react-msaview 9.4.0 → 9.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/bundle/index.js +58 -58
- package/bundle/index.js.map +3 -3
- package/dist/components/MSAViewer.d.ts +2 -8
- package/dist/components/header/menuBarItems.js +1 -4
- package/dist/components/header/menuBarItems.js.map +1 -1
- package/dist/constants.d.ts +0 -1
- package/dist/constants.js +0 -1
- package/dist/constants.js.map +1 -1
- package/dist/model/treeModel.d.ts +0 -9
- package/dist/model/treeModel.js +1 -12
- package/dist/model/treeModel.js.map +1 -1
- package/dist/model.d.ts +4 -8
- package/dist/model.js +3 -7
- package/dist/model.js.map +1 -1
- package/dist/svgTestUtil.d.ts +2 -8
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +3 -3
- package/src/components/header/menuBarItems.ts +0 -4
- package/src/constants.ts +0 -1
- package/src/model/treeModel.ts +0 -13
- package/src/model.ts +3 -7
- package/src/version.ts +1 -1
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@@ -141,7 +141,7 @@ export interface MSAViewerProps {
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* of those props changes and keeps its model across every other change,
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* including a new annotation file. A `ref` holds the current model.
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*/
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declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.RefAttributes<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "
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declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.RefAttributes<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
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drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
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@@ -152,7 +152,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
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drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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}, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
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bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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@@ -548,7 +547,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
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setDrawNodeBubbles(arg: boolean): void;
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setDrawNodeLabels(arg: boolean): void;
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setShowTreeOverview(arg: boolean): void;
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setShowTreeScaleBar(arg: boolean): void;
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setDrawLabels(arg: boolean): void;
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} & {
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setColorSchemeName(name: string): void;
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@@ -969,7 +967,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
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}): void;
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fitHorizontally(maxColWidth?: any): void;
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afterCreate(): void;
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} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "
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} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
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drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
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@@ -980,7 +978,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
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drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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}, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
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bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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@@ -1376,7 +1373,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
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setDrawNodeBubbles(arg: boolean): void;
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setDrawNodeLabels(arg: boolean): void;
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setShowTreeOverview(arg: boolean): void;
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setShowTreeScaleBar(arg: boolean): void;
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setDrawLabels(arg: boolean): void;
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} & {
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setColorSchemeName(name: string): void;
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@@ -1813,7 +1809,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
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drawNodeBubbles: boolean;
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drawNodeLabels: boolean;
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showTreeOverview: boolean;
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showTreeScaleBar: boolean;
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overviewHeight: number;
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columnTracks: ColumnTrackSpec[];
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id: string;
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@@ -1953,7 +1948,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
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drawNodeBubbles: boolean;
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drawNodeLabels: boolean;
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showTreeOverview: boolean;
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showTreeScaleBar: boolean;
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overviewHeight: number;
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columnTracks?: undefined;
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id: string;
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@@ -118,7 +118,7 @@ function outgroupLabel(outgroup) {
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: `Outgroup ${first} … ${rest.at(-1)}`;
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}
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export function treeSubMenu(model) {
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const { drawTree, showBranchLen, labelsAlignRight, drawNodeLabels, drawLabels, treeAreaWidth, showTreeOverview,
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const { drawTree, showBranchLen, labelsAlignRight, drawNodeLabels, drawLabels, treeAreaWidth, showTreeOverview, treeOrder, treeRoot, rotated, } = model;
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return [
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subMenu('Layout', [
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radio('Phylogram', drawTree && showBranchLen, () => {
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@@ -136,9 +136,6 @@ export function treeSubMenu(model) {
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toggle('Tree overview', showTreeOverview, arg => {
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model.setShowTreeOverview(arg);
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}),
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toggle('Scale bar', showTreeScaleBar, arg => {
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model.setShowTreeScaleBar(arg);
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}),
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subMenu('Order', [
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...treeOrders.map(order => radio(treeOrderLabels[order], treeOrder === order, () => {
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model.setTreeOrder(order);
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@@ -1 +1 @@
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+
{"version":3,"file":"menuBarItems.js","sourceRoot":"","sources":["../../../src/components/header/menuBarItems.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,EAAE,sBAAsB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AACvE,OAAO,EAAE,OAAO,EAAE,MAAM,uBAAwB,CAAA;AAChD,OAAO,EAAE,eAAe,EAAE,MAAM,yBAA0B,CAAA;AAC1D,OAAO,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAA;AAChE,OAAO,EAAE,sBAAsB,EAAE,MAAM,yBAAyB,CAAA;AAOhE,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA4B,CAAC,CAAC,CAAA;AACpE,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,+BAAgC,CAAC,CAAC,CAAA;AAC5E,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,kCAAmC,CAAC,CAClD,CAAA;AACD,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,0BAA2B,CAAC,CAAC,CAAA;AAClE,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,0BAA2B,CAAC,CAAC,CAAA;AAClE,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA+B,CAAC,CAAC,CAAA;AAE1E,MAAM,YAAY,GAAG,wCAAwC,CAAA;AAE7D,SAAS,KAAK,CAAC,KAAa,EAAE,OAAgB,EAAE,OAAmB;IACjE,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,OAAgB,EAAE,OAAO,EAAE,OAAO,EAAE,CAAA;AAC5D,CAAC;AAED,SAAS,MAAM,CAAC,KAAa,EAAE,OAAgB,EAAE,GAA2B;IAC1E,OAAO;QACL,KAAK;QACL,IAAI,EAAE,UAAmB;QACzB,OAAO;QACP,OAAO,EAAE,GAAG,EAAE;YACZ,GAAG,CAAC,CAAC,OAAO,CAAC,CAAA;QACf,CAAC;KACF,CAAA;AACH,CAAC;AAED,SAAS,MAAM,CAAC,KAAa,EAAE,OAAmB,EAAE,QAAQ,GAAG,KAAK;IAClE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAA;AACrC,CAAC;AAED,SAAS,OAAO,CAAC,KAAa,EAAE,KAAiB,EAAE,OAAuB;IACxE,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,SAAkB,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,CAAA;AACrE,CAAC;AAED,SAAS,IAAI,CAAI,IAAa,EAAE,KAAU;IACxC,OAAO,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,KAAmB;IAC/C,OAAO;QACL,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,EAAE;YAC1B,MAAM,CAAC,iBAAiB,EAAE,GAAG,EAAE;gBAC7B,KAAK,CAAC,KAAK,EAAE,CAAA;YACf,CAAC,CAAC;SACH,CAAC;QACF,sBAAsB,CAAC,KAAK,CAAC;QAC7B,MAAM,CAAC,gBAAgB,EAAE,GAAG,EAAE;YAC5B,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,eAAe,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,CAAA;QACrE,CAAC,CAAC;QACF,GAAG,IAAI,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE;YAC1B,MAAM,CAAC,uBAAuB,EAAE,GAAG,EAAE;gBACnC,KAAK,CAAC,YAAY,EAAE,CAAA;YACtB,CAAC,CAAC;SACH,CAAC;QACF,MAAM,CAAC,iBAAiB,EAAE,GAAG,EAAE;YAC7B,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,cAAc,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;QACpE,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,KAAmB;IACtC,OAAO;QACL,MAAM,CAAC,SAAS,EAAE,GAAG,EAAE;YACrB,KAAK,CAAC,MAAM,EAAE,CAAA;QAChB,CAAC,CAAC;QACF,MAAM,CAAC,UAAU,EAAE,GAAG,EAAE;YACtB,KAAK,CAAC,OAAO,EAAE,CAAA;QACjB,CAAC,CAAC;QACF,MAAM,CAAC,eAAe,EAAE,GAAG,EAAE;YAC3B,KAAK,CAAC,GAAG,EAAE,CAAA;QACb,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,GAAG,EAAE;YACvB,KAAK,CAAC,eAAe,EAAE,CAAA;QACzB,CAAC,CAAC;QACF,MAAM,CAAC,YAAY,EAAE,GAAG,EAAE;YACxB,KAAK,CAAC,aAAa,EAAE,CAAA;QACvB,CAAC,CAAC;QACF,MAAM,CAAC,YAAY,EAAE,GAAG,EAAE;YACxB,KAAK,CAAC,SAAS,EAAE,CAAA;QACnB,CAAC,CAAC;QACF,MAAM,CAAC,eAAe,EAAE,KAAK,CAAC,UAAU,EAAE,GAAG,CAAC,EAAE;YAC9C,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC1B,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,GAAG,CAAC,GAAG,EAAE,EAAE,EAAE,EAAE,CAAC,CAAA;AAEhC,MAAM,UAAU,WAAW,CAAC,KAAmB;IAC7C,MAAM,EAAE,QAAQ,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,MAAM,GAAG,QAAQ,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,gBAAgB,CAAC,CAAA;IACjE,OAAO;QACL,OAAO,CACL,eAAe,EACf;YACE,KAAK,CAAC,kBAAkB,EAAE,CAAC,QAAQ,EAAE,GAAG,EAAE;gBACxC,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;YAC1B,CAAC,CAAC;YACF,GAAG,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CACtB,KAAK,CACH,GAAG,KAAK,GAAG,CAAC,CAAC,CAAC,2BAA2B,CAAC,CAAC,CAAC,SAAS,GAAG,QAAQ,EAChE,QAAQ,IAAI,gBAAgB,KAAK,GAAG,EACpC,GAAG,EAAE;gBACH,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACvB,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;YAChC,CAAC,CACF,CACF;YACD;gBACE,GAAG,KAAK,CACN,MAAM,CAAC,CAAC,CAAC,SAAS,gBAAgB,SAAS,CAAC,CAAC,CAAC,mBAAmB,EACjE,MAAM,EACN,GAAG,EAAE;oBACH,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;oBACvB,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,kBAAkB;wBAClB,EAAE,KAAK,EAAE,OAAO,EAAE;qBACnB,CAAC,CAAA;gBACJ,CAAC,CACF;gBACD,YAAY,EAAE,KAAK;aACpB;SACF,EACD,QAAQ,CACT;KACF,CAAA;AACH,CAAC;AAED,MAAM,eAAe,GAA8B;IACjD,YAAY,EAAE,kBAAkB;IAChC,KAAK,EAAE,aAAa;IACpB,SAAS,EAAE,+BAA+B;IAC1C,gBAAgB,EAAE,+BAA+B;CAClD,CAAA;AAED,SAAS,aAAa,CAAC,QAAkB;IACvC,MAAM,CAAC,KAAK,EAAE,GAAG,IAAI,CAAC,GAAG,QAAQ,CAAA;IACjC,OAAO,IAAI,CAAC,MAAM,KAAK,CAAC;QACtB,CAAC,CAAC,YAAY,KAAK,EAAE;QACrB,CAAC,CAAC,YAAY,KAAK,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;AAC1C,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAmB;IAC7C,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,cAAc,EACd,UAAU,EACV,aAAa,EACb,gBAAgB,EAChB,SAAS,EACT,QAAQ,EACR,OAAO,GACR,GAAG,KAAK,CAAA;IACT,OAAO;QACL,OAAO,CACL,QAAQ,EACR;YACE,KAAK,CAAC,WAAW,EAAE,QAAQ,IAAI,aAAa,EAAE,GAAG,EAAE;gBACjD,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACvB,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;YAC9B,CAAC,CAAC;YACF,KAAK,CAAC,WAAW,EAAE,QAAQ,IAAI,CAAC,aAAa,EAAE,GAAG,EAAE;gBAClD,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACvB,KAAK,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;YAC/B,CAAC,CAAC;YACF,KAAK,CAAC,aAAa,EAAE,CAAC,QAAQ,EAAE,GAAG,EAAE;gBACnC,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;YAC1B,CAAC,CAAC;SACH,EACD,WAAW,CACZ;QACD,MAAM,CAAC,eAAe,EAAE,gBAAgB,EAAE,GAA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|
package/dist/constants.d.ts
CHANGED
|
@@ -46,7 +46,6 @@ export declare const defaultDrawTree = true;
|
|
|
46
46
|
export declare const defaultDrawNodeBubbles = true;
|
|
47
47
|
export declare const defaultDrawNodeLabels = false;
|
|
48
48
|
export declare const defaultShowTreeOverview = false;
|
|
49
|
-
export declare const defaultShowTreeScaleBar = false;
|
|
50
49
|
export declare const defaultOverviewHeight = 120;
|
|
51
50
|
export declare const maxNeighborJoiningRows = 500;
|
|
52
51
|
export declare const rowTintAlpha = 0.25;
|
package/dist/constants.js
CHANGED
|
@@ -93,7 +93,6 @@ export const defaultDrawTree = true;
|
|
|
93
93
|
export const defaultDrawNodeBubbles = true;
|
|
94
94
|
export const defaultDrawNodeLabels = false;
|
|
95
95
|
export const defaultShowTreeOverview = false;
|
|
96
|
-
export const defaultShowTreeScaleBar = false;
|
|
97
96
|
export const defaultOverviewHeight = 120;
|
|
98
97
|
// Neighbor joining does not run above this many rows. The distance matrix is
|
|
99
98
|
// O(n^2*L) and the join loop O(n^3), both on the main thread with no progress
|
package/dist/constants.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"constants.js","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAEA,sBAAsB;AACtB,MAAM,CAAC,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAClC,MAAM,CAAC,MAAM,eAAe,GAAG,EAAE,CAAA;AACjC,MAAM,CAAC,MAAM,aAAa,GAAG,GAAG,CAAA;AAChC,iFAAiF;AACjF,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC,CAAA;AAClC,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,uBAAuB,GAAG,CAAC,CAAA;AACxC,0EAA0E;AAC1E,2BAA2B;AAC3B,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAA;AACtC,MAAM,CAAC,MAAM,uBAAuB,GAAG,IAAI,CAAA;AAC3C,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAA;AACnC,MAAM,CAAC,MAAM,uBAAuB,GAAG,GAAG,CAAA;AAC1C,MAAM,CAAC,MAAM,qBAAqB,GAAG,KAAK,CAAA;AAC1C,2EAA2E;AAC3E,kEAAkE;AAClE,MAAM,CAAC,MAAM,mBAAmB,GAAG,CAAC,CAAA;AACpC,uEAAuE;AACvE,MAAM,CAAC,MAAM,qBAAqB,GAAG,CAAC,CAAA;AAEtC,yEAAyE;AACzE,8EAA8E;AAC9E,wCAAwC;AACxC,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,GAAG,CAAC;IACzC,MAAM;IACN,KAAK;IACL,gBAAgB;IAChB,iBAAiB;IACjB,KAAK;IACL,QAAQ;CACT,CAAC,CAAA;AAEF,6DAA6D;AAC7D,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;AACnD,MAAM,CAAC,MAAM,qBAAqB,GAAG,IAAI,CAAA;AACzC,MAAM,CAAC,MAAM,iBAAiB,GAAG,KAAK,CAAA;AAEtC,gFAAgF;AAChF,yEAAyE;AACzE,+BAA+B;AAC/B,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,MAAM,EAAE,YAAY,EAAE,UAAU,CAAU,CAAA;AAEzE,MAAM,CAAC,MAAM,qBAAqB,GAAmB,MAAM,CAAA;AAE3D,8EAA8E;AAC9E,2EAA2E;AAC3E,yCAAyC;AACzC,MAAM,CAAC,MAAM,kBAAkB,GAAG,CAAC,CAAA;AACnC,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC,CAAA;AAElC,+EAA+E;AAC/E,sEAAsE;AACtE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAA;AAEvC,+EAA+E;AAC/E,0EAA0E;AAC1E,mDAAmD;AACnD,MAAM,CAAC,MAAM,qBAAqB,GAAG,CAAC,CAAA;AAEtC,MAAM,UAAU,WAAW,CAAC,SAAiB;IAC3C,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,SAAS,GAAG,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;AACjD,CAAC;AAED,2EAA2E;AAC3E,8EAA8E;AAC9E,uCAAuC;AACvC,MAAM,CAAC,MAAM,gBAAgB,GAAG,WAAW,CAAC,gBAAgB,CAAC,CAAA;AAE7D,+EAA+E;AAC/E,iFAAiF;AACjF,0BAA0B;AAC1B,MAAM,CAAC,MAAM,WAAW,GAAG,GAAG,CAAA;AAC9B,MAAM,CAAC,MAAM,YAAY,GAAG,GAAG,CAAA;AAC/B,MAAM,CAAC,MAAM,WAAW,GAAG,EAAE,CAAA;AAE7B,+DAA+D;AAC/D,MAAM,CAAC,MAAM,kBAAkB,GAAG,GAAG,CAAA;AAErC,qBAAqB;AACrB,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAA;AAClC,MAAM,CAAC,MAAM,sBAAsB,GAAG,UAAU,CAAA;AAChD,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAA;AAE1C,sBAAsB;AACtB,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAA;AACrC,MAAM,CAAC,MAAM,uBAAuB,GAAG,KAAK,CAAA;AAC5C,6EAA6E;AAC7E,+EAA+E;AAC/E,+EAA+E;AAC/E,wDAAwD;AACxD,MAAM,CAAC,MAAM,YAAY,GAAG,EAAE,CAAA;AAC9B,MAAM,CAAC,MAAM,eAAe,GAAG,GAAG,CAAA;AAClC,MAAM,CAAC,MAAM,cAAc,GAAG,EAAE,CAAA;AAChC,MAAM,CAAC,MAAM,gBAAgB,GAAG,GAAG,CAAA;AACnC,MAAM,CAAC,MAAM,oBAAoB,GAAG,IAAI,CAAA;AACxC,MAAM,CAAC,MAAM,UAAU,GAAG;IACxB,cAAc;IACd,OAAO;IACP,WAAW;IACX,kBAAkB;CACqB,CAAA;AACzC,MAAM,CAAC,MAAM,gBAAgB,GAAc,cAAc,CAAA;AACzD,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAA;AACnC,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAA;AAC1C,MAAM,CAAC,MAAM,qBAAqB,GAAG,KAAK,CAAA;AAC1C,MAAM,CAAC,MAAM,uBAAuB,GAAG,KAAK,CAAA;AAC5C,MAAM,CAAC,MAAM,qBAAqB,GAAG,GAAG,CAAA;AAExC,6EAA6E;AAC7E,8EAA8E;AAC9E,+EAA+E;AAC/E,iEAAiE;AACjE,MAAM,CAAC,MAAM,sBAAsB,GAAG,GAAG,CAAA;AAEzC,+EAA+E;AAC/E,2EAA2E;AAC3E,YAAY;AACZ,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,CAAA;AAEhC,8EAA8E;AAC9E,qEAAqE;AACrE,MAAM,CAAC,MAAM,mBAAmB,GAAG,SAAS,CAAA;AAC5C,MAAM,CAAC,MAAM,mBAAmB,GAAG,GAAG,CAAA;AAEtC,2EAA2E;AAC3E,6EAA6E;AAC7E,4EAA4E;AAC5E,8EAA8E;AAC9E,6BAA6B;AAC7B,MAAM,CAAC,MAAM,sBAAsB,GAAG,MAAM,CAAA;AAE5C,8EAA8E;AAC9E,8EAA8E;AAC9E,4DAA4D;AAC5D,MAAM,CAAC,MAAM,oBAAoB,GAAG,EAAE,CAAA;AAEtC,wDAAwD;AACxD,MAAM,CAAC,MAAM,kBAAkB,GAAG,EAAE,CAAA;AAEpC,0EAA0E;AAC1E,wCAAwC;AACxC,MAAM,CAAC,MAAM,wBAAwB,GAAG,GAAG,CAAA;AAE3C,+EAA+E;AAC/E,6EAA6E;AAC7E,mEAAmE;AACnE,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAA;AACpC,MAAM,CAAC,MAAM,YAAY,GAAG,gBAAgB,GAAG,CAAC,CAAA"}
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|
@@ -62,11 +62,6 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
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62
62
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* subtree boxed. A click on it focuses the subtree under the pointer
|
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63
63
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*/
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64
64
|
showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
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65
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-
/**
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66
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-
* #property
|
|
67
|
-
* draw the branch-length scale bar above the tree of a phylogram
|
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-
*/
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69
|
-
showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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70
65
|
/**
|
|
71
66
|
* #property
|
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72
67
|
* height of the tree overview band, px
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@@ -113,10 +108,6 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
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|
113
108
|
* #action
|
|
114
109
|
*/
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setShowTreeOverview(arg: boolean): void;
|
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116
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-
/**
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117
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-
* #action
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118
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-
*/
|
|
119
|
-
setShowTreeScaleBar(arg: boolean): void;
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|
120
111
|
/**
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|
121
112
|
* #action
|
|
122
113
|
*/
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package/dist/model/treeModel.js
CHANGED
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@@ -1,5 +1,5 @@
|
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1
1
|
import { types } from '@jbrowse/mobx-state-tree';
|
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2
|
-
import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview,
|
|
2
|
+
import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, treeOrders, } from '../constants.js';
|
|
3
3
|
import { stripDefault } from '../stripDefault.js';
|
|
4
4
|
/**
|
|
5
5
|
* #stateModel Tree
|
|
@@ -66,11 +66,6 @@ export function TreeModelF() {
|
|
|
66
66
|
* subtree boxed. A click on it focuses the subtree under the pointer
|
|
67
67
|
*/
|
|
68
68
|
showTreeOverview: stripDefault(types.boolean, defaultShowTreeOverview),
|
|
69
|
-
/**
|
|
70
|
-
* #property
|
|
71
|
-
* draw the branch-length scale bar above the tree of a phylogram
|
|
72
|
-
*/
|
|
73
|
-
showTreeScaleBar: stripDefault(types.boolean, defaultShowTreeScaleBar),
|
|
74
69
|
/**
|
|
75
70
|
* #property
|
|
76
71
|
* height of the tree overview band, px
|
|
@@ -137,12 +132,6 @@ export function TreeModelF() {
|
|
|
137
132
|
setShowTreeOverview(arg) {
|
|
138
133
|
self.showTreeOverview = arg;
|
|
139
134
|
},
|
|
140
|
-
/**
|
|
141
|
-
* #action
|
|
142
|
-
*/
|
|
143
|
-
setShowTreeScaleBar(arg) {
|
|
144
|
-
self.showTreeScaleBar = arg;
|
|
145
|
-
},
|
|
146
135
|
/**
|
|
147
136
|
* #action
|
|
148
137
|
*/
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"treeModel.js","sourceRoot":"","sources":["../../src/model/treeModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EACL,iBAAiB,EACjB,sBAAsB,EACtB,qBAAqB,EACrB,eAAe,EACf,uBAAuB,EACvB,qBAAqB,EACrB,oBAAoB,EACpB,gBAAgB,EAChB,uBAAuB,EACvB,
|
|
1
|
+
{"version":3,"file":"treeModel.js","sourceRoot":"","sources":["../../src/model/treeModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EACL,iBAAiB,EACjB,sBAAsB,EACtB,qBAAqB,EACrB,eAAe,EACf,uBAAuB,EACvB,qBAAqB,EACrB,oBAAoB,EACpB,gBAAgB,EAChB,uBAAuB,EACvB,UAAU,GACX,MAAM,iBAAiB,CAAA;AACxB,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAIjD;;GAEG;AACH,MAAM,UAAU,UAAU;IACxB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,UAAU,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,iBAAiB,CAAC;QAC1D;;;WAGG;QACH,gBAAgB,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,uBAAuB,CAAC;QAEtE;;;;;WAKG;QACH,aAAa,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAExC;;;;;WAKG;QACH,SAAS,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAEpC;;;;;WAKG;QACH,aAAa,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,oBAAoB,CAAC;QAEhE;;;;;WAKG;QACH,SAAS,EAAE,YAAY,CACrB,KAAK,CAAC,WAAW,CAAY,WAAW,EAAE,CAAC,GAAG,UAAU,CAAC,CAAC,EAC1D,gBAAgB,CACjB;QAED;;;WAGG;QACH,QAAQ,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,eAAe,CAAC;QAEtD;;;WAGG;QACH,eAAe,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,sBAAsB,CAAC;QAEpE;;;;WAIG;QACH,cAAc,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,qBAAqB,CAAC;QAElE;;;;WAIG;QACH,gBAAgB,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,uBAAuB,CAAC;QAEtE;;;WAGG;QACH,cAAc,EAAE,YAAY,CAAC,KAAK,CAAC,MAAM,EAAE,qBAAqB,CAAC;KAClE,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;;WAIG;QACH,gBAAgB,CAAC,CAAqB;YACpC,IAAI,CAAC,aAAa,GAAG,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChE,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;QAC5B,CAAC;QACD;;;;WAIG;QACH,YAAY,CAAC,CAAqB;YAChC,IAAI,CAAC,SAAS,GAAG,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAC9D,CAAC;QAED;;WAEG;QACH,mBAAmB,CAAC,GAAY;YAC9B,IAAI,CAAC,gBAAgB,GAAG,GAAG,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,WAAW,CAAC,GAAY;YACtB,IAAI,CAAC,QAAQ,GAAG,GAAG,CAAA;QACrB,CAAC;QAED;;WAEG;QACH,gBAAgB,CAAC,GAAY;YAC3B,IAAI,CAAC,aAAa,GAAG,GAAG,CAAA;QAC1B,CAAC;QAED;;WAEG;QACH,YAAY,CAAC,KAAgB;YAC3B,IAAI,CAAC,SAAS,GAAG,KAAK,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,kBAAkB,CAAC,GAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,GAAG,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,GAAY;YAC5B,IAAI,CAAC,cAAc,GAAG,GAAG,CAAA;QAC3B,CAAC;QACD;;WAEG;QACH,mBAAmB,CAAC,GAAY;YAC9B,IAAI,CAAC,gBAAgB,GAAG,GAAG,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,aAAa,CAAC,GAAY;YACxB,IAAI,CAAC,UAAU,GAAG,GAAG,CAAA;QACvB,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
|
package/dist/model.d.ts
CHANGED
|
@@ -50,7 +50,7 @@ type FeaturePanelScale = Omit<ResolvedFeaturePanel, 'id' | 'width' | 'offsetX' |
|
|
|
50
50
|
*/
|
|
51
51
|
declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
|
|
52
52
|
maxInlineSnapshotBytes?: number;
|
|
53
|
-
}): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "
|
|
53
|
+
}): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
|
|
54
54
|
drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
55
55
|
labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
56
56
|
treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
|
|
@@ -61,7 +61,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
|
|
|
61
61
|
drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
62
62
|
drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
63
63
|
showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
64
|
-
showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
65
64
|
overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
|
|
66
65
|
}, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
|
|
67
66
|
bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
@@ -668,7 +667,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
|
|
|
668
667
|
setDrawNodeBubbles(arg: boolean): void;
|
|
669
668
|
setDrawNodeLabels(arg: boolean): void;
|
|
670
669
|
setShowTreeOverview(arg: boolean): void;
|
|
671
|
-
setShowTreeScaleBar(arg: boolean): void;
|
|
672
670
|
setDrawLabels(arg: boolean): void;
|
|
673
671
|
} & {
|
|
674
672
|
setColorSchemeName(name: string): void;
|
|
@@ -1760,9 +1758,9 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
|
|
|
1760
1758
|
} & {
|
|
1761
1759
|
/**
|
|
1762
1760
|
* #getter
|
|
1763
|
-
* the branch-length scale bar over the tree,
|
|
1764
|
-
*
|
|
1765
|
-
* too narrow for one
|
|
1761
|
+
* the branch-length scale bar over the tree, the guide of its branch-length
|
|
1762
|
+
* scale: undefined in cladogram mode, with the tree off, or when the tree
|
|
1763
|
+
* area is too narrow for one
|
|
1766
1764
|
*/
|
|
1767
1765
|
readonly treeScaleBar: {
|
|
1768
1766
|
step: number;
|
|
@@ -2440,7 +2438,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
|
|
|
2440
2438
|
drawNodeBubbles: boolean;
|
|
2441
2439
|
drawNodeLabels: boolean;
|
|
2442
2440
|
showTreeOverview: boolean;
|
|
2443
|
-
showTreeScaleBar: boolean;
|
|
2444
2441
|
overviewHeight: number;
|
|
2445
2442
|
columnTracks: ColumnTrackSpec[];
|
|
2446
2443
|
id: string;
|
|
@@ -2580,7 +2577,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
|
|
|
2580
2577
|
drawNodeBubbles: boolean;
|
|
2581
2578
|
drawNodeLabels: boolean;
|
|
2582
2579
|
showTreeOverview: boolean;
|
|
2583
|
-
showTreeScaleBar: boolean;
|
|
2584
2580
|
overviewHeight: number;
|
|
2585
2581
|
columnTracks?: undefined;
|
|
2586
2582
|
id: string;
|
package/dist/model.js
CHANGED
|
@@ -116,7 +116,6 @@ export const preservedOnReset = new Set([
|
|
|
116
116
|
'drawNodeBubbles',
|
|
117
117
|
'drawNodeLabels',
|
|
118
118
|
'showTreeOverview',
|
|
119
|
-
'showTreeScaleBar',
|
|
120
119
|
'overviewHeight',
|
|
121
120
|
'turnedOffTracks',
|
|
122
121
|
'trackHeights',
|
|
@@ -2475,14 +2474,11 @@ function stateModelFactory({ maxInlineSnapshotBytes = defaultMaxInlineSnapshotBy
|
|
|
2475
2474
|
.views(self => ({
|
|
2476
2475
|
/**
|
|
2477
2476
|
* #getter
|
|
2478
|
-
* the branch-length scale bar over the tree,
|
|
2479
|
-
*
|
|
2480
|
-
* too narrow for one
|
|
2477
|
+
* the branch-length scale bar over the tree, the guide of its branch-length
|
|
2478
|
+
* scale: undefined in cladogram mode, with the tree off, or when the tree
|
|
2479
|
+
* area is too narrow for one
|
|
2481
2480
|
*/
|
|
2482
2481
|
get treeScaleBar() {
|
|
2483
|
-
if (!self.showTreeScaleBar) {
|
|
2484
|
-
return undefined;
|
|
2485
|
-
}
|
|
2486
2482
|
return scaleBarLength(self.pxPerBranchLength, self.effectiveTreeAreaWidth - self.marginLeft * 2);
|
|
2487
2483
|
},
|
|
2488
2484
|
/**
|