- Default
trackWidth
removed fromRcsbFvPairwiseAlignment
.
- rcsb-saguaro v3.1.4
- Group Fv tab bug fix
- rcsb-saguaro v3.1.1
- Default
trackWidth
config was removed. The track length will be defined based on the root container
- rcsb-saguaro v3.1.0
- audit fix
- audit fix
- Source taxonomy histogram to barchart
- Old
METAL_COORDINATION
features ignored
MountableComponent
bug fix
- Avoid creating duplicated components in
MountableComponent
- rcsb-saguaro v3.0.9
- rcsb-api-tools v4.3.0
- rcsb-charts v0.2.24
- audit fix
- Multiple dependencies have been updated
- New ligand binding sites annotations
labelList
is no loger an attribute ofRcsbChartInterface
. The logic behind this attribute has been moved torcsb-search-tools
package. Multi-faceting search data will contain alabelPath
list indicating the facets labels
- rcsb-search-tools v0.0.14
- Group carousel resolution single decimal point
- New track builder
UnmodeledTrackBuilder
that merges unmodeled tracks from instances
- rcsb-charts v0.2.23
- audit fix
- rcsb-saguaro v3.0.7
- Multiple dependencies have been updated
- rcsb-api-tools v4.1.14
- Chimeric histogram changed to Taxonomy Sources
- Histogram ranges bounds included when ranges converge
- rcsb-charts v0.2.22
- Added new UniProt histograms:
DISEASE_FACET
,PHENOTYPE_FACET
andINTERPRO_FACET
plot
package exposesRcsbRequestContextManager
- rcsb-saguaro v3.0.7
- rcsb-saguaro v3.0.6
- v6.0.5 duplication
- rcsb-saguaro v3.0.5
- rcsb-saguaro v3.0.4
SingleFacets
cyclic dependency bug fixed
FacetMemberInterface.facetConfig
interface attribute to encode histogram data transformations and other configurationfacetTransform
can be used to transform Search API facets into other facetsbucketClickSearchQuery
can be used to overwrite bucket click eventsmergeDomainMaxValue
has been moved fromFacetMemberInterface.chartConfig
CHIMERIC_FACET
New facet histogram to display wild type vs chimeric protein group distribution
MultipleEntryPropertyCollector
includes polymer entity prd ids
- Types are not anymore exposed from
build/src
- All module classes and types are accessible from
lib/
- Modules format is
ESNext
lib/commonjs
exposes all modules inCommonJS
format
- Modules format is
- Class
RcsbFvTooltip
implements the Sequence Annotation Tooltip element - Interface
RcsbFvTrackDataAnnotationInterface
extendsRcsbFvTrackDataElementInterface
- The main purpose is to encode metadata and sequence annotation regions from the original reference
- This interface has been moved from rcsb-saguaro
MultipleEntryPropertyCollector
includes non-polymer entity to instance and instance to operator relationships
- Sass @import changed to @use
- Styles sheets
scss
refactoring - font-awsome replaced by boxicons
- Multiple dependencies have been updated
- rcsb-saguaro v3.0.3
- Group UI text mod
- Group UI text mod
- Group UI text mod
- bootstrap-icons to @fortawesome/fontawesome-free
- Group UI titles camel-cased
RcsbRequestTools.getMultipleObjectProperties
return all values bug fixed
RcsbRequestContextManager
maps store promises- Simplified
RcsbRequestTools
- New type
ChartObjectIdType
to identify included and excluded distribution areas in group summary pages - Strict typed
FacetMemberInterface.attribute
andRcsbChartInterface.attribute
toRcsbSearchAttributeType
- Histograms based on ChatJS
- tooltip and axis ticks added to the facet store items
- Using rcsb-search-tools
- Search requests use rcsb-search-tools methods
FacetTools.ts
SearchQueryTools.ts
- rcsb-charts v0.2.21
- rcsb-saguaro v2.5.12
- rcsb-api-tools v4.1.13
- Multiple dependencies updated
- Uniprot unknown annotation type bug fixed
- Uniprot Group Alignment bug fixed
- Removing gap columns in group views
mergeTrackBuilders
new method to merge track builders
- Uniprot Entity pLDDT filter bug fixed
- Improved performance of track logo generation
- Avoid overlap check for annotation area and block-area tracks and alignment tracks
- Duplicated cache bug fix
- Support for single logo request in sequence groups view
- Next page cache in sequence groups view
- Fix npm tag
- New builder for external data providers
buildDataProviderFv
- Exposed track factories
GroupChartEvents.clickEvent
callsSearchQueryContextManager.updateSearchQuery
to add the new histogram/bar condition to the current query- Only
SearchQueryContextManager
trigger the observers callingSearchQueryContextManager.next
RcsbGroupSearchQueryComponent
constructor initializesSearchQueryContextManager
configuration
externalUiComponents
exposes two attributesadd
to provide additionalUiComponentType
componentsreplace
to replace defaultUiComponentType
for external ones
buildInstanceSequenceFv
parameterInstanceSequenceConfig.defaultValue
points to label_asym_id instead of label_auth_idtrackConfigModifier.alignment
includes the full alignment responseAlignmentResponse
and alignment member index as parametersTagDelimiter
has been moved to@rcsb/rcsb-api-tools
module
- tsc strictNullChecks true
- Using rcsb-charts
- rcsb-saguaro v2.5.9
- Missing white space
- Removed 1D3D link in entry groups
- Auditing vulnerabilities
- Auditing vulnerabilities
- Auditing vulnerabilities
- Cache entity collisions fixed
- rcsb-saguaro v2.5.8
- Uniprot Group Alignment entity track title color bug fix
- Uniprot Group Alignment pagination
- rcsb-saguaro v2.5.5
- No changes. Published mistake
- SearchQuery propagated trough group carousel link
- Page button is not rendered in single page MSA
RcsbFvGroupAlignmentBuilder
additionalConfig.page
bug fixed
- Enabling 1D-3D Alignment link for Sequence Identity carousels
- External filters are available for annotations and alignments. Filters are applied in collector methods
- rcsb-saguaro v2.5.4
- Exposed configuration
RcsbFvAdditionalConfig.externalUiComponents
to add external UI elements. Currently, only available forbuildSequenceIdentityAlignmentFv
- Exposed group histogram layout configuration
GroupChartAdditionalProperties.layoutConfig
. Currently, it includes the histogram title (string|undefined
)
RcsbFvGroupAlignment
display aligned track using observed/unobserved and local scores color codes
UniprotAlignmentTrackFactory
renamed toMsaAlignmentTrackFactory
- External track Alignment Variation memory leak bug fixed
- rcsb-api-tools v4.1.1
- Victory tooltip
dx
attribute has been decreased to avoid tooltip disappear in Safari
- rcsb-saguaro v2.2.16
- Removed SwissModel packages
buildSequenceIdentityAlignmentFv
boardConfig
overwriting bug fixed
- Exposed
buildSequenceIdentityAlignmentFv
to display sequence identity group alignments
buildUniprotMultipleEntitySequenceFv
boardConfig
overwriting bug fixed
- rcsb-saguaro v2.2.15
- rcsb-saguaro v2.2.14
- rcsb-saguaro v2.2.13
- rcsb-saguaro v2.2.12
- rcsb-saguaro v2.2.11
- rcsb-saguaro v2.2.10
- rcsb-saguaro v2.2.9
- rcsb-saguaro v2.2.8
- rcsb-saguaro v2.2.7
TagDelimiter
exposes methods to parse RCSB PDB object identifiers- Removed alignment element sorting
- Large alignments lists do not block dropdown buttons
RcsbGroupWeb.RcsbResidueChart
new package to display residue properties histograms- It can display any positional feature at entry and instance level
- It cannot filter properties
ChartConfigInterface.chartDisplayConfig
allows to overwriteCharTools
display properties (sizes, padding, fontsize, ...)
AnnotationCollector
class does not format collected data anymore. The only responsibility of this class is to dispatch positional featuresSeqeunceCollector
class has been renamed toAlignmentCollector
and it does not format data anymore. The only responsibility of this class is to dispatch alignment dataRcsbFvFactories
is a new package to format data from the 1d-coordinate sever into track configuration objectsRcsbFvRowConfigInterface
. Tracks are grouped in blocks. In most cases one block represents alignments and a second block positional featuresRcsvFvBlockFactoryInterface
functional interface that defines a block factoryBlockManager
package defines the logic of how positional features are organized into tracks
RcsvFvTrackFactoryInterface
functional interface that defines a track factoryWebTools
package renamed toRcsbFvComponents
- Class
SelectButtonManager
abstracts creation of select dropdown menus- Dropdowns menu are fake-unmounted using
Root::render(undefined)
- Dropdowns menu are fake-unmounted using
ChartTools
readonly static attributes are not public anymore.ChartTools.getConfig
allows to getCharTools
attributes
- rcsb-saguaro v2.2.6
- React 18
- Multiple dependencies updated
- Client initializers were not overwriting
rcsbRequestClient
attributes RcsbCoreQueryInterface::client
attribute has been converted togetClient
function that returns the actual client. The function is passed as a constructor parameterSearchRequestProperty::client
attribute has been converted togetClient
function that returns the actual client. The function is passed as a constructor parameter
- rcsb-api-tools v4.0.4
- Moving request configuration methods
initializeBorregoClient
,initializeYosemiteClient
andinitializeArchesClient
intoRcsbRequestContextManager
- Exposing request configuration methods
initializeBorregoClient
,initializeYosemiteClient
andinitializeArchesClient
- Alignments are not sorted by default.
BuildAlignmentsInterface
provides configuration for sorting.
- Dropdown change callbacks include the module object (
RcsbFvModulePublicInterface
)
- Builder methods returned objets
RcsbFvModulePublicInterface
update their attributes when dropdown changes update PFV content - Dropdown change callbacks pass the whole
PolymerEntityInstanceInterface
object
- Checking undefined
RcsbFvAdditionalConfig
inbuildUniprotMultipleEntitySequenceFv
- Exposing optional parameter
UniprotSequenceConfig
inbuildMultipleAlignmentSequenceFv
method to define dropdown changes callbacks - Exposing optional parameter
RcsbFvAdditionalConfig
inbuildMultipleAlignmentSequenceFv
method
- Including ASA buried filter in UniProt instance module
- rcsb-api-tools v4.0.1
- rcsb-saguaro v2.0.6
- Histogram visualization of RCSB PDB search API
RcsbSearch
new package to communicate with RCSB Search APIRcsbFvUI
new package to build UI menusRcsbChartWeb
new package to display histogram chartsRcsbGroupWeb
new package to display RCSB PDB Group web components
- rcsb-api-tools v4.0.0
- rcsb-saguaro v2.0.5
- Context manager
rcsbFvCtxManager
is only responsible for handling PFVs - New Context manager
rcsbRequestCtxManager
responsible for API requests- All API requests should be done through this class (currently, not happening)
- rcsb-saguaro update 2.0.4
- rcsb-api-tools update 3.0.2
- Auditing vulnerabilities
- Minor type fix in react-select. New select option type
SelectOptionProps
InstanceSequenceConfig
external methods defined inselectButtonOptionProps
do not need to importcomponents.Option
from react-select. TheSelectButton
class will include it as a children component
- Minor type fix in react-select
- Minor type fix
- Minor type fix
- react-select type definition fixed
- Multiple dependencies updated
- rcsb-api-tools v2.3.1
- Added interface
CollectAnnotationsInterface
for generating new annotations internally (not exposed)annotationGenerator?(annotations: Array<AnnotationFeatures>)
generates new annotations from the collected onesannotationFilter?(annotations: Array<AnnotationFeatures>)
filter the collected annotations- Both methods are called before annotations processing and thus, they should be configured in
RcsbAnnotationConfig.ac.json
or equivalent config file - Checking content before adding generated features
- New callback attribute
InstanceSequenceConfig
>beforeChangeCallback
. This function is called when instance dropdown menu changes and before rendering the new 1D RcsbFv. The callback may return aRcsbContextType
object that will be included in theadditionalConfig
- Added two new classes (
AssemblyInterfacesCollector
andAssemblyInterfacesTranslate
) to collect and handle assembly and interface id relationships - Exposing all feature types in a single object
FeatureType
(file:src/RcsbExport/FeatureType.ts
) - New package
RcsbExport
to expose classes and methods outside the library ExternalTrackBuilderInterface
methods return a promise and are executed asynchronous
- Exposed methods for creating dropdown menus. Class
RcsbFvUI
static methodscreateSelectButton
creates a select dropdown menuaddSelectButton
adds a second menu. Only an additional button can be created (replaced if a new one is created)clearSelectButton
clear all menus
- Removed interface
CollectAnnotationsInterface
attributeNameaddTargetInTitle
- Added
titleSuffix
andtrackTitle
attributes toCollectAnnotationsInterface
- These new attributes are defined as async functions (ann: AnnotationFeatures, d: Feature) => Promise<string|undefined> to provide or modify track titles based on the features content
- New
RcsbFvInterface
module- Interface
InstanceSequenceConfig
provides a new attributemodule
to choose between theRcsbFvInstance
or RcsbFvInterface` modules
- Interface
- New classes to collect and translate instance/interface ids relationships from data api
RcsbQueryInterfaceInstances
,InterfaceInstanceCollector
andInterfaceInstanceTranslate
- Dropdown title configuration is exposed in
InstanceSequenceConfig
attributeNamedropdownTitle
RcsbFvAdditionalConfig
missing inRcsbFvBuilder.buildMultipleInstanceSequenceFv
fixed
ExternalTrackBuilderInterface
available throughRcsbFvAdditionalConfig
for allRcsbFvBuilder
types In addition, it includes the query context as additional parameter for processing and addition methodsprocessAlignmentAndFeatures
includes the query context as part of the input parametersaddTo
includes the query context as part of the input parametersfilterFeatures
new method for filtering positional featuresfilterAlignments
new method for filtering alignment data
Changed setTimeout
calls to 'rxjs' asyncScheduler
- rcsb-saguaro update 2.0.0
AnnotationCollectorInterface
new annotation features gettergetAnnotationFeatures
ExternalTrackBuilderInterface
interface to build tracks from the collected annotations and alignmentsSequenceCollectorInterface
new alignment response gettergetAlignmentResponse
SequenceCollectorInterface
collect
method accepts a new optional argumentfilter?:Array<string>
to filter targets in the alignment- No more
Map
inheritance inAnnotationTrack
. Now it delegatesMap
methods - rcsb-saguaro update 1.11.0
- Using rcsb-api-tools
- Loader spinner added
- rcsb-saguaro update 1.10.1
STEREO_OUTLIER
pin display
STEREO_OUTLIER
andPEPTIDE
config added
AnnotationTrack
annotationConfig
bug fixed
SequenceCollectorInterface
collect
bug fixed
- Annotation multidimensional value support
- Disorder and hydropathy tracks
- rcsb-saguaro-api update 2.1.0
- Fixed unchecked
annotationConfig
null - Added display for
CALCIUM_BINDING_REGION
- Fixed duplication of annotations in UniProt modules
- rcsb-saguaro-api update
- New class
AnnotationTrackManager
to process and format track annotations - Support for multiple
AnnotationConfigInterface
- Antibody and domain DBs config added
merged_types
defines the annotation display priority when multiple annotations share the same location
- UniProt with no PDB bug fixed
- Removed all Group/Search API related methods
- Inheritance to composition for collector classes
- async/await promise style
- Recursive waits migrated to rxjx Observables
- PFV unique building method
- Context Manager rcsbFv build new board config param
- Select button default value title bug fixed
- rcsb-saguaro update 1.8.4
- RcsbFvWebApp.setBoardConfig and RcsbFvWebApp.getRcsbFv have been removed.
- Custom board config must be defined in RcsbFvAdditionalConfig (Some RcsbFvWebApp methods do not support additional configs yet)
- Builder methods return RcsbFvModulePublicInterface
- RcsbRequestContextManager never duplicates requests. It tracks individual request status ("available"|"pending")
- rcsb-saguaro update 1.8.1
- PFAM config added
- Mogul track height
- Mogul config bug fixed
- Mogul outliers transformed to continuous
- New annotation type MEMBRANE_SEGMENT
- ignore annotation type attributeName bug fixed
- Undefined end in block elements bug fixed
- Typed types
- New class AnnotationTrack transforms Feature into RcsbFvTrackDataElementInterface
- Added commented code to handle FeaturePositionValue as Arrays
Dependency update
- rcsb-saguaro update 1.8.0
Dependency update
- rcsb-saguaro update 1.7.4
- Displaying nucleic (non-protein) entities/instances
- Track configuration attributeName "ignore" can be used to ignore annotations based on its type
- rcsb-saguaro update 1.7.3
- open_end attributeName bug fixed
- Instance default value bug fixed
- Composite merging bug fixed
- New tracks merged
- New annotation map property displayCooccurrence avoids merging positional co-occurrent features
- rcsb-saguaro update 1.6.0
- rcsb-saguaro update 1.5.1
- rcsb-saguaro update 1.5.0
- rcsb-saguaro update 1.4.1
- rcsb-saguaro update 1.4.0
- rcsb-saguaro update 1.3.0
- rcsb-saguaro update 1.2.1
- rcsb-saguaro update 1.2.0
- Chromosome Fv Module: fixed null/empty sequence bug
- rcsb-saguaro update
- Track instance related title changed to X[auth Y]
- Initial release