@rcsb/rcsb-saguaro-app 4.0.2 → 4.0.6

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rcsb/rcsb-saguaro-app",
-  "version": "4.0.2",
+  "version": "4.0.6",
   "description": "RCSB 1D Saguaro Web App",
   "main": "build/dist/app.js",
   "files": [
@@ -17,7 +17,7 @@
     "tsc": "tsc",
     "clean": "del-cli build/*json build/src",
     "cleanAll": "npm run clean && del-cli build/dist",
-    "buildDoc": "npx typedoc ./src/RcsbFv.ts && sed -i '' '/---/d' docs/index.html",
+    "buildDoc": "npx typedoc ./src/app.ts && sed -i '' '/---/d' docs/index.html",
     "cpExamples": "ncp examples docs/examples",
     "buildAllDoc": "npm run buildDoc && npm run cpExamples",
     "test": "echo \"Error: no test specified\" && exit 1"
@@ -49,7 +49,6 @@
     "@types/lodash": "^4.14.176",
     "@types/react": "^17.0.39",
     "@types/react-dom": "^17.0.11",
-    "@types/react-select": "^5.0.1",
     "babel-loader": "^8.1.0",
     "bootstrap": "^5.1.3",
     "css-loader": "^6.5.1",
@@ -60,7 +59,6 @@
     "react": "^17.0.2",
     "react-bootstrap": "^2.1.2",
     "react-dom": "^17.0.2",
-    "react-select": "^5.2.2",
     "sass": "^1.43.5",
     "sass-loader": "^12.3.0",
     "style-loader": "^3.3.1",
@@ -77,6 +75,7 @@
     "@rcsb/rcsb-api-tools": "^3.0.0",
     "@rcsb/rcsb-saguaro": "^2.0.1",
     "ideogram": "^1.33.0",
+    "react-select": "^5.2.2",
     "rxjs": "^6.6.0"
   },
   "bugs": {

package/CHANGELOG.md

@@ -1,262 +0,0 @@
-# RCSB Saguaro App Changelog
-
-[Semantic Versioning](https://semver.org/)
-
-## [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` attribute `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` attribute `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
-- RcsbFvContextManager 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 attribute 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 attribute "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 attribute 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 <b>displayCooccurrence</b> 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 and Dependency update
-- rcsb-saguaro update
-- Chromosome Fv Module: fixed null/empty sequence bug
-
-## [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