+ Occupancy annotation row shows number of
+ ungapped positions in each column of the alignment.
+
+ -
+ Tree/PCA calculation menu items merged to
+ a calculation dialog box
+
+ -
+ Revised implementation of PCA for speed
+ and memory efficiency (~30x faster)
+
+ -
+ Revised implementation of sequence
+ similarity scores as used by Tree, PCA, Shading Consensus
+ and other calculations
+
+ -
+ Score matrices are stored as resource
+ files within the Jalview codebase
+
+ -
+ Trees computed on Sequence Feature
+ Similarity may have different topology due to increased
+ precision
+
+
+ Rendering
+
+ -
+ More robust colours and shader
+ model for alignments and groups
+
+ -
+ Custom shading schemes created via groovy
+ scripts
+
+
+ Overview
+
+ -
+ Efficiency improvements for interacting
+ with alignment and overview windows
+
+ -
+ Scrolling of wrapped alignment views via
+ overview
+
+ -
+ Hidden columns and sequences can be
+ omitted in Overview
+
+ -
+ Click-drag in visible area allows fine
+ adjustment of visible position
+
+
+
+ Data import/export
- - More robust colours and shader model for alignments and groups
- - Custom shading schemes created via groovy scripts
- - linked scrolling of CDS/Protein views via Overview or sequence motif search operations
- - Efficiency improvements for interacting with alignment and overview windows
-
Posterior probability annotation from
Stockholm files imported as sequence associated annotation
+ -
+ More robust per-sequence positional
+ annotation input/output via stockholm flatfile
+
+ -
+ Sequence names don't include file
+ extension when importing structure files without embedded
+ names or PDB accessions
+
+ -
+ Drag and drop load of AAIndex and NCBI
+ format sequence substitution matrices
+
- Application
+ User Interface
-
-
- Experimental Features Checkbox in Desktop's Tools
- menu to hide or show untested features in the application.
+ Experimental Features Checkbox in
+ Desktop's Tools menu to hide or show untested features in
+ the application.
+
+ -
+ Linked scrolling of CDS/Protein views
+ via Overview or sequence motif search operations
+
+ -
+ Amend sequence features dialog box can be
+ opened by double clicking gaps within sequence feature
+ extent
+
+ -
+ Status bar message shown when not enough
+ aligned positions were available to create a 3D structure
+ superposition.
- - Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera
- - Faster Chimera/Jalview communication by file-based command exchange
- - URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB
- - Updated JABAWS client to v2.2
- Experimental features
+ 3D Structure
-
+ Hidden regions in alignment views are not
+ coloured in linked structure views
+
+ -
+ Faster Chimera/Jalview communication by
+ file-based command exchange
+
+ -
+ Structure chooser automatically shows
+ Cached Structures rather than querying the PDBe if
+ structures are already available for sequences
+
+ -
+ Structures imported via URL are cached in
+ the Jalview project rather than downloaded again when the
+ project is reopened.
+
+ -
New entries in the Chimera menu
to transfer Chimera's structure attributes as Jalview
- features, and vice-versa.
+ features, and vice-versa (Experimental
+ Feature)
- Applet
+ Web Services
+
+ -
+ Updated JABAWS client to v2.2
+
+ -
+ Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services
+
+ -
+ URLs for viewing database
+ cross-references provided by identifiers.org and the
+ EMBL-EBI's MIRIAM DB
+
+
+
+ Scripting
+
+ -
+ FileFormatI interface for describing and
+ identifying file formats (instead of String constants)
+
+ -
+ FeatureCounter script refactored for
+ efficiency when counting all displayed features (not
+ backwards compatible with 2.10.1)
+
+
+ Example files
-
+ -
+ Graduated feature colour style example
+ included in the example feature file
+
+
+ Documentation
+
+ -
+ Release notes reformatted for readability
+ with the built-in Java help viewer
+
+ -
+ Find documentation updated with 'search
+ sequence description' option
+
Test Suite
- Added PrivelegedAccessor to test suite
- Prevent or clear modal dialogs raised during tests
-
+
+ -
+ External service integration tests for
+ Uniprot REST Free Text Search Client
+
+ -
+ Added PrivilegedAccessor to test suite
+
+ -
+ Prevent or clear modal dialogs raised
+ during tests
+
- |
- General
+ |
+
+ Calculations
-
Fixed incorrect value in BLOSUM 62 score
- matrix - C->R should be '3'
Old matrix restored with
- this one-line groovy script:
jalview.schemes.ResidueProperties.BLOSUM62[4][1]=3
+ matrix - C->R should be '-3'
Old matrix restored
+ with this one-line groovy script:
jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
- -
+
-
Fixed Jalview's treatment of gaps in PCA
- and substitution matrix based Tree calculations.
In
+ and substitution matrix based Tree calculations.
In
earlier versions of Jalview, gaps matching gaps were
penalised, and gaps matching non-gaps penalised even more.
In the PCA calculation, gaps were actually treated as
- non-gaps - so different costs were applied, which mean't
+ non-gaps - so different costs were applied, which meant
Jalview's PCAs were different to those produced by
SeqSpace.
Jalview now treats gaps in the same way as
- SeqSpace (ie it scores them as 0). To restore pre-2.10.2
- behaviour
- jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
- 2.10.1 mode
- jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
- restore 2.10.2 mode
-
- - Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view
- - Hidden regions in alignment views are not coloured in linked structure views
- - Current selection lost if popup menu opened on a region of alignment without groups
- - Popup menu not always shown for regions of an alignment with overlapping groups
- - Finder double counts if both a sequence's name and description match
- - Hiding column selection containing two hidden regions results in incorrect hidden regions
- - PCA calculation could hang when generating output report when working with highly redundant alignments
- - Cannot configure feature colours with lightGray or darkGray via features file
- - Overview window visible region moves erratically when hidden rows or columns are present
- - Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring
- - Protein specific colours only offered in colour and group colour menu for protein alignments
- - 'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups
- - Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds
- - Percentage identity and conservation menu items do not show a tick or allow shading to be disabled
- - Conservation shading or PID threshold lost when base colourscheme changed if slider not visible
- - Sequence features shown in tooltip for gaps before start of features
+ SeqSpace (ie it scores them as 0).
Enter
+ the following in the Groovy console to restore pre-2.10.2
+ behaviour:
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+ // for 2.10.1 mode
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
+ // to restore 2.10.2 mode
Note:
+ these settings will affect all subsequent tree and PCA
+ calculations (not recommended)
+
+ -
+ Fixed off-by-one bug that affected
+ scaling of branch lengths for trees computed using
+ Sequence Feature Similarity.
+
+ -
+ PCA calculation could hang when
+ generating output report when working with highly
+ redundant alignments
+
+ -
+ Sort by features includes features to
+ right of selected region when gaps present on right-hand
+ boundary
+
- Application
+ User Interface
- - Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)
- - Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds
- - Feature settings panel does not update as new features are added to alignment
- - Structure viewer's View -> Colour By view selection menu changes colours of alignment views
- - Proxy server address and port always appear enabled in Preferences->Connections
- - Spurious exceptions in console raised from alignment calculation workers after alignment has been closed
- - Typo in selection popup menu - Create groups now 'Create Group'
- - CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work
- - Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'
- - DAS registry not found exceptions removed from console output
- - Above PID colour threshold not recovered when alignment view imported from project
-
+ -
+ Reopening Colour by annotation dialog
+ doesn't reselect a specific sequence's associated
+ annotation after it was used for colouring a view
+
+ -
+ Current selection lost if popup menu
+ opened on a region of alignment without groups
+
+ -
+ Popup menu not always shown for regions
+ of an alignment with overlapping groups
+
+ -
+ Finder double counts if both a sequence's
+ name and description match
+
+ -
+ Hiding column selection containing two
+ hidden regions results in incorrect hidden regions
+
+ -
+ 'Apply to all groups' setting when
+ changing colour does not apply Conservation slider value
+ to all groups
+
+ -
+ Percentage identity and conservation menu
+ items do not show a tick or allow shading to be disabled
+
+ -
+ Conservation shading or PID threshold
+ lost when base colourscheme changed if slider not visible
+
+ -
+ Sequence features shown in tooltip for
+ gaps before start of features
+
+ -
+ Graduated feature colour threshold not
+ restored to UI when feature colour is edited
+
+ -
+ Vertical scrollbar jumps one page-width at
+ a time when scrolling vertically in wrapped mode.
+
+ -
+ Structure and alignment overview update
+ as graduate feature colour settings are modified via the
+ dialog box
+
+ -
+ Overview window doesn't always update
+ when a group defined on the alignment is resized
+
+ -
+ Mouseovers on left/right scale region in
+ wrapped view result in positional status updates
+
+
+ -
+ Status bar doesn't show position for
+ ambiguous amino acid and nucleotide symbols
+
+ -
+ Copy consensus sequence failed if
+ alignment included gapped columns
+
+ -
+ Minimum size set for Jalview windows so
+ widgets don't permanently disappear
+
+ -
+ Cannot select or filter quantitative
+ annotation that are shown only as column labels (e.g.
+ T-Coffee column reliability scores)
+
+ -
+ Exception thrown if trying to create a
+ sequence feature on gaps only
+
+ -
+ Features created with 'New feature'
+ button from a Find inherit previously defined feature type
+ rather than the Find query string
+
+ -
+ incorrect title in output window when
+ exporting tree calculated in Jalview
+
+ -
+ Hiding sequences at bottom of alignment
+ and then revealing them reorders sequences on the
+ alignment
+
+ -
+ Group panel in sequence feature settings
+ doesn't update to reflect available set of groups after
+ interactively adding or modifying features
+
+ -
+ Sequence Database chooser unusable on
+ Linux
+
+ -
+ Hide insertions in PopUp->Selection menu
+ only excluded gaps in current sequence and ignored
+ selection.
+
+
+ Rendering
+
+ -
+ Overview window visible region moves
+ erratically when hidden rows or columns are present
+
+ -
+ Per-residue colourschemes applied via the
+ Structure Viewer's colour menu don't correspond to
+ sequence colouring
+
+ -
+ Protein specific colours only offered in
+ colour and group colour menu for protein alignments
+
+ -
+ Colour threshold slider doesn't update to
+ reflect currently selected view or group's shading
+ thresholds
+
+ -
+ Feature colour thresholds not respected
+ when rendered on overview and structures when opacity at
+ 100%
+
+ -
+ User defined gap colour not shown in
+ overview when features overlaid on alignment
+
+
+ Data import/export
+
+ -
+ Very large alignments take a long time to
+ load
+
+ -
+ Per-sequence RNA secondary structures
+ added after a sequence was imported are not written to
+ Stockholm File
+
+ -
+ WUSS notation for simple pseudoknots lost
+ when importing RNA secondary structure via Stockholm
+
+ -
+ Secondary structure arrows for [] and {}
+ not shown in correct direction for simple pseudoknots
+
+ -
+ Cannot configure feature colours
+ with lightGray or darkGray via features file (but can
+ specify lightgray)
+
+ -
+ Above PID colour threshold not recovered
+ when alignment view imported from project
+
+ -
+ No mappings generated between
+ structure and sequences extracted from structure files
+ imported via URL and viewed in Jmol
+
+ -
+ Structures loaded via URL are saved in
+ Jalview Projects rather than fetched via URL again when
+ the project is loaded and the structure viewed
+
+
+ Web Services
+
+ -
+ EnsemblGenomes example failing after
+ release of Ensembl v.88
+
+ -
+ Proxy server address and port always
+ appear enabled in Preferences->Connections
+
+ -
+ DAS registry not found exceptions
+ removed from console output
+
+ -
+ Cannot retrieve protein products from
+ Ensembl by Peptide ID
+
+ -
+ Incorrect PDB-Uniprot mappings
+ created from SIFTs, and spurious 'Couldn't open structure
+ in Chimera' errors raised after April 2017 update (problem
+ due to 'null' string rather than empty string used for
+ residues with no corresponding PDB mapping).
+
+
+ Application UI
+
+ -
+ User Defined Colours not added to Colour
+ menu
+
+ -
+ Easier creation of colours for all 'Lower
+ case' residues (button in colourscheme editor debugged and
+ new documentation and tooltips added)
+
+ -
+ Text colour threshold's 'Cancel' button
+ doesn't restore group-specific text colour thresholds
+
+ -
+ Feature settings panel does not update as
+ new features are added to alignment
+
+ -
+ Cancel in feature settings reverts
+ changes to feature colours via the Amend features dialog
+
+ -
+ Null pointer exception when attempting to
+ edit graduated feature colour via amend features dialog
+ box
+
+ -
+ Structure viewer's View -> Colour By view
+ selection menu changes colours of alignment views
+
+ -
+ Spurious exceptions in console raised
+ from alignment calculation workers after alignment has
+ been closed
+
+ -
+ Typo in selection popup menu - Create
+ groups now 'Create Group'
+
+ -
+ CMD/CTRL and G or Shift G for
+ Create/Undefine group doesn't always work
+
+ -
+ Tree Viewer's Print Dialog doesn't get
+ shown again after pressing 'Cancel'
+
+ -
+ Trackpad horizontal scroll gesture
+ adjusts start position in wrap mode
+
+ -
+ Status bar doesn't show positions for
+ ambiguous amino acids
+
+ -
+ cDNA Consensus annotation not shown in
+ CDS/Protein view after CDS sequences added for aligned
+ proteins
+
+ -
+ User defined colourschemes called 'User
+ Defined' don't appear in Colours menu
+
Applet
- - Features not rendered as transparent on overview or linked structure view
- - Colour group by conservation doesn't work (since 2.8)
- - Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme
+ -
+ Switching between Nucleotide and Protein
+ score models doesn't always result in an updated PCA plot
+
+ -
+ Features not rendered as transparent on
+ overview or linked structure view
+
+ -
+ Colour group by conservation doesn't
+ work (since 2.8)
+
+ -
+ Hitting Cancel after applying
+ user-defined colourscheme doesn't restore original
+ colourscheme
+
+
+ Test Suite
+
+ -
+ Unit test failure:
+ jalview.ws.jabaws.RNAStructExportImport setup fails
+
+ -
+ Unit test failure:
+ jalview.ws.sifts.SiftsClientTest due to compatibility
+ problems with deep array comparison equality asserts in
+ successive versions of TestNG
+
+ -
+ Relocated StructureChooserTest and
+ ParameterUtilsTest Unit tests to Network suite
+
New Known Issues
- - Protein/CDS view scrolling not always in phase after a sequence motif find operation
- - Status bar doesn't show positions for ambiguous amino acids
- - Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols
+ -
+ Protein/CDS view scrolling not always in
+ phase after a sequence motif find operation
+
+ -
+ Importing annotation file with rows
+ containing just upper and lower case letters are
+ interpreted as WUSS RNA secondary structure symbols
+
+ -
+ Cannot load and display Newick trees
+ reliably from eggnog Ortholog database
+
+ -
+ Status bar shows 'Marked x columns
+ containing features of type Highlight' when 'B' is pressed
+ to mark columns containing highlighted regions.
+
+ -
+ Dropping a PDB file onto a sequence
+ doesn't always add secondary structure annotation.
+
-
- |
+
|
|
@@ -200,7 +675,8 @@ li:before {
for all consensus calculations
- Jmol updated to version 14.6.4 (released 3rd Oct 2016)
+ Jmol updated to version 14.6.4 (released
+ 3rd Oct 2016)
Updated Jalview's Certum code signing certificate
for 2016-2017
@@ -228,9 +704,9 @@ li:before {
New keystroke (B) and Select highlighted
- columns menu item to mark columns containing
- highlighted regions (e.g. from structure selections or results
- of a Find operation)
+ columns menu item to mark columns containing highlighted
+ regions (e.g. from structure selections or results of a
+ Find operation)
Command line option for batch-generation
@@ -330,73 +806,78 @@ li:before {
lysozyme results in a PDB Client error dialog box
- Structure View's mapping report switched ranges for PDB and sequence for SIFTS
- SIFTS 'Not_Observed' residues mapped to non-existant coordindate data
+ Structure View's mapping report switched
+ ranges for PDB and sequence for SIFTS
+
+
+ SIFTS 'Not_Observed' residues mapped to non-existant
+ coordindate data
+
-
|
-
-
- |
- Application
+ |
+
+ |
+ Application
+
+ - 3D Structure chooser opens with 'Cached structures'
+ view if structures already loaded
+ - Progress bar reports models as they are loaded to
+ structure views
+ |
+
+
+ General
- - 3D Structure chooser opens with 'Cached structures'
- view if structures already loaded
- - Progress bar reports models as they are loaded to
- structure views
- |
-
-
- General
-
- - Colour by conservation always enabled and no tick
- shown in menu when BLOSUM or PID shading applied
- - FER1_ARATH and FER2_ARATH labels were switched in
- example sequences/projects/trees
-
- Application
-
- - Jalview projects with views of local PDB structure
- files saved on Windows cannot be opened on OSX
- - Multiple structure views can be opened and
- superposed without timeout for structures with multiple
- models or multiple sequences in alignment
- - Cannot import or associated local PDB files without
- a PDB ID HEADER line
- - RMSD is not output in Jmol console when
- superposition is performed
- - Drag and drop of URL from Browser fails for Linux
- and OSX versions earlier than El Capitan
- - ENA client ignores invalid content from ENA server
- - Exceptions are not raised in console when ENA
- client attempts to fetch non-existent IDs via Fetch DB
- Refs UI option
- - Exceptions are not raised in console when a new
- view is created on the alignment
- - OSX right-click fixed for group selections:
- CMD-click to insert/remove gaps in groups and CTRL-click
- to open group pop-up menu
-
- Build and deployment
-
- - URL link checker now copes with multi-line anchor
- tags
-
- New Known Issues
-
- - Drag and drop from URL links in browsers do not
- work on Windows
-
- |
+ Colour by conservation always enabled and no tick
+ shown in menu when BLOSUM or PID shading applied
+ FER1_ARATH and FER2_ARATH labels were switched in
+ example sequences/projects/trees
+
+ Application
+
+ - Jalview projects with views of local PDB structure
+ files saved on Windows cannot be opened on OSX
+ - Multiple structure views can be opened and superposed
+ without timeout for structures with multiple models or
+ multiple sequences in alignment
+ - Cannot import or associated local PDB files without a
+ PDB ID HEADER line
+ - RMSD is not output in Jmol console when superposition
+ is performed
+ - Drag and drop of URL from Browser fails for Linux and
+ OSX versions earlier than El Capitan
+ - ENA client ignores invalid content from ENA server
+ - Exceptions are not raised in console when ENA client
+ attempts to fetch non-existent IDs via Fetch DB Refs UI
+ option
+ - Exceptions are not raised in console when a new view
+ is created on the alignment
+ - OSX right-click fixed for group selections: CMD-click
+ to insert/remove gaps in groups and CTRL-click to open group
+ pop-up menu
+
+ Build and deployment
+
+ - URL link checker now copes with multi-line anchor
+ tags
+
+ New Known Issues
+
+ - Drag and drop from URL links in browsers do not work
+ on Windows
+
+
+
|
@@ -407,8 +888,8 @@ li:before {
| General
-
- Updated Spanish translations.
-
+ Updated Spanish translations.
+
-
Jmol now primary parser
for importing structure data to Jalview. Enables mmCIF and
@@ -698,7 +1179,7 @@ li:before {
load even when Consensus calculation is disabled
-
- Remove right on penultimate column of
+ Remove right on penultimate column of
alignment does nothing
@@ -786,7 +1267,8 @@ li:before {
Enable 'Get Cross-References' in menu
- after fetching cross-references, and restoring from project
+ after fetching cross-references, and restoring from
+ project
Mouseover of a copy of a sequence is not
@@ -851,7 +1333,8 @@ li:before {
Unable to read old Jalview projects that
contain non-XML data added after Jalvew wrote project.
- Newly created annotation row reorders
+
+ Newly created annotation row reorders
after clicking on it to create new annotation for a
column.
@@ -923,9 +1406,12 @@ li:before {
Applet
- Split frame example added to applet examples page
- Build and Deployment
+ Build and Deployment
- - New ant target for running Jalview's test suite
+ -
+ New ant target for running Jalview's test
+ suite
+
|
@@ -1313,10 +1799,10 @@ li:before {
Deployment and Documentation
+ General
+ --> Deployment and Documentation
- 2G and 1G options in launchApp have no effect on
memory allocation
@@ -1524,8 +2010,7 @@ li:before {
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
- Export/import group and sequence associated line
@@ -2154,11 +2639,6 @@ li:before {
- 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
@@ -2186,8 +2666,8 @@ li:before {
- 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
@@ -2611,11 +3091,6 @@ li:before {
- 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'
@@ -2630,11 +3105,6 @@ li:before {
- 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
@@ -2646,11 +3116,6 @@ li:before {
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
-
-
-
-
-
|