X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=89a39a32698ac269d7fddac823fb99eef4d647bb;hb=c350f93c6fac69b6a8a65645f0e89e26451df146;hp=330105383188fb25083a8910b4d3542b7c063c6c;hpb=6bfa5b3f409851b020aacf1f5c033842c4b1fde8;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 3301053..89a39a3 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;
}
-
@@ -70,64 +70,203 @@ li:before {
|
- General
+ 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
+
+ -
+ Linked scrolling of CDS/Protein views
+ via Overview or sequence motif search operations
+
+ -
+ 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
- - Hidden columns and sequences can be omitted in Overview
-
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.
+
+ -
+ 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
-
+ 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
+ Feauture)
- 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 readibility
+ with the built-in Java help viewer
+
+ -
+ Find documentation updated with 'search
+ sequence description' option
+
Test Suite
- Added PrivilegedAccessor 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
@@ -135,7 +274,7 @@ li:before {
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
@@ -145,63 +284,366 @@ li:before {
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
- - Sequence position for ambiguous codon not shown in status bar
+ -
+ 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
- - No mappings generated between structure and sequences extracted from structure files imported via URL
+ -
+ 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
+
+ -
+ Hidden regions in alignment views are not
+ coloured in linked structure views
+
+ -
+ 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 Newick trees 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.
+
-
-
- |
+
|
@@ -212,7 +654,8 @@ 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
@@ -240,9 +683,9 @@ 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
@@ -342,73 +785,78 @@ 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
+
+
+
@@ -419,8 +867,8 @@ li:before {
| General
-
- Updated Spanish translations.
-
+ Updated Spanish translations.
+
-
Jmol now primary parser
for importing structure data to Jalview. Enables mmCIF and
@@ -710,7 +1158,7 @@ li:before {
load even when Consensus calculation is disabled
-
- Remove right on penultimate column of
+ Remove right on penultimate column of
alignment does nothing
@@ -798,7 +1246,8 @@ 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
@@ -863,7 +1312,8 @@ 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.
@@ -935,9 +1385,12 @@ 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
+
|
@@ -1325,10 +1778,10 @@ li:before {
Deployment and Documentation
+ General
+ --> Deployment and Documentation
- 2G and 1G options in launchApp have no effect on
memory allocation
@@ -1536,8 +1989,7 @@ 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
@@ -2166,11 +2618,6 @@ 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
@@ -2198,8 +2645,8 @@ 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
@@ -2623,11 +3070,6 @@ 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'
@@ -2642,11 +3084,6 @@ 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
@@ -2658,11 +3095,6 @@ li:before {
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
-
-
-
-
-
|