Add datamodel docs

lib/apidocs/DataModel.md

@@ -0,0 +1,87 @@
+---
+id: datamodel
+title: DataModel
+---
+
+Note: this document is automatically generated from mobx-state-tree objects in
+our source code.
+
+### Source file
+
+[src/DataModel.ts](https://github.com/GMOD/react-msaview/blob/main/lib/src/DataModel.ts)
+
+the data stored for the model. this is sometimes temporary in the case that
+e.g. msaFilehandle is available on the parent model, because then the msa
+data will not be persisted in saved session snapshots, it will be fetched
+from msaFilehandle at startup
+
+### DataModel - Properties
+#### property: msa
+
+
+
+```js
+// type signature
+IMaybe<ISimpleType<string>>
+// code
+msa: types.maybe(types.string)
+```
+
+#### property: tree
+
+
+
+```js
+// type signature
+IMaybe<ISimpleType<string>>
+// code
+tree: types.maybe(types.string)
+```
+
+#### property: treeMetadata
+
+
+
+```js
+// type signature
+IMaybe<ISimpleType<string>>
+// code
+treeMetadata: types.maybe(types.string)
+```
+
+
+
+
+
+
+
+
+### DataModel - Actions
+#### action: setMSA
+
+
+
+```js
+// type signature
+setMSA: (msa?: string) => void
+```
+
+#### action: setTree
+
+
+
+```js
+// type signature
+setTree: (tree?: string) => void
+```
+
+#### action: setTreeMetadata
+
+
+
+```js
+// type signature
+setTreeMetadata: (treeMetadata?: string) => void
+```
+
+

lib/apidocs/MsaView.md

@@ -15,23 +15,6 @@ extends
 - DialogQueueSessionMixin
 
 ### MsaView - Properties
-#### property: annotatedRegions
-
-current "annotated regions"
-
-```js
-// type signature
-IArrayType<IModelType<{ start: ISimpleType<number>; end: ISimpleType<number>; attributes: IType<Record<string, string[]>, Record<string, string[]>, Record<string, string[]>>; }, {}, _NotCustomized, _NotCustomized>>
-// code
-annotatedRegions: types.array(
-        types.model({
-          start: types.number,
-          end: types.number,
-          attributes: types.frozen<Record<string, string[]>>(),
-        }),
-      )
-```
-
 #### property: bgColor
 
 draw MSA tiles with a background color
@@ -108,26 +91,7 @@ autorun
 // type signature
 IOptionalIType<IModelType<{ tree: IMaybe<ISimpleType<string>>; msa: IMaybe<ISimpleType<string>>; treeMetadata: IMaybe<ISimpleType<string>>; }, { ...; }, _NotCustomized, _NotCustomized>, [...]>
 // code
-data: types.optional(
-        types
-          .model({
-            tree: types.maybe(types.string),
-            msa: types.maybe(types.string),
-            treeMetadata: types.maybe(types.string),
-          })
-          .actions(self => ({
-            setTree(tree?: string) {
-              self.tree = tree
-            },
-            setMSA(msa?: string) {
-              self.msa = msa
-            },
-            setTreeMetadata(treeMetadata?: string) {
-              self.treeMetadata = treeMetadata
-            },
-          })),
-        { tree: '', msa: '' },
-      )
+data: types.optional(DataModelF(), { tree: '', msa: '' })
 ```
 
 #### property: drawNodeBubbles
@@ -279,7 +243,7 @@ showBranchLen: true
 
 #### property: showOnly
 
-array of tree nodes to show (invert of collapsed)
+focus on particular subtree
 
 ```js
 // type signature
@@ -383,15 +347,6 @@ BasicTrack[]
 any
 ```
 
-#### getter: annotationTrackModels
-
-
-
-```js
-// type
-BasicTrack[]
-```
-
 #### getter: blanks
 
 
@@ -407,7 +362,7 @@ any[]
 
 ```js
 // type
-number[][]
+any[]
 ```
 
 #### getter: blocksX
@@ -416,7 +371,7 @@ number[][]
 
 ```js
 // type
-number[]
+any[]
 ```
 
 #### getter: blocksY
@@ -425,7 +380,7 @@ number[]
 
 ```js
 // type
-number[]
+any[]
 ```
 
 #### getter: boxTrackModels
@@ -549,6 +504,15 @@ boolean
 
 
 
+```js
+// type
+number
+```
+
+#### getter: maxScrollX
+
+
+
 ```js
 // type
 number
@@ -675,6 +639,15 @@ number
 
 total height of track area (px)
 
+```js
+// type
+number
+```
+
+#### getter: totalWidth
+
+
+
 ```js
 // type
 number
@@ -689,6 +662,15 @@ number
 BasicTrack[]
 ```
 
+#### getter: treeAreaWidthMinusMargin
+
+
+
+```js
+// type
+number
+```
+
 #### getter: treeMetadata
 
 
@@ -792,15 +774,6 @@ rowSpecificBpToPx: (rowName: string, position: number) => number
 
 
 ### MsaView - Actions
-#### action: addAnnotation
-
-add a new annotated region, in 'global' coordinates
-
-```js
-// type signature
-addAnnotation: (start: number, end: number, attributes: Record<string, string[]>) => void
-```
-
 #### action: addStructureToSelection
 
 add to the selected structures
@@ -819,15 +792,6 @@ addStructureToSelection: (elt: ModelCreationType<ExtractCFromProps<{ id: ISimple
 addUniprotTrack: (node: { name: string; accession: string; }) => void
 ```
 
-#### action: clearAnnotationClickBoundaries
-
-internal, used for annotation click-and-drag state
-
-```js
-// type signature
-clearAnnotationClickBoundaries: () => void
-```
-
 #### action: clearHidden
 
 
@@ -864,6 +828,15 @@ doScrollX: (deltaX: number) => void
 doScrollY: (deltaY: number) => void
 ```
 
+#### action: exportSVG
+
+
+
+```js
+// type signature
+exportSVG: (opts: { theme: Theme; includeMinimap?: boolean; exportType: string; }) => Promise<void>
+```
+
 #### action: hideNode
 
 
@@ -891,15 +864,6 @@ remove from the selected structures
 removeStructureFromSelection: (elt: ModelCreationType<ExtractCFromProps<{ id: ISimpleType<string>; structure: IModelType<{ pdb: ISimpleType<string>; startPos: ISimpleType<number>; endPos: ISimpleType<number>; }, {}, _NotCustomized, _NotCustomized>; range: IMaybe<...>; }>>) => void
 ```
 
-#### action: setAnnotationClickBoundaries
-
-internal, used for annotation click-and-drag state
-
-```js
-// type signature
-setAnnotationClickBoundaries: (left: number, right: number) => void
-```
-
 #### action: setBgColor
 
 

lib/src/DataModel.ts

@@ -0,0 +1,46 @@
+import { types } from 'mobx-state-tree'
+
+/**
+ * #stateModel DataModel
+ * the data stored for the model. this is sometimes temporary in the case that
+ * e.g. msaFilehandle is available on the parent model, because then the msa
+ * data will not be persisted in saved session snapshots, it will be fetched
+ * from msaFilehandle at startup
+ */
+export function DataModelF() {
+  return types
+    .model({
+      /**
+       * #property
+       */
+      tree: types.maybe(types.string),
+      /**
+       * #property
+       */
+      msa: types.maybe(types.string),
+      /**
+       * #property
+       */
+      treeMetadata: types.maybe(types.string),
+    })
+    .actions(self => ({
+      /**
+       * #action
+       */
+      setTree(tree?: string) {
+        self.tree = tree
+      },
+      /**
+       * #action
+       */
+      setMSA(msa?: string) {
+        self.msa = msa
+      },
+      /**
+       * #action
+       */
+      setTreeMetadata(treeMetadata?: string) {
+        self.treeMetadata = treeMetadata
+      },
+    }))
+}

lib/src/model.ts

@@ -5,6 +5,8 @@ import { hierarchy, cluster, HierarchyNode } from 'd3-hierarchy'
 import { ascending } from 'd3-array'
 import Stockholm from 'stockholm-js'
 import { saveAs } from 'file-saver'
+import { Theme } from '@mui/material'
+
 // jbrowse
 import { FileLocation, ElementId } from '@jbrowse/core/util/types/mst'
 import { FileLocation as FileLocationType } from '@jbrowse/core/util/types'
@@ -35,9 +37,9 @@ import { UniprotTrack } from './UniprotTrack'
 import { StructureModel } from './StructureModel'
 import { DialogQueueSessionMixin } from './DialogQueue'
 import { renderToSvg } from './renderToSvg'
-import { Theme } from '@mui/material'
 import { blocksX, blocksY } from './calculateBlocks'
 import measureTextCanvas from './measureTextCanvas'
+import { DataModelF } from './DataModel'
 
 export interface RowDetails {
   [key: string]: unknown
@@ -274,26 +276,7 @@ const model = types
        * data from the loaded tree/msa/treeMetadata, generally loaded by
        * autorun
        */
-      data: types.optional(
-        types
-          .model({
-            tree: types.maybe(types.string),
-            msa: types.maybe(types.string),
-            treeMetadata: types.maybe(types.string),
-          })
-          .actions(self => ({
-            setTree(tree?: string) {
-              self.tree = tree
-            },
-            setMSA(msa?: string) {
-              self.msa = msa
-            },
-            setTreeMetadata(treeMetadata?: string) {
-              self.treeMetadata = treeMetadata
-            },
-          })),
-        { tree: '', msa: '' },
-      ),
+      data: types.optional(DataModelF(), { tree: '', msa: '' }),
     }),
   )
   .volatile(() => ({