@datagrok-libraries/bio 5.45.11 → 5.46.1

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Files changed (11) hide show
  1. package/CHANGELOG.md +8 -0
  2. package/package.json +2 -2
  3. package/src/pdb/auto-dock-service.d.ts +1 -0
  4. package/src/pdb/auto-dock-service.d.ts.map +1 -1
  5. package/src/pdb/auto-dock-service.js.map +1 -1
  6. package/src/utils/cell-renderer-consts.d.ts +1 -0
  7. package/src/utils/cell-renderer-consts.d.ts.map +1 -1
  8. package/src/utils/cell-renderer-monomer-placer.d.ts +7 -2
  9. package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
  10. package/src/utils/cell-renderer-monomer-placer.js +18 -8
  11. package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/CHANGELOG.md CHANGED
@@ -1,5 +1,13 @@
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  # bio changelog
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+ ## 5.46.1 (2024-12-02)
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+
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+ Add terminate method to the IAutoDockService interface
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+
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+ ## 5.46.0 (2024-11-19)
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+
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+ Sequence renderer: Support font resize
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+
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  ## 5.45.11 (2024-11-15)
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12
 
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  Async cell renderer correct invalidation
package/package.json CHANGED
@@ -8,12 +8,12 @@
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  "access": "public"
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  },
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  "friendlyName": "Datagrok bio library",
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- "version": "5.45.11",
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+ "version": "5.46.1",
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  "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
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  "dependencies": {
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  "@datagrok-libraries/chem-meta": "^1.2.7",
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  "@datagrok-libraries/gridext": "^1.3.73",
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- "@datagrok-libraries/ml": "^6.7.4",
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+ "@datagrok-libraries/ml": "^6.7.5",
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  "@datagrok-libraries/utils": "^4.3.7",
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  "@deck.gl/core": "8.8.12",
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  "cash-dom": "^8.1.5",
package/src/pdb/auto-dock-service.d.ts CHANGED
@@ -36,6 +36,7 @@ export interface IAutoDockService {
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  */
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  dockLigand(receptor: BiostructureData, ligand: BiostructureData, autodockGpf: string, poseCount?: number, posColName?: string): Promise<DG.DataFrame>;
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  dockLigandColumn(receptor: BiostructureData, ligandCol: DG.Column<string>, autodockGpf: string, poseCount?: number, posColName?: string): Promise<DG.DataFrame>;
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+ terminate(): Promise<void>;
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  }
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  export declare function getAutoDockService(): Promise<IAutoDockService>;
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  //# sourceMappingURL=auto-dock-service.d.ts.map
package/src/pdb/auto-dock-service.d.ts.map CHANGED
@@ -1 +1 @@
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package/src/pdb/auto-dock-service.js.map CHANGED
@@ -1 +1 @@
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package/src/utils/cell-renderer-consts.d.ts CHANGED
@@ -10,6 +10,7 @@ export declare const enum MmcrTemps {
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  highlightDifference = ".mm.cellRenderer.highlightDifference",
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  gapLength = ".mm.cellRenderer.gapLength",
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  monomerPlacer = ".mm.cellRenderer.monomerPlacer",
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+ fontSize = ".mm.cellRenderer.fontSize",
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  rendererSettingsChanged = ".mm.cellRenderer.settingsChanged",
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  overriddenLibrary = ".mm.cellRenderer.overriddenLibrary"
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  }
package/src/utils/cell-renderer-consts.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
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package/src/utils/cell-renderer-monomer-placer.d.ts CHANGED
@@ -4,9 +4,10 @@ import { CellRendererBackBase } from './cell-renderer-back-base';
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  import { ILogger } from './logger';
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  import { IMonomerLibBase } from '../types/index';
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  type MonomerPlacerProps = {
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- monomerCharWidth: number;
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  separatorWidth: number;
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  monomerToShort: MonomerToShortFunc;
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+ font: string;
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+ fontCharWidth: number;
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  };
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  export declare const undefinedColor = "rgb(100,100,100)";
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  export declare function hitBounds(bounds: number[], x: number): number | null;
@@ -15,7 +16,7 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
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  private readonly propsProvider;
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  private colWidth;
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  private _monomerLengthList;
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- private separatorWidth;
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+ private get separatorWidth();
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  props: MonomerPlacerProps;
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  private _processedRows;
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  private _processedMaxVisibleSeqLength;
@@ -30,6 +31,10 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
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  /** View is required to subscribe and handle for data frame changes */
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  constructor(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>, logger: ILogger, monomerLengthLimit: number, propsProvider: () => MonomerPlacerProps);
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  init(): Promise<void>;
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+ static getFontSettings(tableCol?: DG.Column): {
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+ font: string;
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+ fontWidth: number;
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+ };
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  toLog(): string;
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  protected getMonomerLib(): IMonomerLibBase | null;
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  protected reset(): void;
package/src/utils/cell-renderer-monomer-placer.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/src/utils/cell-renderer-monomer-placer.js CHANGED
@@ -32,6 +32,8 @@ export function hitBounds(bounds, x) {
32
32
  return null;
33
33
  }
34
34
  export class MonomerPlacer extends CellRendererBackBase {
35
+ // width of separator symbol
36
+ get separatorWidth() { return this.props?.fontCharWidth ? this.props?.fontCharWidth : 5; }
35
37
  /** View is required to subscribe and handle for data frame changes */
36
38
  constructor(gridCol, tableCol, logger, monomerLengthLimit, propsProvider) {
37
39
  super(gridCol, tableCol, logger);
@@ -39,8 +41,6 @@ export class MonomerPlacer extends CellRendererBackBase {
39
41
  this.propsProvider = propsProvider;
40
42
  this.colWidth = 0;
41
43
  this._monomerLengthList = null;
42
- // width of separator symbol
43
- this.separatorWidth = 5;
44
44
  this._processedMaxVisibleSeqLength = 0;
45
45
  this._monomerLengthMap = {}; // caches the lengths to save time on g.measureText
46
46
  this._monomerStructureMap = {}; // caches the atomic structures of monomers
@@ -81,6 +81,16 @@ export class MonomerPlacer extends CellRendererBackBase {
81
81
  }));
82
82
  this.reset();
83
83
  }
84
+ static getFontSettings(tableCol) {
85
+ const fontFamily = 'monospace';
86
+ let fontSize = 12;
87
+ if (tableCol && tableCol.temp[".mm.cellRenderer.fontSize" /* MmcrTemps.fontSize */] &&
88
+ typeof tableCol.temp[".mm.cellRenderer.fontSize" /* MmcrTemps.fontSize */] === 'number' && !isNaN(tableCol.temp[".mm.cellRenderer.fontSize" /* MmcrTemps.fontSize */]))
89
+ fontSize = Math.max(tableCol.temp[".mm.cellRenderer.fontSize" /* MmcrTemps.fontSize */], 1);
90
+ // monospace ratio
91
+ const fontWidth = fontSize * 0.6;
92
+ return { font: `${fontSize}px ${fontFamily}`, fontWidth };
93
+ }
84
94
  toLog() {
85
95
  return `MonomerPlacer<${this.viewerId}>`;
86
96
  }
@@ -131,7 +141,7 @@ export class MonomerPlacer extends CellRendererBackBase {
131
141
  if (this._monomerLengthList === null)
132
142
  this._monomerLengthList = new Array(this.tableCol.length).fill(null);
133
143
  const sh = this.seqHelper.getSeqHandler(this.tableCol);
134
- const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
144
+ const minMonWidth = this.props.separatorWidth + 1 * this.props.fontCharWidth;
135
145
  const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth);
136
146
  const seqSS = sh.getSplitted(rowIdx);
137
147
  const visibleSeqLength = Math.min(maxVisibleSeqLength, seqSS.length);
@@ -143,7 +153,7 @@ export class MonomerPlacer extends CellRendererBackBase {
143
153
  const seqMonLabel = seqSS.getOriginal(seqMonI);
144
154
  const shortMon = this.props.monomerToShort(seqMonLabel, this.monomerLengthLimit);
145
155
  const separatorWidth = sh.isSeparator() ? this.separatorWidth : this.props.separatorWidth;
146
- const seqMonWidth = separatorWidth + shortMon.length * this.props.monomerCharWidth;
156
+ const seqMonWidth = separatorWidth + shortMon.length * this.props.fontCharWidth;
147
157
  res[seqMonI] = seqMonWidth;
148
158
  seqWidth += seqMonWidth;
149
159
  if (seqWidth > this.colWidth)
@@ -178,7 +188,7 @@ export class MonomerPlacer extends CellRendererBackBase {
178
188
  return { startIdx: 0, endIdx: Math.min(this.tableCol.length, 10) };
179
189
  }
180
190
  })();
181
- const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
191
+ const minMonWidth = this.props.separatorWidth + 1 * this.props.fontCharWidth;
182
192
  const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth);
183
193
  for (let seqIdx = startIdx; seqIdx < endIdx; seqIdx++) {
184
194
  if (this._processedRows.get(seqIdx) && maxVisibleSeqLength <= this._processedMaxVisibleSeqLength)
@@ -192,7 +202,7 @@ export class MonomerPlacer extends CellRendererBackBase {
192
202
  for (let seqMonI = 0; seqMonI < visibleSeqLength; ++seqMonI) {
193
203
  const seqMonLabel = seqSS.getOriginal(seqMonI);
194
204
  const shortMon = this.props.monomerToShort(seqMonLabel, this.monomerLengthLimit);
195
- const seqMonWidth = this.props.separatorWidth + shortMon.length * this.props.monomerCharWidth;
205
+ const seqMonWidth = this.props.separatorWidth + shortMon.length * this.props.fontCharWidth;
196
206
  res[seqMonI] = Math.max(res[seqMonI] ?? 0, seqMonWidth);
197
207
  seqWidth += seqMonWidth;
198
208
  if (seqWidth >= this.colWidth)
@@ -265,13 +275,13 @@ export class MonomerPlacer extends CellRendererBackBase {
265
275
  g.beginPath();
266
276
  g.rect(x + this.padding, y + this.padding, w - this.padding - 1, h - this.padding * 2);
267
277
  g.clip();
268
- g.font = '12px monospace';
278
+ g.font = this.props?.font ?? '12px monospace';
269
279
  g.textBaseline = 'top';
270
280
  //TODO: can this be replaced/merged with splitSequence?
271
281
  const units = tableCol.meta.units;
272
282
  const aligned = tableCol.getTag(bioTAGS.aligned);
273
283
  const separator = tableCol.getTag(bioTAGS.separator) ?? '';
274
- const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
284
+ const minMonWidth = this.props.separatorWidth + 1 * this.props.fontCharWidth;
275
285
  const splitLimit = Math.ceil(w / minMonWidth);
276
286
  const tempReferenceSequence = tableCol.temp["reference-sequence" /* tempTAGS.referenceSequence */];
277
287
  const tempCurrentWord = this.tableCol.temp["current-word" /* tempTAGS.currentWord */];
package/src/utils/cell-renderer-monomer-placer.js.map CHANGED
@@ -1 +1 @@
1
- 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