The Alignment Calculations Dialog

Extract Scores ... (optional)
This + option is only visible if Jalview detects one or more + white-space separated values in the description line of the + alignment sequences.
When selected, these numbers are + parsed into sequence associated annotation which can then be + used to sort the alignment via the Sort by→Score menu. +

Autocalculate Consensus
For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy calculations performed after @@ -614,7 +595,7 @@ in Jalview 2.8.1

'Standard Databases' will check sequences against - the EBI databases plus any active DAS sequence sources<
+ the EBI databases plus any active DAS sequence sources Other sub-menus allow you to pick a specific source to query - sources are listed alphabetically according to their nickname. diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 8032348..c7a1c87 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -53,37 +53,19 @@ window.
-

Calculate Tree
Functions - for calculating trees on the alignment or the currently selected - region. See calculating - trees. - -

Neighbour Joining Using PAM250
-
Neighbour Joining Using Sequence - Feature Similarity
Neighbour Joining Using Blosum62
-
Neighbour Joining Using % Identity
Average Distance Using PAM250
-
Average Distance Using Sequence - Feature Similarity
Average Distance Using Blosum62
Average Distance Using % Identity

Calculate Tree or PCA ...
Opens the + calculations dialog for + for calculating trees or + principle component analysis + plots on the alignment or the currently selected + region. +
+

Pairwise Alignments
Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.

Principal Component Analysis
Shows - a spatial clustering of the sequences based on similarity scores - calculated over the alignment.. See Principal Component - Analysis. -

Extract Scores ... (optional)
This option is only visible if Jalview detects one or more white-space separated values in the description line of the diff --git a/help/html/releases.html b/help/html/releases.html index 5376db8..ea9bbf5 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; } - @@ -70,20 +70,55 @@ li:before {
- 2.10.2
- 8/8/2017 + 2.10.2
8/8/2017

General
-
Revised implementation of PCA for speed and memory efficiency (~30x faster)
-
Trees computed on Sequence Feature Similarity may have different topology due to increased precision
-
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
+
+ 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 +
+
+
+
+ Tree/PCA calculation menu items merged to + a calculation dialog box +
+
+ 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 @@ -93,20 +128,74 @@ li:before { extension when importing structure files without embedded names or PDB accessions
-
Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent
-
Graduated feature colour style example included in the example feature file
+
+ Amend sequence features dialog box can be + opened by double clicking gaps within sequence feature + extent +
+
+ Graduated feature colour style example + included in the example feature file +
+
+ Occupancy annotation row shows number of + ungapped positions in each column of the alignment. +
+
+ File extension pruned from Sequence ID + for sequences derived from structure files without + embedded database accession +
+
+ Status bar message shown when not enough + aligned positions were available to create a 3D structure + superposition. +
+
+ More robust per-sequence positional + annotation input/output via stockholm flatfile +
+
Application

- - 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. +
+
+ 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 +
+
+ Drag and drop load of AAIndex and NCBI + format sequence substitution matrices +
+
+ 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.
-
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
@@ -118,25 +207,49 @@ li:before {
Applet
-
+
+ +

Test Suite
-
Added PrivilegedAccessor to test suite
-
Prevent or clear modal dialogs raised during tests
-
- Scripting -
-
FileFormatI interface for describing and identifying file formats (instead of String constants)
-
+
+ Added PrivilegedAccessor to test suite +
+
+ Prevent or clear modal dialogs raised + during tests +
+
+ External service integration tests for + Uniprot REST Free Text Search Client +
+
+ 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) +
+
+ + +

-
+
+
General

Fixed incorrect value in BLOSUM 62 score - 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 + 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 @@ -154,85 +267,380 @@ 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
-
Very large alignments take a long time to load
-
Graduated feature colour threshold not restored to UI when feature colour is edited
-
Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%
-
Structure and alignment overview update as graduate feature colour settings are modified via the dialog box
-
Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.
-
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 shows position for ambiguous amino acid and nucleotide symbols
-
Copy consensus sequence failed if alignment included gapped columns
-
User defined gap colour not shown in overview when features overlaid on alignment
-
- Documentation -
-
Release notes reformatted for readibility with the built-in Java help viewer
+
+ Fixed off-by-one bug that affected + scaling of branch lengths for trees computed using + Sequence Feature Similarity. +
+
+ 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 +
+
+ Very large alignments take a long time to + load +
+
+ Graduated feature colour threshold not + restored to UI when feature colour is edited +
+
+ Feature colour thresholds not respected + when rendered on overview and structures when opacity at + 100% +
+
+ Structure and alignment overview update + as graduate feature colour settings are modified via the + dialog box +
+
+ Vertical scrollbar jumps one page-width at + a time when scrolling vertically in wrapped mode. +
+
+ 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 shows position for ambiguous + amino acid and nucleotide symbols +
+
+ Copy consensus sequence failed if + alignment included gapped columns +
+
+ User defined gap colour not shown in + overview when features overlaid on alignment +
+
+ 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) +
+
+ Gap colours in user-defined colourschemes + are not shown +
+
+ Exception thrown if trying to create a + sequence feature on gaps only +
+
+ Sort by features includes features to + right of selected region when gaps present on right-hand + boundary +
+
+ 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 +
+
+ 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 +
+
+ 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 +
+
+ +
+
+ +
+
+ +
+
+ Documentation +
+
+ Release notes reformatted for readibility + with the built-in Java help viewer +
+
+ Find documentation updated with 'search + sequence description' option +

Application
-
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
+
+ Sequence Database chooser doesn't show + available databases panel on Linux +
+
+ EnsemblGenomes example failing after + release of Ensembl v.88 +
+
+ 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 +
+
+ 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 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
-
Trackpad horizontal scroll gesture adjusts start position in wrap mode
-
Status bar doesn't show positions for ambiguous amino acids
-
Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns
-
Cannot retrieve protein products from Ensembl by Peptide ID
-
cDNA Consensus annotation not shown in CDS/Protein view after CDS sequences added for aligned proteins
+
+ Trackpad horizontal scroll gesture + adjusts start position in wrap mode +
+
+ Status bar doesn't show positions for + ambiguous amino acids +
+
+ Hide insertions in PopUp menu excludes + gaps in selection, current sequence and only within + selected columns +
+
+ Cannot retrieve protein products from + Ensembl by Peptide ID +
+
+ cDNA Consensus annotation not shown in + CDS/Protein view after CDS sequences added for aligned + proteins +
+
+ 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). +
+ +
Applet
-
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
+
+ +
+
+ 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 +

New Known Issues
-
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
+
+ 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. +

Test Suite -
Unit test failure: jalview.ws.jabaws.RNAStructExportImport setup fails
-
+
+
+ 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 +
+
-
+ +
- 2.10.1
- 29/11/2016 + 2.10.1
29/11/2016

@@ -243,7 +651,8 @@ 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
@@ -271,9 +680,9 @@ 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 @@ -373,73 +782,78 @@ 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 + - - -
- 2.10.0b1
- 25/10/2016 -
- - Application + +
+ 2.10.0b1
+ 25/10/2016 +
+ + 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
+
+
+ @@ -450,8 +864,8 @@ li:before { General

- Updated Spanish translations. -
+ Updated Spanish translations. +
Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and @@ -741,7 +1155,7 @@ li:before { load even when Consensus calculation is disabled

- Remove right on penultimate column of + Remove right on penultimate column of alignment does nothing

@@ -829,7 +1243,8 @@ 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 @@ -894,7 +1309,8 @@ 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.
@@ -966,9 +1382,12 @@ 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 +

@@ -1356,10 +1775,10 @@ li:before { Deployment and Documentation +
+
General +
+
--> Deployment and Documentation

2G and 1G options in launchApp have no effect on memory allocation
@@ -1567,8 +1986,7 @@ 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 @@ -2197,11 +2615,6 @@ 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
@@ -2229,8 +2642,8 @@ 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 @@ -2654,11 +3067,6 @@ 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'
@@ -2673,11 +3081,6 @@ 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 @@ -2689,11 +3092,6 @@ li:before {
WsDbFetch query/result association resolved
Tree leaf to sequence mapping improved
Smooth fonts switch moved to FontChooser dialog box. - - - - -
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 8a0436d..60769a4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -32,15 +32,16 @@ highlights are below.

-
New UI, and faster and more configurable implementation for PCA, Neighbour-Joining and UPGMA Trees
+
New UI, and faster and more configurable + implementation for PCA, Neighbour-Joining and UPGMA Trees
Menu entries for calculating PCA and different types of tree have been replaced by a single Calculations dialog box. The - underlying implementation for the PCA and tree calculations have been - made faster and more memory efficient. A new framework has also been - created for the score models used to calculate distances between - sequences. This framework allows import of substitution matrices in - NCBI and AAIndex format, and custom score models to be created via a - groovy script.
+ underlying implementation for the PCA and tree calculations have + been made faster and more memory efficient. A new framework has + also been created for the score models used to calculate distances + between sequences. This framework allows import of substitution + matrices in NCBI and AAIndex format, and custom score models to be + created via a groovy script.
Update to JABAWS 2.2
Jalview's alignment, protein conservation analysis, and protein disorder and RNA secondary structure prediction services are now provided by
Find and the free + text search system (for querying Uniprot and the PDBe).

Experimental Features @@ -80,5 +84,16 @@ the Chimera viewer's Chimera menu allow positional annotation to be exchanged between Chimera and Jalview. +
+ Scripting
New groovy examples + demonstrate Jalview 2.10.2 APIs for creation of data-driven + colourschemes, and custom alignment file handlers. The FeatureAnnotationWorker + introduced in Jalview 2.10 has also been refactored to allow + efficient counting across multiple feature types. Please be aware + that feature counter scripts created for earlier versions will not + execute in Jalview 2.10.2. +
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 45988fb..d472ef8 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -4423,13 +4423,6 @@ public class Jalview2XML } // recover view properties and display parameters - if (view.getViewName() != null) - { - af.viewport.viewName = view.getViewName(); - af.setInitialTabVisible(); - } - af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), - view.getHeight()); af.viewport.setShowAnnotation(view.getShowAnnotation()); af.viewport.setAbovePIDThreshold(view.getPidSelected()); @@ -4463,6 +4456,14 @@ public class Jalview2XML af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view .isShowUnconserved() : false); af.viewport.getRanges().setStartRes(view.getStartRes()); + + if (view.getViewName() != null) + { + af.viewport.viewName = view.getViewName(); + af.setInitialTabVisible(); + } + af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), + view.getHeight()); // startSeq set in af.alignPanel.updateLayout below af.alignPanel.updateLayout(); ColourSchemeI cs = null; diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java index ec53e93..2176719 100755 --- a/src/jalview/gui/SliderPanel.java +++ b/src/jalview/gui/SliderPanel.java @@ -365,7 +365,7 @@ public class SliderPanel extends GSliderPanel } if (forConservation) { - if (!scheme.conservationApplied()) + if (!scheme.conservationApplied() && sg != null) { /* * first time the colour scheme has had Conservation shading applied diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 5a7a27f..70f16d9 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -641,6 +641,20 @@ public abstract class AlignmentViewport implements AlignViewportI, { if (getConservationSelected()) { + int retry = 0; + synchronized (this) + { + while (isCalcInProgress() && retry < 10) + { + try + { + wait(50); + retry++; + } catch (InterruptedException e) + { + } + } + } residueShading.setConservation(hconservation); } residueShading.alignmentChanged(alignment, hiddenRepSequences); diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java index 67098ae..af9c045 100644 --- a/test/jalview/gui/AlignFrameTest.java +++ b/test/jalview/gui/AlignFrameTest.java @@ -544,10 +544,11 @@ public class AlignFrameTest assertEquals(af.alignPanel.getViewName(), "View 1"); AlignViewport av2 = af.getViewport(); assertNotSame(av, av2); + assertSame(av2, af.alignPanel.av); rs = av2.getResidueShading(); assertNotSame(av.getResidueShading(), rs); assertEquals(rs.getThreshold(), 10); - assertTrue(rs.conservationApplied()); + assertTrue(rs.conservationApplied(), rs.toString()); assertEquals(rs.getConservationInc(), 20); assertEquals(av2.getAlignment().getGroups().size(), 1); sg = av2.getAlignment().getGroups().get(0);