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Package detail

@rcsb/rcsb-saguaro-app

rcsb1.6kMIT6.4.1TypeScript support: included

RCSB 1D Saguaro Web App

1D, viewer, sequence, annotations, gene, protein, PDB, RCSB, UniProt

readme

rcsb-saguaro-app

RCSB Saguaro Web Application is an open-source library built on the top of the RCSB Saguaro 1D Feature Viewer and designed to display protein features at the RCSB Web Site. The package collects protein annotations from the 1D Coordinate Server and the main RCSB Data API and generates preconfigures Protein Feature Summaries. The package allows access to RCSB Saguaro methods to add or change displayed data.

When using rcsb-saguaro, please cite:

Joan Segura, Yana Rose, John Westbrook, Stephen K Burley, Jose M Duarte. RCSB Protein Data Bank 1D tools and services, Bioinformatics, 2020; https://doi.org/10.1093/bioinformatics/btaa1012

Node Module Installation

npm install @rcsb/rcsb-saguaro-app

CDN JavaScript

<script src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@6.0.0/build/app.min.js" type="text/javascript"></script>

Testing

  • npm install
  • npm run devServer
  • Go to http://localhost:9000/UniprotGroupFv.html

JavaScript Examples

The full collection of examples can be edit and modified at CODEPEN

Library Documentation

TypeScript classes documentation can be found here.

Main Class and Methods

RcsbFvWebApp calss provides a collection of methods to display preconfigured features over PDB and UniProt sequences as displayed at RCSB PDB web site. Additionally, it allows to configure board size and set up feature click events.

  • RcsbFvWebApp.buildUniprotFv(elementId: string, upAcc: string)
  • RcsbFvWebApp.buildEntityFv(elementId: string, entityId: string)
  • RcsbFvWebApp.buildInstanceFv(elementId: string, instanceId: string)
  • RcsbFvWebApp.buildUniprotEntityFv(elementId: string, upAcc: string, entityId: string)
  • RcsbFvWebApp.buildUniprotEntityInstanceFv(elementId: string, upAcc: string, entityId: string, instanceId: string)

  • RcsbFvWebApp.setBoardConfig(boardConfigData: RcsbFvBoardConfigInterface)

  • RcsbFvWebApp.getRcsbFv(elementId: string)

GraphQL configuration

Building TypeScript interfaces
  • Files ["src/RcsbServerConfig/codegen.borrego.json", "src/RcsbServerConfig/codegen.yosemite.json"]
  • Borrego Interfaces: graphql-codegen --config src/RcsbServerConfig/codegen.borrego.json
  • Yosemite Interfaces: graphql-codegen --config src/RcsbServerConfig/codegen.yosemite.json
  • Generated Sources: "src/RcsbGraphQL/Types"
    IntelliJ schemas
  • Config Files: ["src/RcsbGraphQL/Queries/Borrego/.graphqlconfig", "src/RcsbGraphQL/Queries/Yosemite/.graphqlconfig"]
  • Generated Schemas: ["src/RcsbGraphQL/Queries/Borrego/schema.graphql", "src/RcsbGraphQL/Queries/Yosemite/schema.graphql"]

New RCSB data-api request method

  • A new graphql query defined in src/RcsbGraphQL/Queries/Yosemite (e.g. QueryAssemblyInterfaces.graphql)
  • A new request class using rcsb-api-tools defined in src/RcsbGraphQL (e.g. RcsbQueryAssemblyInterfaces.ts)
  • A new method in the RcsbClient class defined in src/RcsbGraphQL/RcsbClient.ts (e.g. requestAssemblyInterfaces)
    • This method must used the request class defined above
  • A new collector class based on the request class in src/RcsbCollectTools/Translators (e.g. AssemblyInterfacesCollector)
    • This class must call the method defined above
    • This class may transform the RCSB data-api schema into a more convenient interface
  • A new translator class defined in src/RcsbUtils (e.g. AssemblyInterfacesTranslate)
    • The constructor gets the data collected by the above class
    • The class exposes the methods needs to provide the relationships between RCSB objects of different granularity
  • A new method in the RcsbRequestContextManager defined in src/RcsbFvWeb/RcsbFvBuilder
    • This method must avoid duplicate requests

Testing

Different testing example are available in the src/RcsbFvExamples folder

  • npm install
  • npm run devServer

Go to:

  • http://localhost:9000/EntitySummaryFv.html
  • http://localhost:9000/InstanceSequenceFv.html
  • http://localhost:9000/UniprotGroupFv.html ...

Contributing

All contributions are welcome. Please, make a pull request or open an issue.

License

The MIT License

Copyright (c) 2019 - now, RCSB PDB and contributors

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

changelog

RCSB Saguaro App Changelog

Semantic Versioning

[6.4.1] - 2025-05-20

Dependency update

  • rcsb-api-tools v5.1.1

[6.4.0] - 2025-05-20

Improvements

  • IHM support

Dependency update

  • rcsb-api-tools v5.1.0

[6.3.11] - 2025-04-08

Improvements

  • Next page caching for group-alignments view
  • Concurrent alignments and annotations for group-annotations view

[6.3.10] - 2025-04-03

Bug Fix

  • Global Binding Site track counting bug fixed

[6.3.9] - 2025-04-03

Configuration

  • Uniprot group view does not compute sequence-variation track

Bug Fix

  • Uniprot group view does not remove alignment gaps

[6.3.8] - 2025-04-02

Improvements

  • Group carouse dynamic min-height style
  • Local icons
  • Group alignment filter by instance-id

Dependency update

  • rcsb-api-tools v5.0.0
  • rcsb-search-tools v0.0.15
  • audit fix
  • Updated all dependencies

[6.3.7] - 2025-01-29

Configuration

  • Track name config

[6.3.6] - 2025-01-28

Configuration

  • New validation features

[6.3.5] - 2025-01-14

Bug fix

  • Try to fix empty artifact

[6.3.4] - 2025-01-14

Configuration

  • Suppress new validation data

[6.3.3] - 2024-11-01

Configuration

  • Default trackWidth removed from RcsbFvPairwiseAlignment.

[6.3.2] - 2024-10-04

Dependency update

  • rcsb-saguaro v3.1.4

[6.3.1] - 2024-10-03

Bug fix

  • Group Fv tab bug fix

Dependency update

  • rcsb-saguaro v3.1.1

[6.3.0] - 2024-09-26

Configuration

  • Default trackWidth config was removed. The track length will be defined based on the root container

Dependency update

  • rcsb-saguaro v3.1.0

[6.2.6] - 2024-09-12

Dependency update

  • audit fix

[6.2.5] - 2024-08-23

Dependency update

  • audit fix

[6.2.4] - 2024-08-23

Configuration

  • Source taxonomy histogram to barchart
  • Old METAL_COORDINATION features ignored

    Bug fix

  • MountableComponent bug fix

[6.2.3] - 2024-08-22

Improvement

  • Avoid creating duplicated components in MountableComponent

[6.2.2] - 2024-08-21

Dependency update

  • rcsb-saguaro v3.0.9
  • rcsb-api-tools v4.3.0
  • rcsb-charts v0.2.24
  • audit fix
  • Multiple dependencies have been updated

[6.2.1] - 2024-08-20

Configuration

  • New ligand binding sites annotations

[6.2.0] - 2024-08-20

Minor Refactor

  • labelList is no loger an attribute of RcsbChartInterface. The logic behind this attribute has been moved to rcsb-search-tools package. Multi-faceting search data will contain a labelPath list indicating the facets labels

Dependency update

  • rcsb-search-tools v0.0.14

[6.1.1] - 2024-07-23

Improvement

  • Group carousel resolution single decimal point

[6.1.0] - 2024-05-16

New feature

  • New track builder UnmodeledTrackBuilder that merges unmodeled tracks from instances

[6.0.14] - 2024-04-02

Dependency update

  • rcsb-charts v0.2.23
  • audit fix

[6.0.13] - 2024-03-06

Dependency update

  • rcsb-saguaro v3.0.7
  • Multiple dependencies have been updated

[6.0.12] - 2024-02-09

Dependency update

  • rcsb-api-tools v4.1.14

[6.0.11] - 2024-01-30

Display

  • Chimeric histogram changed to Taxonomy Sources

Bug fix

  • Histogram ranges bounds included when ranges converge

Dependency update

  • rcsb-charts v0.2.22

[6.0.10] - 2024-01-12

Improvement

  • Added new UniProt histograms: DISEASE_FACET, PHENOTYPE_FACET and INTERPRO_FACET

[6.0.9] - 2024-01-10

Improvement

  • plot package exposes RcsbRequestContextManager

[6.0.8] - 2023-12-07

Dependency update

  • rcsb-saguaro v3.0.7

[6.0.7] - 2023-12-07

Dependency update

  • rcsb-saguaro v3.0.6

[6.0.6] - 2023-12-07

Deprecated

  • v6.0.5 duplication

[6.0.5] - 2023-11-30

Dependency update

  • rcsb-saguaro v3.0.5

[6.0.4] - 2023-11-29

Dependency update

  • rcsb-saguaro v3.0.4

[6.0.3] - 2023-11-28

Bug fix

  • SingleFacets cyclic dependency bug fixed

[6.0.2] - 2023-11-28

Improvement

  • FacetMemberInterface.facetConfig interface attribute to encode histogram data transformations and other configuration
    • facetTransform can be used to transform Search API facets into other facets
    • bucketClickSearchQuery can be used to overwrite bucket click events
    • mergeDomainMaxValue has been moved from FacetMemberInterface.chartConfig
  • CHIMERIC_FACET New facet histogram to display wild type vs chimeric protein group distribution

[6.0.1] - 2023-11-27

Improvement

  • MultipleEntryPropertyCollector includes polymer entity prd ids

[6.0.0] - 2023-11-22

Breaking changes

  • 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 in CommonJS format

Improvement

  • Class RcsbFvTooltip implements the Sequence Annotation Tooltip element
  • Interface RcsbFvTrackDataAnnotationInterface extends RcsbFvTrackDataElementInterface
    • 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

Code refactoring

  • Sass @import changed to @use
  • Styles sheets scss refactoring
  • font-awsome replaced by boxicons

Dependency update

  • Multiple dependencies have been updated
  • rcsb-saguaro v3.0.3

[5.1.5] - 2023-09-18

Display

  • Group UI text mod

[5.1.4] - 2023-09-13

Display

  • Group UI text mod

[5.1.3] - 2023-09-13

Display

  • Group UI text mod

[5.1.2] - 2023-09-12

Refactoring

  • bootstrap-icons to @fortawesome/fontawesome-free
  • Group UI titles camel-cased

Bug fix

  • RcsbRequestTools.getMultipleObjectProperties return all values bug fixed

[5.1.1] - 2023-09-08

Code refactoring

  • RcsbRequestContextManager maps store promises
  • Simplified RcsbRequestTools

[5.1.0] - 2023-09-07

Improvement

  • New type ChartObjectIdType to identify included and excluded distribution areas in group summary pages
  • Strict typed FacetMemberInterface.attribute and RcsbChartInterface.attribute to RcsbSearchAttributeType
  • Histograms based on ChatJS
  • tooltip and axis ticks added to the facet store items

    Refactoring

  • Using rcsb-search-tools
  • Search requests use rcsb-search-tools methods
    • FacetTools.ts
    • SearchQueryTools.ts

      Dependency update

  • rcsb-charts v0.2.21

[5.0.8] - 2023-07-11

Dependency update

  • rcsb-saguaro v2.5.12
  • rcsb-api-tools v4.1.13
  • Multiple dependencies updated

[5.0.7] - 2023-05-16

Bug fix

  • Uniprot unknown annotation type bug fixed

[5.0.6] - 2023-05-16

Bug fix

  • Uniprot Group Alignment bug fixed

[5.0.5] - 2023-05-09

Improvements

  • Removing gap columns in group views
  • mergeTrackBuilders new method to merge track builders

    Bug fix

  • Uniprot Entity pLDDT filter bug fixed

[5.0.4] - 2023-05-03

Improvements

  • Improved performance of track logo generation
  • Avoid overlap check for annotation area and block-area tracks and alignment tracks

[5.0.3] - 2023-05-02

Bug fix

  • Duplicated cache bug fix

[5.0.2] - 2023-04-27

Improvements

  • Support for single logo request in sequence groups view
  • Next page cache in sequence groups view

[5.0.1] - 2023-04-25

No changes

  • Fix npm tag

[5.0.0] - 2023-04-25

New Features

  • New builder for external data providers buildDataProviderFv
  • Exposed track factories

Refactoring

  • GroupChartEvents.clickEvent calls SearchQueryContextManager.updateSearchQuery to add the new histogram/bar condition to the current query
  • Only SearchQueryContextManager trigger the observers calling SearchQueryContextManager.next
  • RcsbGroupSearchQueryComponent constructor initializes SearchQueryContextManager configuration

Breaking changes

  • externalUiComponents exposes two attributes
    • add to provide additional UiComponentType components
    • replace to replace default UiComponentType for external ones
  • buildInstanceSequenceFv parameter InstanceSequenceConfig.defaultValue points to label_asym_id instead of label_auth_id
  • trackConfigModifier.alignment includes the full alignment response AlignmentResponse and alignment member index as parameters TagDelimiter has been moved to @rcsb/rcsb-api-tools module

Improvements

  • tsc strictNullChecks true

Dependency update

  • Using rcsb-charts
  • rcsb-saguaro v2.5.9

[4.5.14] - 2023-04-12

Bug fix

  • Missing white space

[4.5.13] - 2023-04-12

Bug fix

  • Removed 1D3D link in entry groups

    Dependency update

  • Auditing vulnerabilities

[4.5.12] - 2023-03-02

Dependency update

  • Auditing vulnerabilities

[4.5.11] - 2023-03-02

Dependency update

  • Auditing vulnerabilities

[4.5.10] - 2023-03-02

Bug fix

  • Cache entity collisions fixed

[4.5.9] - 2023-01-20

Dependency update

  • rcsb-saguaro v2.5.8

[4.5.8] - 2022-12-09

Bug fix

  • Uniprot Group Alignment entity track title color bug fix

[4.5.7] - 2022-12-05

Display improvement

  • Uniprot Group Alignment pagination

[4.5.6] - 2022-11-28

Dependency update

  • rcsb-saguaro v2.5.5

[4.5.5] - 2022-11-28

No change

  • No changes. Published mistake

[4.5.4] - 2022-11-23

Bug fix

  • SearchQuery propagated trough group carousel link

[4.5.3] - 2022-11-23

Bug fix

  • Page button is not rendered in single page MSA
  • RcsbFvGroupAlignmentBuilder additionalConfig.page bug fixed

[4.5.2] - 2022-11-23

Improvement

  • Enabling 1D-3D Alignment link for Sequence Identity carousels

[4.5.1] - 2022-11-23

Improvement

  • External filters are available for annotations and alignments. Filters are applied in collector methods

    Dependency update

  • rcsb-saguaro v2.5.4

[4.5.0] - 2022-11-10

Improvement

  • Exposed configuration RcsbFvAdditionalConfig.externalUiComponents to add external UI elements. Currently, only available for buildSequenceIdentityAlignmentFv

[4.4.16] - 2022-11-04

Display improvement

  • Exposed group histogram layout configuration GroupChartAdditionalProperties.layoutConfig. Currently, it includes the histogram title (string|undefined)

[4.4.15] - 2022-11-03

Display improvement

  • RcsbFvGroupAlignment display aligned track using observed/unobserved and local scores color codes

    Minor refactor

  • UniprotAlignmentTrackFactory renamed to MsaAlignmentTrackFactory

    Bug fix

  • External track Alignment Variation memory leak bug fixed
  • Dependency update

  • rcsb-api-tools v4.1.1

[4.4.14] - 2022-10-17

Minor display

  • Victory tooltip dx attribute has been decreased to avoid tooltip disappear in Safari

[4.4.13] - 2022-10-17

Dependency update

  • rcsb-saguaro v2.2.16

Update

  • Removed SwissModel packages

[4.4.12] - 2022-10-07

Bug fix

  • buildSequenceIdentityAlignmentFv boardConfig overwriting bug fixed

[4.4.11] - 2022-10-07

Improvement

  • Exposed buildSequenceIdentityAlignmentFv to display sequence identity group alignments

[4.4.10] - 2022-09-23

Bug fix

  • buildUniprotMultipleEntitySequenceFv boardConfig overwriting bug fixed

[4.4.9] - 2022-09-13

Dependency update

  • rcsb-saguaro v2.2.15

[4.4.8] - 2022-09-13

Dependency update

  • rcsb-saguaro v2.2.14

[4.4.7] - 2022-09-13

Dependency update

  • rcsb-saguaro v2.2.13

[4.4.6] - 2022-09-13

Dependency update

  • rcsb-saguaro v2.2.12

[4.4.5] - 2022-09-12

Dependency update

  • rcsb-saguaro v2.2.11

[4.4.4] - 2022-09-12

Dependency update

  • rcsb-saguaro v2.2.10

[4.4.3] - 2022-09-06

Dependency update

  • rcsb-saguaro v2.2.9

[4.4.2] - 2022-09-06

Dependency update

  • rcsb-saguaro v2.2.8

[4.4.1] - 2022-09-01

Dependency update

  • rcsb-saguaro v2.2.7

[4.4.0] - 2022-08-31

Improvements

  • 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 overwrite CharTools display properties (sizes, padding, fontsize, ...)

Code refactoring

  • AnnotationCollector class does not format collected data anymore. The only responsibility of this class is to dispatch positional features
  • SeqeunceCollector class has been renamed to AlignmentCollector and it does not format data anymore. The only responsibility of this class is to dispatch alignment data
  • RcsbFvFactories is a new package to format data from the 1d-coordinate sever into track configuration objects RcsbFvRowConfigInterface. Tracks are grouped in blocks. In most cases one block represents alignments and a second block positional features
  • RcsvFvBlockFactoryInterface functional interface that defines a block factory
    • BlockManager package defines the logic of how positional features are organized into tracks
  • RcsvFvTrackFactoryInterface functional interface that defines a track factory
  • WebTools package renamed to RcsbFvComponents
  • Class SelectButtonManager abstracts creation of select dropdown menus
    • Dropdowns menu are fake-unmounted using Root::render(undefined)
  • ChartTools readonly static attributes are not public anymore.
    • ChartTools.getConfig allows to get CharTools attributes

Dependency update

  • rcsb-saguaro v2.2.6
  • React 18
  • Multiple dependencies updated

[4.3.6] - 2022-05-26

Bug fixes

  • Client initializers were not overwriting rcsbRequestClient attributes
  • RcsbCoreQueryInterface::client attribute has been converted to getClient function that returns the actual client. The function is passed as a constructor parameter
  • SearchRequestProperty::client attribute has been converted to getClient function that returns the actual client. The function is passed as a constructor parameter

[4.3.5] - 2022-05-20

Dependency update

  • rcsb-api-tools v4.0.4

[4.3.4] - 2022-05-20

Improvements

  • Moving request configuration methods initializeBorregoClient, initializeYosemiteClient and initializeArchesClient into RcsbRequestContextManager

[4.3.3] - 2022-05-18

Improvements

  • Exposing request configuration methods initializeBorregoClient, initializeYosemiteClient and initializeArchesClient

[4.3.2] - 2022-05-05

Improvements

  • Alignments are not sorted by default. BuildAlignmentsInterface provides configuration for sorting.

[4.3.1] - 2022-04-25

Improvements

  • Dropdown change callbacks include the module object (RcsbFvModulePublicInterface)

[4.3.0] - 2022-04-22

Improvements

  • Builder methods returned objets RcsbFvModulePublicInterface update their attributes when dropdown changes update PFV content
  • Dropdown change callbacks pass the whole PolymerEntityInstanceInterface object

[4.2.2] - 2022-04-20

Bug fixes

  • Checking undefined RcsbFvAdditionalConfig in buildUniprotMultipleEntitySequenceFv

[4.2.1] - 2022-04-20

Improvement

  • Exposing optional parameter UniprotSequenceConfig in buildMultipleAlignmentSequenceFv method to define dropdown changes callbacks
  • Exposing optional parameter RcsbFvAdditionalConfig in buildMultipleAlignmentSequenceFv method

[4.1.3] - 2022-04-20

Display improvement

  • Including ASA buried filter in UniProt instance module

[4.1.2] - 2022-04-14

Dependency update

  • rcsb-api-tools v4.0.1

[4.1.1] - 2022-04-14

Dependency update

  • rcsb-saguaro v2.0.6

[4.1.0] - 2022-04-13

New features

  • Histogram visualization of RCSB PDB search API
    • RcsbSearch new package to communicate with RCSB Search API
    • RcsbFvUI new package to build UI menus
    • RcsbChartWeb new package to display histogram charts
    • RcsbGroupWeb new package to display RCSB PDB Group web components

Dependency update

  • rcsb-api-tools v4.0.0
  • rcsb-saguaro v2.0.5

Code refactoring

  • 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)

[4.0.7] - 2022-04-07

Dependency update

  • rcsb-saguaro update 2.0.4
  • rcsb-api-tools update 3.0.2
  • Auditing vulnerabilities

[4.0.6] - 2022-02-15

Minor bug fix

  • Minor type fix in react-select. New select option type SelectOptionProps
  • InstanceSequenceConfig external methods defined in selectButtonOptionProps do not need to import components.Option from react-select. The SelectButton class will include it as a children component

[4.0.5] - 2022-02-15

Minor bug fix

  • Minor type fix in react-select

[4.0.4] - 2022-02-15

Minor bug fix

  • Minor type fix

[4.0.4] - 2022-02-15

Minor bug fix

  • Minor type fix

[4.0.3] - 2022-02-14

Minor bug fix

  • react-select type definition fixed

[4.0.2] - 2022-02-14

Dependency update

  • Multiple dependencies updated

[4.0.1] - 2022-02-08

Dependency update

  • rcsb-api-tools v2.3.1

[4.0.0] - 2022-02-08

Annotation collector improvements

  • Added interface CollectAnnotationsInterface for generating new annotations internally (not exposed)
    • annotationGenerator?(annotations: Array<AnnotationFeatures>) generates new annotations from the collected ones
    • annotationFilter?(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 a RcsbContextType object that will be included in the additionalConfig
  • Added two new classes (AssemblyInterfacesCollector and AssemblyInterfacesTranslate) 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

[3.4.0] - 2021-12-07

UI improvements

  • Exposed methods for creating dropdown menus. Class RcsbFvUI static methods
    • createSelectButton creates a select dropdown menu
    • addSelectButton adds a second menu. Only an additional button can be created (replaced if a new one is created)
    • clearSelectButton clear all menus

[3.3.0] - 2021-11-30

Annotations configuration improvements

  • Removed interface CollectAnnotationsInterface attributeName addTargetInTitle
  • Added titleSuffix and trackTitle attributes to CollectAnnotationsInterface
    • 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 attribute module to choose between the RcsbFvInstance or RcsbFvInterface` modules
  • New classes to collect and translate instance/interface ids relationships from data api
    • RcsbQueryInterfaceInstances, InterfaceInstanceCollector and InterfaceInstanceTranslate

[3.2.1] - 2021-11-10

Minor configuration

  • Dropdown title configuration is exposed in InstanceSequenceConfig attributeName dropdownTitle

[3.1.1] - 2021-11-02

Bug fix

  • RcsbFvAdditionalConfig missing in RcsbFvBuilder.buildMultipleInstanceSequenceFv fixed

[3.1.0] - 2021-10-27

External track builder improvements

  • ExternalTrackBuilderInterface available through RcsbFvAdditionalConfig for all RcsbFvBuilder types In addition, it includes the query context as additional parameter for processing and addition methods
    • processAlignmentAndFeatures includes the query context as part of the input parameters
    • addTo includes the query context as part of the input parameters
    • filterFeatures new method for filtering positional features
    • filterAlignments new method for filtering alignment data

[3.0.0] - 2021-10-15

Minor code refactor

Changed setTimeout calls to 'rxjs' asyncScheduler

Breaking changes

  • rcsb-saguaro update 2.0.0

[2.4.0] - 2021-10-08

Minor code refactor and improvements

  • AnnotationCollectorInterface new annotation features getter getAnnotationFeatures
  • ExternalTrackBuilderInterface interface to build tracks from the collected annotations and alignments
  • SequenceCollectorInterface new alignment response getter getAlignmentResponse
  • SequenceCollectorInterface collect method accepts a new optional argument filter?:Array<string> to filter targets in the alignment
  • No more Map inheritance in AnnotationTrack. Now it delegates Map methods
  • rcsb-saguaro update 1.11.0

[2.3.6] - 2021-10-04

Dependency update

  • Using rcsb-api-tools

[2.3.5] - 2021-09-16

Display Improvement

  • Loader spinner added
  • rcsb-saguaro update 1.10.1

[2.3.4] - 2021-08-30

Display config

  • STEREO_OUTLIER pin display

[2.3.3] - 2021-08-30

Display config

  • STEREO_OUTLIER and PEPTIDE config added

[2.3.2] - 2021-08-30

Bug correction

  • AnnotationTrack annotationConfig bug fixed

[2.3.1] - 2021-08-24

Bug correction

  • SequenceCollectorInterface collect bug fixed

[2.3.0] - 2021-08-24

Improvements

  • Annotation multidimensional value support
  • Disorder and hydropathy tracks
  • rcsb-saguaro-api update 2.1.0

[2.2.2] - 2021-08-23

Bug correction

  • Fixed unchecked annotationConfig null
  • Added display for CALCIUM_BINDING_REGION

[2.2.1] - 2021-08-20

Bug correction

  • Fixed duplication of annotations in UniProt modules
  • rcsb-saguaro-api update

[2.2.0] - 2021-08-12

Code refactor

  • New class AnnotationTrackManager to process and format track annotations
  • Support for multiple AnnotationConfigInterface

[2.1.0] - 2021-08-11

Display config

  • Antibody and domain DBs config added
  • merged_types defines the annotation display priority when multiple annotations share the same location

[2.0.2] - 2021-07-19

Bug correction

  • UniProt with no PDB bug fixed

[2.0.1] - 2021-07-16

Code cleaning

  • Removed all Group/Search API related methods

[2.0.0] - 2021-07-16

Code refactor, deprecations and bug fixes

  • 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

    Breaking changes

  • 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

[1.4.8] - 2021-06-15

Optimization

  • RcsbRequestContextManager never duplicates requests. It tracks individual request status ("available"|"pending")

[1.4.7] - 2021-06-14

Dependency update

  • rcsb-saguaro update 1.8.1

[1.4.6] - 2021-06-09

Display config

  • PFAM config added

[1.4.5] - 2021-06-03

Bug fix

  • Mogul track height

[1.4.4] - 2021-06-03

Bug fix

  • Mogul config bug fixed

[1.4.3] - 2021-06-03

Data display

  • Mogul outliers transformed to continuous
  • New annotation type MEMBRANE_SEGMENT

[1.4.2] - 2021-06-03

Bug fix

  • ignore annotation type attributeName bug fixed

[1.4.1] - 2021-06-02

Bug fix

  • Undefined end in block elements bug fixed

[1.4.0] - 2021-06-02

Improvements

  • Typed types
  • New class AnnotationTrack transforms Feature into RcsbFvTrackDataElementInterface
  • Added commented code to handle FeaturePositionValue as Arrays

[1.3.2] - 2021-05-31

Improvements

Dependency update

  • rcsb-saguaro update 1.8.0

[1.3.1] - 2021-05-31

Improvements

Dependency update

  • rcsb-saguaro update 1.7.4

[1.3.0] - 2021-05-18

Improvements

  • Displaying nucleic (non-protein) entities/instances
  • Track configuration attributeName "ignore" can be used to ignore annotations based on its type

[1.2.3] - 2021-05-13

Dependency update

  • rcsb-saguaro update 1.7.3

[1.2.2] - 2021-04-30

Bug fix

  • open_end attributeName bug fixed
  • Instance default value bug fixed

[1.2.1] - 2021-04-28

Bug fix and data display config

  • Composite merging bug fixed
  • New tracks merged

[1.2.0] - 2021-04-28

Dependency update and config improvement

  • New annotation map property displayCooccurrence avoids merging positional co-occurrent features
  • rcsb-saguaro update 1.6.0

[1.1.9] - 2021-04-22

Dependency update

  • rcsb-saguaro update 1.5.1

[1.1.8] - 2021-04-21

Dependency update

  • rcsb-saguaro update 1.5.0

[1.1.7] - 2021-04-19

Dependency update

  • rcsb-saguaro update 1.4.1

[1.1.6] - 2021-04-19

Dependency update

  • rcsb-saguaro update 1.4.0

[1.1.5] - 2021-04-15

Dependency update

  • rcsb-saguaro update 1.3.0

[1.1.4] - 2021-02-23

Dependency update

  • rcsb-saguaro update 1.2.1

[1.1.3] - 2021-03-29

Dependency update

  • rcsb-saguaro update 1.2.0

[1.1.2] - 2021-03-25

Bug fix

  • Chromosome Fv Module: fixed null/empty sequence bug

    Dependency update

  • rcsb-saguaro update

[1.1.1] - 2021-02-23

Data display

  • Track instance related title changed to X[auth Y]

[1.1.0] - 2021-02-23

General

  • Initial release