react-msaview 3.2.1 → 3.2.2

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.
Files changed (48) hide show
  1. package/bundle/index.js +11 -11
  2. package/dist/components/msa/renderMSABlock.js +30 -26
  3. package/dist/components/msa/renderMSABlock.js.map +1 -1
  4. package/dist/components/tree/dialogs/TreeNodeInfoDialog.js +2 -3
  5. package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map +1 -1
  6. package/dist/components/tree/renderTreeCanvas.js +5 -5
  7. package/dist/components/tree/renderTreeCanvas.js.map +1 -1
  8. package/dist/model/DialogQueue.d.ts +1 -1
  9. package/dist/model.d.ts +23 -24
  10. package/dist/model.js +37 -13
  11. package/dist/model.js.map +1 -1
  12. package/dist/parseNewick.d.ts +4 -4
  13. package/dist/parseNewick.js +7 -7
  14. package/dist/parseNewick.js.map +1 -1
  15. package/dist/parsers/ClustalMSA.d.ts +4 -4
  16. package/dist/parsers/ClustalMSA.js +2 -2
  17. package/dist/parsers/ClustalMSA.js.map +1 -1
  18. package/dist/parsers/EmfMSA.d.ts +27 -0
  19. package/dist/parsers/EmfMSA.js +53 -0
  20. package/dist/parsers/EmfMSA.js.map +1 -0
  21. package/dist/parsers/EmfTree.d.ts +5 -0
  22. package/dist/parsers/EmfTree.js +8 -0
  23. package/dist/parsers/EmfTree.js.map +1 -0
  24. package/dist/parsers/FastaMSA.js +2 -2
  25. package/dist/parsers/FastaMSA.js.map +1 -1
  26. package/dist/parsers/StockholmMSA.js +2 -2
  27. package/dist/parsers/StockholmMSA.js.map +1 -1
  28. package/dist/reparseTree.js +2 -2
  29. package/dist/reparseTree.js.map +1 -1
  30. package/dist/util.d.ts +3 -3
  31. package/dist/util.js +1 -1
  32. package/dist/util.js.map +1 -1
  33. package/dist/version.d.ts +1 -1
  34. package/dist/version.js +1 -1
  35. package/package.json +4 -3
  36. package/src/components/msa/renderMSABlock.ts +42 -38
  37. package/src/components/tree/dialogs/TreeNodeInfoDialog.tsx +6 -2
  38. package/src/components/tree/renderTreeCanvas.ts +2 -2
  39. package/src/model.ts +38 -19
  40. package/src/parseNewick.ts +7 -7
  41. package/src/parsers/ClustalMSA.ts +2 -2
  42. package/src/parsers/EmfMSA.ts +66 -0
  43. package/src/parsers/EmfTree.ts +9 -0
  44. package/src/parsers/FastaMSA.ts +2 -2
  45. package/src/parsers/StockholmMSA.ts +2 -2
  46. package/src/reparseTree.ts +3 -3
  47. package/src/util.ts +5 -5
  48. package/src/version.ts +1 -1
package/dist/components/msa/renderMSABlock.js CHANGED
@@ -43,17 +43,19 @@ function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, })
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  for (const node of visibleLeaves) {
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  const { data: { name }, } = node;
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  const y = node.x;
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- const str = columns[name].slice(xStart, xEnd);
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- for (let i = 0; i < str.length; i++) {
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- const letter = str[i];
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- const color = colorSchemeName === 'clustalx_protein_dynamic'
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- ? getClustalXColor(colStats[xStart + i], colStatsSums[xStart + i], model, name, xStart + i)
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- : colorSchemeName === 'percent_identity_dynamic'
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- ? getPercentIdentityColor(colStats[xStart + i], colStatsSums[xStart + i], model, name, xStart + i)
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- : colorScheme[letter.toUpperCase()];
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- if (bgColor) {
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- ctx.fillStyle = color || theme.palette.background.default;
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- ctx.fillRect(i * colWidth + offsetX - (offsetX % colWidth), y - rowHeight, colWidth, rowHeight);
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+ const str = columns[name]?.slice(xStart, xEnd);
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+ if (str) {
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+ for (let i = 0; i < str.length; i++) {
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+ const letter = str[i];
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+ const color = colorSchemeName === 'clustalx_protein_dynamic'
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+ ? getClustalXColor(colStats[xStart + i], colStatsSums[xStart + i], model, name, xStart + i)
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+ : colorSchemeName === 'percent_identity_dynamic'
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+ ? getPercentIdentityColor(colStats[xStart + i], colStatsSums[xStart + i], model, name, xStart + i)
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+ : colorScheme[letter.toUpperCase()];
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+ if (bgColor) {
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+ ctx.fillStyle = color || theme.palette.background.default;
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+ ctx.fillRect(i * colWidth + offsetX - (offsetX % colWidth), y - rowHeight, colWidth, rowHeight);
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+ }
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  }
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  }
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  }
@@ -64,21 +66,23 @@ function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart,
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  for (const node of visibleLeaves) {
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  const { data: { name }, } = node;
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  const y = node.x;
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- const str = columns[name].slice(xStart, xEnd);
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- for (let i = 0; i < str.length; i++) {
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- const letter = str[i];
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- const color = colorScheme[letter.toUpperCase()];
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- const contrast = contrastLettering
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- ? contrastScheme[letter.toUpperCase()] || 'black'
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- : 'black';
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- const x = i * colWidth + offsetX - (offsetX % colWidth);
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- // note: -rowHeight/4 matches +rowHeight/4 in tree
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- ctx.fillStyle = actuallyShowDomains
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- ? 'black'
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- : bgColor
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- ? contrast
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- : color || 'black';
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- ctx.fillText(letter, x + colWidth / 2, y - rowHeight / 4);
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+ const str = columns[name]?.slice(xStart, xEnd);
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+ if (str) {
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+ for (let i = 0; i < str.length; i++) {
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+ const letter = str[i];
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+ const color = colorScheme[letter.toUpperCase()];
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+ const contrast = contrastLettering
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+ ? contrastScheme[letter.toUpperCase()] || 'black'
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+ : 'black';
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+ const x = i * colWidth + offsetX - (offsetX % colWidth);
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+ // note: -rowHeight/4 matches +rowHeight/4 in tree
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+ ctx.fillStyle = actuallyShowDomains
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+ ? 'black'
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+ : bgColor
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+ ? contrast
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+ : color || 'black';
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+ ctx.fillText(letter, x + colWidth / 2, y - rowHeight / 4);
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+ }
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  }
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  }
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  }
package/dist/components/msa/renderMSABlock.js.map CHANGED
@@ -1 +1 @@
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1
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package/dist/components/tree/dialogs/TreeNodeInfoDialog.js CHANGED
@@ -7,15 +7,14 @@ import SequenceTextArea from '../../SequenceTextArea';
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  const TreeNodeInfoDialog = observer(function ({ info, model, nodeName, onClose, }) {
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  const { treeMetadata, rows } = model;
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  const metadata = treeMetadata[nodeName];
10
- const [name, sequence] = rows.find(f => f[0] === nodeName);
10
+ const res = rows.find(f => f[0] === nodeName);
11
11
  return (React.createElement(Dialog, { onClose: () => {
12
12
  onClose();
13
13
  }, open: true, title: "Tree node info", maxWidth: "xl" },
14
14
  React.createElement(DialogContent, null,
15
15
  React.createElement(BaseCard, { title: "Attributes" },
16
16
  React.createElement(Attributes, { attributes: { nodeName, ...info } })),
17
- React.createElement(BaseCard, { title: "Sequence" },
18
- React.createElement(SequenceTextArea, { str: [[name, sequence]] })),
17
+ React.createElement(BaseCard, { title: "Sequence" }, res ? (React.createElement(SequenceTextArea, { str: [res] })) : (React.createElement("div", null, "Sequence not found"))),
19
18
  metadata ? (React.createElement(BaseCard, { title: "Extra metadata" },
20
19
  React.createElement(Attributes, { attributes: metadata }))) : null)));
21
20
  });
package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"TreeNodeInfoDialog.js","sourceRoot":"","sources":["../../../../src/components/tree/dialogs/TreeNodeInfoDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,UAAU,EACV,QAAQ,GACT,MAAM,mDAAmD,CAAA;AAI1D,OAAO,gBAAgB,MAAM,wBAAwB,CAAA;AAErD,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,IAAI,EACJ,KAAK,EACL,QAAQ,EACR,OAAO,GAMR;IACC,MAAM,EAAE,YAAY,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,QAAQ,GAAG,YAAY,CAAC,QAAQ,CAAC,CAAA;IACvC,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,QAAQ,CAAC,CAAA;IAC7C,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;YACZ,OAAO,EAAE,CAAA;QACX,CAAC,EACD,IAAI,QACJ,KAAK,EAAC,gBAAgB,EACtB,QAAQ,EAAC,IAAI;QAEb,oBAAC,aAAa;YACZ,oBAAC,QAAQ,IAAC,KAAK,EAAC,YAAY;gBAC1B,oBAAC,UAAU,IAAC,UAAU,EAAE,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAI,CACxC;YACX,oBAAC,QAAQ,IAAC,KAAK,EAAC,UAAU,IACvB,GAAG,CAAC,CAAC,CAAC,CACL,oBAAC,gBAAgB,IAAC,GAAG,EAAE,CAAC,GAAG,CAAC,GAAI,CACjC,CAAC,CAAC,CAAC,CACF,sDAA6B,CAC9B,CACQ;YACV,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,QAAQ,IAAC,KAAK,EAAC,gBAAgB;gBAC9B,oBAAC,UAAU,IAAC,UAAU,EAAE,QAAQ,GAAI,CAC3B,CACZ,CAAC,CAAC,CAAC,IAAI,CACM,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}
package/dist/components/tree/renderTreeCanvas.js CHANGED
@@ -62,10 +62,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
62
62
  }
63
63
  }
64
64
  export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
65
- const { fontSize, showBranchLen, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree,
66
- // eslint-disable-next-line @typescript-eslint/no-unused-vars
67
- rowHeight: _rowHeight, // this is needed for redrawing after zoom change
68
- } = model;
65
+ const { fontSize, showBranchLen, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, } = model;
69
66
  const by = blockSizeYOverride || blockSize;
70
67
  if (labelsAlignRight) {
71
68
  ctx.textAlign = 'right';
@@ -133,7 +130,10 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
133
130
  }
134
131
  export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
135
132
  clickMap?.clear();
136
- const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, showTreeText, marginLeft, nref, } = model;
133
+ const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, showTreeText, marginLeft, nref,
134
+ // eslint-disable-next-line @typescript-eslint/no-unused-vars
135
+ rowHeight: _rowHeight, // this is needed for redrawing after zoom change
136
+ } = model;
137
137
  const by = blockSizeYOverride || blockSize;
138
138
  ctx.resetTransform();
139
139
  // this is a bogus use of nref, it is never less than 0. we just are using it
package/dist/components/tree/renderTreeCanvas.js.map CHANGED
@@ -1 +1 @@
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1
+ 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package/dist/model/DialogQueue.d.ts CHANGED
@@ -8,7 +8,7 @@ export declare function DialogQueueSessionMixin(): import("mobx-state-tree").IMo
8
8
  /**
9
9
  * #getter
10
10
  */
11
- readonly DialogComponent: DialogComponentType;
11
+ readonly DialogComponent: DialogComponentType | undefined;
12
12
  /**
13
13
  * #getter
14
14
  */
package/dist/model.d.ts CHANGED
@@ -7,6 +7,7 @@ import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types'
7
7
  export declare function isGzip(buf: Buffer): boolean;
8
8
  import { type NodeWithIds, type NodeWithIdsAndLength } from './util';
9
9
  import ClustalMSA from './parsers/ClustalMSA';
10
+ import EmfMSA from './parsers/EmfMSA';
10
11
  import StockholmMSA from './parsers/StockholmMSA';
11
12
  import FastaMSA from './parsers/FastaMSA';
12
13
  import type { InterProScanResults } from './launchInterProScan';
@@ -68,22 +69,17 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
68
69
  locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
69
70
  uri: import("mobx-state-tree").ISimpleType<string>;
70
71
  baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
71
- internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree" /**
72
- * #property
73
- * array of tree parent nodes that are 'collapsed' (all children are
74
- * hidden)
75
- */).ISimpleType<string>>;
72
+ internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
76
73
  internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
77
- internetAccountType: import("mobx-state-tree" /**
78
- * #property
79
- * array of tree leaf nodes that are 'collapsed' (just that leaf node
80
- * is hidden)
81
- */).ISimpleType<string>;
74
+ internetAccountType: import("mobx-state-tree").ISimpleType<string>;
82
75
  authInfo: import("mobx-state-tree").IType<any, any, any>;
83
76
  }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
84
77
  }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
85
78
  locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
86
- name: import("mobx-state-tree").ISimpleType<string>;
79
+ name: import("mobx-state-tree" /**
80
+ * #property
81
+ * turned off tracks
82
+ */).ISimpleType<string>;
87
83
  blobId: import("mobx-state-tree").ISimpleType<string>;
88
84
  }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
89
85
  locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
@@ -102,16 +98,17 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
102
98
  blobId: import("mobx-state-tree").ISimpleType<string>;
103
99
  }> | import("mobx-state-tree").ModelSnapshotType<{
104
100
  locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
105
- localPath: import("mobx-state-tree").ISimpleType<string>;
101
+ localPath: import("mobx-state-tree" /**
102
+ * #volatile
103
+ * resize handle width between tree and msa area, px
104
+ */).ISimpleType<string>;
106
105
  }>, import("mobx-state-tree").ModelInstanceType<{
107
- locationType: import(
108
- /**
106
+ locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
107
+ name: import("mobx-state-tree").ISimpleType<string>;
108
+ blobId: import("mobx-state-tree" /**
109
109
  * #volatile
110
110
  * the currently mouse-hovered row
111
- */
112
- "mobx-state-tree").ISimpleType<"BlobLocation">;
113
- name: import("mobx-state-tree").ISimpleType<string>;
114
- blobId: import("mobx-state-tree").ISimpleType<string>;
111
+ */).ISimpleType<string>;
115
112
  }, {}> | import("mobx-state-tree").ModelInstanceType<{
116
113
  locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
117
114
  localPath: import("mobx-state-tree").ISimpleType<string>;
@@ -121,8 +118,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
121
118
  } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
122
119
  locationType: import("mobx-state-tree" /**
123
120
  * #volatile
124
- * a dummy variable that is incremented when ref changes so autorun for
125
- * drawing canvas commands will run
121
+ * the currently mouse-click column
126
122
  */).ISimpleType<"UriLocation">;
127
123
  uri: import("mobx-state-tree").ISimpleType<string>;
128
124
  baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -131,7 +127,9 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
131
127
  * #volatile
132
128
  */).IModelType<{
133
129
  internetAccountType: import("mobx-state-tree").ISimpleType<string>;
134
- authInfo: import("mobx-state-tree").IType<any, any, any>;
130
+ authInfo: import("mobx-state-tree" /**
131
+ * #volatile
132
+ */).IType<any, any, any>;
135
133
  }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
136
134
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
137
135
  msaFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
@@ -258,7 +256,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
258
256
  }, {
259
257
  queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
260
258
  } & {
261
- readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType;
259
+ readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
262
260
  readonly DialogProps: any;
263
261
  } & {
264
262
  removeActiveDialog(): void;
@@ -456,6 +454,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
456
454
  setData(data: {
457
455
  msa?: string;
458
456
  tree?: string;
457
+ treeMetadata?: string;
459
458
  }): void;
460
459
  /**
461
460
  * #action
@@ -541,7 +540,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
541
540
  /**
542
541
  * #getter
543
542
  */
544
- readonly MSA: StockholmMSA | FastaMSA | ClustalMSA | null;
543
+ readonly MSA: StockholmMSA | FastaMSA | EmfMSA | ClustalMSA | null;
545
544
  /**
546
545
  * #getter
547
546
  */
@@ -820,7 +819,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
820
819
  description: string;
821
820
  start: number;
822
821
  end: number;
823
- }[] | undefined>;
822
+ }[]>;
824
823
  } & {
825
824
  /**
826
825
  * #getter
package/dist/model.js CHANGED
@@ -23,6 +23,7 @@ import palettes from './ggplotPalettes';
23
23
  import TextTrack from './components/TextTrack';
24
24
  // parsers
25
25
  import ClustalMSA from './parsers/ClustalMSA';
26
+ import EmfMSA from './parsers/EmfMSA';
26
27
  import StockholmMSA from './parsers/StockholmMSA';
27
28
  import FastaMSA from './parsers/FastaMSA';
28
29
  import parseNewick from './parseNewick';
@@ -33,6 +34,7 @@ import { DialogQueueSessionMixin } from './model/DialogQueue';
33
34
  import { TreeF } from './model/treeModel';
34
35
  import { MSAModelF } from './model/msaModel';
35
36
  import { mouseOverCoordToGlobalCoord, globalCoordToRowSpecificCoord, } from './rowCoordinateCalculations';
37
+ import EmfTree from './parsers/EmfTree';
36
38
  /**
37
39
  * #stateModel MsaView
38
40
  * extends
@@ -90,7 +92,7 @@ function stateModelFactory() {
90
92
  * #property
91
93
  * height of each row, px
92
94
  */
93
- rowHeight: 20,
95
+ rowHeight: 18,
94
96
  /**
95
97
  * #property
96
98
  * scroll position, Y-offset, px
@@ -105,7 +107,7 @@ function stateModelFactory() {
105
107
  * #property
106
108
  * width of columns, px
107
109
  */
108
- colWidth: 16,
110
+ colWidth: 14,
109
111
  /**
110
112
  * #property
111
113
  * filehandle object for the tree
@@ -154,7 +156,11 @@ function stateModelFactory() {
154
156
  * data from the loaded tree/msa/treeMetadata, generally loaded by
155
157
  * autorun
156
158
  */
157
- data: types.optional(DataModelF(), { tree: '', msa: '' }),
159
+ data: types.optional(DataModelF(), {
160
+ tree: '',
161
+ msa: '',
162
+ treeMetadata: '',
163
+ }),
158
164
  /**
159
165
  * #property
160
166
  */
@@ -513,10 +519,15 @@ function stateModelFactory() {
513
519
  if (Stockholm.sniff(text)) {
514
520
  return new StockholmMSA(text, self.currentAlignment);
515
521
  }
516
- if (text.startsWith('>')) {
522
+ else if (text.startsWith('>')) {
517
523
  return new FastaMSA(text);
518
524
  }
519
- return new ClustalMSA(text);
525
+ else if (text.startsWith('SEQ')) {
526
+ return new EmfMSA(text);
527
+ }
528
+ else {
529
+ return new ClustalMSA(text);
530
+ }
520
531
  }
521
532
  return null;
522
533
  },
@@ -530,14 +541,27 @@ function stateModelFactory() {
530
541
  * #getter
531
542
  */
532
543
  get tree() {
533
- const ret = self.data.tree
534
- ? generateNodeIds(parseNewick(self.data.tree))
535
- : this.MSA?.getTree() || {
544
+ const text = self.data.tree;
545
+ let ret;
546
+ if (text) {
547
+ let t;
548
+ if (text.startsWith('SEQ')) {
549
+ const r = new EmfTree(text);
550
+ t = r.data.tree;
551
+ }
552
+ else {
553
+ t = text;
554
+ }
555
+ ret = generateNodeIds(parseNewick(t));
556
+ }
557
+ else {
558
+ ret = this.MSA?.getTree() || {
536
559
  noTree: true,
537
- branchset: [],
560
+ children: [],
538
561
  id: 'empty',
539
562
  name: 'empty',
540
563
  };
564
+ }
541
565
  return reparseTree(ret);
542
566
  },
543
567
  /**
@@ -557,10 +581,10 @@ function stateModelFactory() {
557
581
  * #getter
558
582
  */
559
583
  get root() {
560
- let hier = hierarchy(this.tree, d => d.branchset)
561
- // todo: investigate whether needed, typescript says branchset always true
584
+ let hier = hierarchy(this.tree, d => d.children)
585
+ // todo: investigate whether needed, typescript says children always true
562
586
  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
563
- .sum(d => (d.branchset ? 0 : 1))
587
+ .sum(d => (d.children ? 0 : 1))
564
588
  .sort((a, b) => ascending(a.data.length || 1, b.data.length || 1));
565
589
  if (self.showOnly) {
566
590
  const res = hier.find(n => n.data.id === self.showOnly);
@@ -653,7 +677,7 @@ function stateModelFactory() {
653
677
  * #getter
654
678
  */
655
679
  get fontSize() {
656
- return Math.min(Math.max(6, self.rowHeight - 8), 18);
680
+ return Math.min(Math.max(6, self.rowHeight - 3), 18);
657
681
  },
658
682
  /**
659
683
  * #getter
package/dist/model.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/parseNewick.d.ts CHANGED
@@ -34,13 +34,13 @@
34
34
  * Converted to JSON:
35
35
  * {
36
36
  * name: "F",
37
- * branchset: [
37
+ * children: [
38
38
  * {name: "A", length: 0.1},
39
39
  * {name: "B", length: 0.2},
40
40
  * {
41
41
  * name: "E",
42
42
  * length: 0.5,
43
- * branchset: [
43
+ * children: [
44
44
  * {name: "C", length: 0.3},
45
45
  * {name: "D", length: 0.4}
46
46
  * ]
@@ -50,9 +50,9 @@
50
50
  *
51
51
  * Converted to JSON, but with no names or lengths:
52
52
  * {
53
- * branchset: [
53
+ * children: [
54
54
  * {}, {}, {
55
- * branchset: [{}, {}]
55
+ * children: [{}, {}]
56
56
  * }
57
57
  * ]
58
58
  * }
package/dist/parseNewick.js CHANGED
@@ -34,13 +34,13 @@
34
34
  * Converted to JSON:
35
35
  * {
36
36
  * name: "F",
37
- * branchset: [
37
+ * children: [
38
38
  * {name: "A", length: 0.1},
39
39
  * {name: "B", length: 0.2},
40
40
  * {
41
41
  * name: "E",
42
42
  * length: 0.5,
43
- * branchset: [
43
+ * children: [
44
44
  * {name: "C", length: 0.3},
45
45
  * {name: "D", length: 0.4}
46
46
  * ]
@@ -50,9 +50,9 @@
50
50
  *
51
51
  * Converted to JSON, but with no names or lengths:
52
52
  * {
53
- * branchset: [
53
+ * children: [
54
54
  * {}, {}, {
55
- * branchset: [{}, {}]
55
+ * children: [{}, {}]
56
56
  * }
57
57
  * ]
58
58
  * }
@@ -65,13 +65,13 @@ export default function parse(s) {
65
65
  const token = tokens[i];
66
66
  const subtree = {};
67
67
  switch (token) {
68
- case '(': // new branchset
69
- tree.branchset = [subtree];
68
+ case '(': // new children
69
+ tree.children = [subtree];
70
70
  ancestors.push(tree);
71
71
  tree = subtree;
72
72
  break;
73
73
  case ',': // another branch
74
- ancestors.at(-1)?.branchset.push(subtree);
74
+ ancestors.at(-1)?.children.push(subtree);
75
75
  tree = subtree;
76
76
  break;
77
77
  case ')': // optional name next