@datagrok/sequence-translator 1.3.2 → 1.3.4

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.3.2",
+  "version": "1.3.4",
   "author": {
     "name": "Alexey Choposky",
     "email": "achopovsky@datagrok.ai"

package/src/apps/pattern/view/svg-utils/strands-block.ts

@@ -1,5 +1,5 @@
 import {NUCLEOTIDES} from '../../../common/model/const';
-import {STRAND, STRANDS, TERMINUS} from '../../model/const';
+import {STRAND, STRANDS, TERMINI, TERMINUS} from '../../model/const';
 import {PatternConfiguration} from '../../model/types';
 import {isOverhangNucleotide} from '../../model/utils';
 import {SVG_CIRCLE_SIZES, SVG_ELEMENT_COLORS, SVG_TEXT_FONT_SIZES} from './const';
@@ -19,6 +19,7 @@ const RIGHT_LABEL_WIDTH = 20;
 export class StrandsBlock extends SVGBlockBase {
   private strands: SVGBlockBase[];
   private labels: SVGBlockBase[];
+  private terminalModifications: SVGBlockBase[];
   constructor(
     svgElementFactory: SVGElementFactory,
     config: PatternConfiguration,
@@ -30,16 +31,22 @@ export class StrandsBlock extends SVGBlockBase {
     this.strands = strandTypes
       .map((strand) => new SingleStrandBlock(this.svgElementFactory, config, yShift, strand));
 
+
+    this.terminalModifications = strandTypes.map(
+      (strandType, idx) =>
+        new TerminalModificationLabels(this.svgElementFactory, config, yShift, strandType, this.strands[idx] as SingleStrandBlock)
+    );
     this.labels = strandTypes.map(
       (strandType, idx) =>
-        new StrandLabel(this.svgElementFactory, config, yShift, strandType, this.strands[idx] as SingleStrandBlock)
+        new StrandLabel(this.svgElementFactory, config, yShift, strandType, this.terminalModifications[idx] as TerminalModificationLabels)
     );
   }
 
   get svgElements(): SVGElement[] {
     const elements = [
       ...this.strands,
-      ...this.labels
+      ...this.terminalModifications,
+      ...this.labels,
     ].map((block) => block.svgElements).flat();
     return elements;
   }
@@ -255,11 +262,10 @@ class StrandLabel extends SVGBlockBase {
     protected config: PatternConfiguration,
     protected yShift: number,
     private strand: STRAND,
-    private strandSvgWrapper: SingleStrandBlock
+    private terminalModifications: TerminalModificationLabels
   ) {
     super(svgElementFactory, config, yShift);
     this._svgElements = this.createSVGElements();
-    // this.strandSvgWrapper.shiftElements({x: this.getLeftLabelWidth(), y: 0});
   }
 
   private createSVGElements(): SVGElement[] {
@@ -300,7 +306,7 @@ class StrandLabel extends SVGBlockBase {
     const text = `  ${terminus}`;
     const textDimensions = TextDimensionsCalculator.getTextDimensions(text, SVG_TEXT_FONT_SIZES.NUCLEOBASE);
     const position = {
-      x: SENSE_STRAND_HORIZONTAL_SHIFT + this.strandSvgWrapper.getContentWidth() + 5,
+      x: SENSE_STRAND_HORIZONTAL_SHIFT + this.terminalModifications.getContentWidth() + 5,
       y: getStrandCircleYShift(this.strand, this.yShift) + textDimensions.height / 3
     };
 
@@ -317,7 +323,92 @@ class StrandLabel extends SVGBlockBase {
   }
 
   getContentWidth(): number {
-    return this.strandSvgWrapper.getContentWidth() + this.getLeftLabelWidth() + this.getRightLabelWidth() + SENSE_STRAND_PADDING;
+    return this.terminalModifications.getContentWidth() + this.getLeftLabelWidth() +
+      this.getRightLabelWidth() + SENSE_STRAND_PADDING;
+  }
+
+  getContentHeight(): number {
+    return this.terminalModifications.getContentHeight();
+  }
+}
+
+class TerminalModificationLabels extends SVGBlockBase {
+  private _svgElements: SVGElement[];
+  constructor(
+    protected svgElementFactory: SVGElementFactory,
+    protected config: PatternConfiguration,
+    protected yShift: number,
+    private strand: STRAND,
+    private strandSvgWrapper: SingleStrandBlock
+  ) {
+    super(svgElementFactory, config, yShift);
+    this._svgElements = this.createSVGElements();
+  }
+
+  private createSVGElements(): SVGElement[] {
+    const elements = this.createTerminalModifications();
+    return elements;
+  }
+
+  private getTerminalModification(terminus: TERMINUS): string {
+    const terminalModification = this.config.strandTerminusModifications[this.strand][terminus];
+    return terminalModification;
+  }
+
+  private getTerminalModificationTextDimensions(terminus: TERMINUS): {width: number, height: number} {
+    const terminalModification = this.getTerminalModification(terminus);
+    const textDimensions = TextDimensionsCalculator
+      .getTextDimensions(terminalModification, SVG_TEXT_FONT_SIZES.NUCLEOBASE);
+    return textDimensions;
+  }
+
+  private getLeftTerminus(): TERMINUS {
+    return this.strand === STRAND.SENSE ? TERMINUS.FIVE_PRIME : TERMINUS.THREE_PRIME;
+  }
+
+  private createTerminalModification(terminus: TERMINUS): SVGTextElement {
+    const terminalModification = this.getTerminalModification(terminus);
+    const dimensions = this.getTerminalModificationTextDimensions(terminus);
+
+    const isLeft = terminus === this.getLeftTerminus();
+    const xShift = isLeft ? SENSE_STRAND_HORIZONTAL_SHIFT :
+      SENSE_STRAND_HORIZONTAL_SHIFT +
+      this.getTerminalModificationTextDimensions(this.getLeftTerminus()).width +
+      this.strandSvgWrapper.getContentWidth();
+    const position = {
+      x: xShift,
+      y: getStrandCircleYShift(this.strand, this.yShift) + dimensions.height / 3
+    };
+    if (isLeft) {
+      this.strandSvgWrapper.shiftElements({
+        x: dimensions.width,
+        y: 0
+      });
+    }
+
+    return this.svgElementFactory.createTextElement(
+      terminalModification,
+      position,
+      SVG_TEXT_FONT_SIZES.NUCLEOBASE,
+      SVG_ELEMENT_COLORS.MODIFICATION_TEXT
+    );
+  }
+
+  private createTerminalModifications(): SVGTextElement[] {
+    const termini = (this.strand === STRAND.ANTISENSE) ? TERMINI : Array.from(TERMINI).reverse();
+    const textElements = termini.map((terminus) => this.createTerminalModification(terminus));
+    return textElements;
+  }
+
+  get svgElements(): SVGElement[] {
+    return this._svgElements;
+  }
+
+  getContentWidth(): number {
+    return this.strandSvgWrapper.getContentWidth() +
+      TERMINI
+        .map((terminus) => this.getTerminalModificationTextDimensions(terminus).width)
+        .reduce((acc, curr) => acc += curr, 0);
   }
 
   getContentHeight(): number {

package/src/apps/pattern/view/svg-utils/svg-block-base.ts

@@ -17,21 +17,13 @@ export abstract class SVGBlockBase {
   shiftElements(shift: {x: number, y: number}): void {
     this.svgElements.forEach((element) => {
       const transform = element.getAttribute('transform') || '';
-      const match = transform.match(/translate\(([^,]+),([^,]+)\)/);
-      const x = match ? parseFloat(match[1]) : 0;
-      const y = match ? parseFloat(match[2]) : 0;
-      const newTransform = `translate(${x + shift.x},${y + shift.y})`;
+      // const match = transform.match(/translate\(([^,]+),([^,]+)\)/);
+      // const x = match ? parseFloat(match[1]) : 0;
+      // const y = match ? parseFloat(match[2]) : 0;
+      const newTransform = `translate(${shift.x},${shift.y})`;
       element.setAttribute('transform', `${transform} ${newTransform}`);
     });
   }
 
-  adjustContentWithinGlobalContainer(globalWidth: number): void {
-    const contentWidth = this.getContentWidth();
-    if (contentWidth < globalWidth) {
-      const shift = (globalWidth - contentWidth) / 2;
-      this.shiftElements({x: shift, y: 0});
-    }
-  }
-
   abstract getContentWidth(): number;
 }

package/src/package.ts

@@ -1,5 +1,6 @@
-import DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
 
 import {MonomerLibWrapper} from './apps/common/model/monomer-lib/lib-wrapper';
 import {OligoToolkitPackage} from './apps/common/model/oligo-toolkit-package';

package/src/polytool/pt-conversion.ts

@@ -268,8 +268,12 @@ export class Chain {
 function getHelms(sequences: string[], rules: Rules): string[] {
   const helms = new Array<string>(sequences.length);
   for (let i = 0; i < sequences.length; i++) {
-    const chain = Chain.fromNotation(sequences[i], rules);
-    helms[i] = chain.getHelm();
+    if (sequences[i] === undefined)
+      helms[i] = '';
+    else {
+      const chain = Chain.fromNotation(sequences[i], rules);
+      helms[i] = chain.getHelm();
+    }
   }
 
   return helms;
@@ -288,20 +292,20 @@ export async function addTransformedColumn(
   addCommonTags(targetHelmCol);
   targetHelmCol.setTag('units', NOTATION.HELM);
 
+  if (addHelm) {
+    targetHelmCol.setTag('cell.renderer', 'helm');
+    df.columns.add(targetHelmCol);
+  }
+
   const molCol = await grok.functions.call('Bio:getMolFromHelm', {
     'df': df,
     'helmCol': targetHelmCol,
     'chiralityEngine': chiralityEngine
   });
 
-
   molCol.name = df.columns.getUnusedName('molfile(' + sequencesCol.name + ')');
   molCol.semType = DG.SEMTYPE.MOLECULE;
 
-  if (addHelm) {
-    targetHelmCol.setTag('cell.renderer', 'helm');
-    df.columns.add(targetHelmCol);
-  }
   df.columns.add(molCol, true);
   await grok.data.detectSemanticTypes(df);
 }