@datagrok/sequence-translator 0.0.1 → 0.0.5

package/src/drawAxolabsPattern.ts

@@ -1,8 +1,8 @@
-import {axolabsMap} from "./axolabsMap";
+import {axolabsMap} from './axolabsMap';
 
 // https://uxdesign.cc/star-rating-make-svg-great-again-d4ce4731347e
-function getPointsToDrawStar(centerX: number, centerY: number) {
-  const innerCirclePoints = 5;  // a 5 point star
+function getPointsToDrawStar(centerX: number, centerY: number): string {
+  const innerCirclePoints = 5; // a 5 point star
   const innerRadius = 15 / innerCirclePoints;
   const innerOuterRadiusRatio = 2; // outter circle is x2 the inner
   const outerRadius = innerRadius * innerOuterRadiusRatio;
@@ -12,9 +12,9 @@ function getPointsToDrawStar(centerX: number, centerY: number) {
 
   let points = '';
   for (let i = 0; i < totalNumberOfPoints; i++) {
-    let r = (i % 2 == 0) ? outerRadius : innerRadius;
-    let currentX = centerX + Math.cos(i * angle + angleOffsetToCenterStar) * r;
-    let currentY = centerY + Math.sin(i * angle + angleOffsetToCenterStar) * r;
+    const r = (i % 2 == 0) ? outerRadius : innerRadius;
+    const currentX = centerX + Math.cos(i * angle + angleOffsetToCenterStar) * r;
+    const currentY = centerY + Math.sin(i * angle + angleOffsetToCenterStar) * r;
     points += currentX + ',' + currentY + ' ';
   }
   return points;
@@ -35,121 +35,137 @@ function getTextWidth(text: string, font: number): number {
   return 2 * context.measureText(text).width;
 }
 
-function getTextInsideCircle(bases: string[], index: number, nucleotideCounter: number, numberOfNucleotides: number, enumerateModifications: string[]): string {
-  return (bases[index].slice(-3) == "(o)") || !enumerateModifications.includes(bases[index]) ? "" :
+function getTextInsideCircle(
+  bases: string[], index: number, nucleotideCounter: number,
+  numberOfNucleotides: number, enumerateModifications: string[]): string {
+  return (bases[index].slice(-3) == '(o)') || !enumerateModifications.includes(bases[index]) ? '' :
     ['A', 'G', 'C', 'U', 'T'].includes(bases[index]) ? bases[index] : String(numberOfNucleotides - nucleotideCounter);
 }
 
-function getFontColorVisibleOnBackground(rgbString: string) {
-  const rgbIntList = rgbString.match(/\d+/g)!.map(e => Number(e));
-  return (rgbIntList[0] * 0.299 + rgbIntList[1] * 0.587 + rgbIntList[2] * 0.114) > 186 ? '#333333' : '#ffffff';
+function getFontColorVisibleOnBackground(rgbString: string): string {
+  const rgbIntList = rgbString.match(/\d+/g)!.map((e) => Number(e));
+  return (rgbIntList[0] * 0.299 + rgbIntList[1] * 0.587 + rgbIntList[2] * 0.114) > 186 ? '#33333' : '#ffffff';
 }
 
 function getBaseColor(base: string): string {
-  return axolabsMap[base]["color"];
+  return axolabsMap[base]['color'];
 }
 
-export function drawAxolabsPattern(patternName: string, asExists: boolean, ssBases: string[], asBases: string[], ssPtoStatuses: boolean[], asPtoStatuses: boolean[],
-                                   ssThreeModification: string, ssFiveModification: string, asThreeModification: string, asFiveModification: string, comment: string,
-                                   enumerateModifications: string[]) {
-
+export function drawAxolabsPattern(
+  patternName: string, asExists: boolean, ssBases: string[],
+  asBases: string[], ssPtoStatuses: boolean[], asPtoStatuses: boolean[],
+  ssThreeModification: string, ssFiveModification: string,
+  asThreeModification: string, asFiveModification: string, comment: string,
+  enumerateModifications: string[]) {
   function getEquidistantXForLegend(index: number): number {
     return Math.round((index + startFrom) * width / (uniqueBases.length + startFrom) + legendRadius);
   }
 
   function getXOfBaseCircles(index: number, rightOverhangs: number): number {
-    return widthOfRightModification + (resultingNumberOfNucleotidesInStrands - index + rightOverhangs + 1) * baseDiameter;
+    return widthOfRightModification +
+      (resultingNumberOfNucleotidesInStrands - index + rightOverhangs + 1) * baseDiameter;
   }
 
   function getShiftToAlignNumberInsideCircle(bases: string[], generalIndex: number, nucleotideIndex: number): number {
-    return (nucleotideIndex < 10 || ['A', 'G', 'C', 'U', 'T'].includes(bases[generalIndex])) ? shiftToAlignOneDigitNumberInsideCircle : shiftToAlignTwoDigitNumberInsideCircle;
+    return (nucleotideIndex < 10 || ['A', 'G', 'C', 'U', 'T'].
+      includes(bases[generalIndex])) ? shiftToAlignOneDigitNumberInsideCircle : shiftToAlignTwoDigitNumberInsideCircle;
   }
 
   const svg = {
-    xmlns: "http://www.w3.org/2000/svg",
+    xmlns: 'http://www.w3.org/2000/svg',
     render: function(width: number, height: number) {
       const e = document.createElementNS(this.xmlns, 'svg');
-      e.setAttribute("id", "mySvg");
-      e.setAttribute("width", String(width));
-      e.setAttribute("height", String(height));
+      e.setAttribute('id', 'mySvg');
+      e.setAttribute('width', String(width));
+      e.setAttribute('height', String(height));
       return e;
     },
     circle: function(x: number, y: number, radius: number, color: string) {
       const e = document.createElementNS(this.xmlns, 'circle');
-      e.setAttribute("cx", String(x));
-      e.setAttribute("cy", String(y));
-      e.setAttribute("r", String(radius));
-      e.setAttribute("fill", color);
+      e.setAttribute('cx', String(x));
+      e.setAttribute('cy', String(y));
+      e.setAttribute('r', String(radius));
+      e.setAttribute('fill', color);
       return e;
     },
     text: function(text: string, x: number, y: number, fontSize: number, color: string) {
       const e = document.createElementNS(this.xmlns, 'text');
-      e.setAttribute("x", String(x));
-      e.setAttribute("y", String(y));
-      e.setAttribute("font-size", String(fontSize));
-      e.setAttribute("font-weight", "normal");
-      e.setAttribute("font-family", "Arial");
-      e.setAttribute("fill", color);
+      e.setAttribute('x', String(x));
+      e.setAttribute('y', String(y));
+      e.setAttribute('font-size', String(fontSize));
+      e.setAttribute('font-weight', 'normal');
+      e.setAttribute('font-family', 'Arial');
+      e.setAttribute('fill', color);
       e.innerHTML = text;
       return e;
     },
     star: function(x: number, y: number, fill: string) {
-      const e = document.createElementNS(this.xmlns, "polygon");
-      e.setAttribute("points", getPointsToDrawStar(x, y));
-      e.setAttribute("fill", fill);
+      const e = document.createElementNS(this.xmlns, 'polygon');
+      e.setAttribute('points', getPointsToDrawStar(x, y));
+      e.setAttribute('fill', fill);
       return e;
-    }
+    },
   };
 
   ssBases = ssBases.reverse();
   ssPtoStatuses = ssPtoStatuses.reverse();
 
-  const baseRadius = 15,
-    shiftToAlignTwoDigitNumberInsideCircle = -10,
-    shiftToAlignOneDigitNumberInsideCircle = -5,
-    legendRadius = 6,
-    psLinkageRadius = 5,
-    baseFontSize = 17,
-    legendFontSize = 14,
-    psLinkageColor = 'red',
-    fontColor = 'var(--grey-6)',
-    titleFontColor = 'black',
-    modificationsColor = 'red',
-    ssLeftText = "SS: 5'",
-    asLeftText = "AS: 3'",
-    ssRightText = "3'",
-    asRightText = "5'";
+  const baseRadius = 15;
+  const shiftToAlignTwoDigitNumberInsideCircle = -10;
+  const shiftToAlignOneDigitNumberInsideCircle = -5;
+  const legendRadius = 6;
+  const psLinkageRadius = 5;
+  const baseFontSize = 17;
+  const legendFontSize = 14;
+  const psLinkageColor = 'red';
+  const fontColor = 'var(--grey-6)';
+  const titleFontColor = 'black';
+  const modificationsColor = 'red';
+  const ssLeftText = 'SS: 5\'';
+  const asLeftText = 'AS: 3\'';
+  const ssRightText = '3\'';
+  const asRightText = '5\'';
 
   const ssRightOverhangs = countOverhangsOnTheRightEdge(ssBases);
   const asRightOverhangs = countOverhangsOnTheRightEdge(asBases);
-  const resultingNumberOfNucleotidesInStrands = Math.max(ssBases.length - ssRightOverhangs, asBases.length - asRightOverhangs),
-    baseDiameter = 2 * baseRadius,
-    widthOfBases = baseDiameter * (resultingNumberOfNucleotidesInStrands + Math.max(ssRightOverhangs, asRightOverhangs)),
-    widthOfLeftModification = Math.max(getTextWidth(ssThreeModification, baseFontSize), getTextWidth(asFiveModification, baseFontSize)),
-    widthOfRightModification = Math.max(getTextWidth(ssFiveModification, baseFontSize), getTextWidth(asThreeModification, baseFontSize)),
-    widthOfLeftText = Math.max(getTextWidth(ssLeftText, baseFontSize), getTextWidth(asLeftText, baseFontSize)),
-    widthOfRightText = Math.max(getTextWidth(ssRightText, baseFontSize), getTextWidth(asRightText, baseFontSize)),
-    width = widthOfLeftText + widthOfLeftModification + widthOfBases + widthOfRightModification + widthOfRightText + baseDiameter,
-    height = asExists ? 11 * baseRadius : 9 * baseRadius,
-    xOfTitle = baseRadius,// Math.round(width / 4),
-    uniqueBases = asExists ? [...new Set(ssBases.concat(asBases))] : [...new Set(ssBases)],
-    isPtoExist = asExists ? [...new Set(ssPtoStatuses.concat(asPtoStatuses))].includes(true) : [...new Set(ssPtoStatuses)].includes(true),
-    startFrom = isPtoExist ? 1 : 0,
-    xOfLeftTexts = 0,
-    xOfLeftModifications = xOfLeftTexts + widthOfLeftText - 5,
-    xOfSsRightModifications = ssRightOverhangs * baseDiameter + getXOfBaseCircles(-0.5, 0),
-    xOfAsRightModifications = asRightOverhangs * baseDiameter + getXOfBaseCircles(-0.5, 0),
-    xOfRightTexts = Math.max(xOfSsRightModifications, xOfAsRightModifications) + widthOfLeftModification + baseDiameter * (Math.max(ssRightOverhangs, asRightOverhangs)),
-    yOfTitle = baseRadius,
-    yOfSsTexts = 4 * baseRadius,
-    yOfAsTexts = 7 * baseRadius,
-    yOfComment = asExists ? 11 * baseRadius : 8.5 * baseRadius,
-    yOfSsCircles = 3.5 * baseRadius,
-    yOfAsCircles = 6.5 * baseRadius,
-    yOfCirclesInLegends = asExists ? 9 * baseRadius : 6 * baseRadius,
-    yOfTextLegend = asExists ? 9.5 * baseRadius - 3 : yOfAsCircles - 3;
-
-  let image = svg.render(width, height);
+  const resultingNumberOfNucleotidesInStrands =
+    Math.max(ssBases.length - ssRightOverhangs, asBases.length - asRightOverhangs);
+  const baseDiameter = 2 * baseRadius;
+  const widthOfBases =
+    baseDiameter * (resultingNumberOfNucleotidesInStrands + Math.max(ssRightOverhangs, asRightOverhangs));
+  const widthOfLeftModification =
+    Math.max(getTextWidth(ssThreeModification, baseFontSize), getTextWidth(asFiveModification, baseFontSize));
+  const widthOfRightModification =
+    Math.max(getTextWidth(ssFiveModification, baseFontSize), getTextWidth(asThreeModification, baseFontSize));
+  const widthOfLeftText = Math.max(getTextWidth(ssLeftText, baseFontSize), getTextWidth(asLeftText, baseFontSize));
+  const widthOfRightText = Math.max(getTextWidth(ssRightText, baseFontSize), getTextWidth(asRightText, baseFontSize));
+  const width =
+    widthOfLeftText + widthOfLeftModification + widthOfBases +
+    widthOfRightModification + widthOfRightText + baseDiameter;
+  const height = asExists ? 11 * baseRadius : 9 * baseRadius;
+  const xOfTitle = baseRadius; // Math.round(width / 4),
+  const uniqueBases = asExists ? [...new Set(ssBases.concat(asBases))] : [...new Set(ssBases)];
+  const isPtoExist =
+    asExists ? [...new Set(ssPtoStatuses.concat(asPtoStatuses))].includes(true) :
+      [...new Set(ssPtoStatuses)].includes(true);
+  const startFrom = isPtoExist ? 1 : 0;
+  const xOfLeftTexts = 0;
+  const xOfLeftModifications = xOfLeftTexts + widthOfLeftText - 5;
+  const xOfSsRightModifications = ssRightOverhangs * baseDiameter + getXOfBaseCircles(-0.5, 0);
+  const xOfAsRightModifications = asRightOverhangs * baseDiameter + getXOfBaseCircles(-0.5, 0);
+  const xOfRightTexts =
+    Math.max(xOfSsRightModifications, xOfAsRightModifications) +
+      widthOfLeftModification + baseDiameter * (Math.max(ssRightOverhangs, asRightOverhangs));
+  const yOfTitle = baseRadius;
+  const yOfSsTexts = 4 * baseRadius;
+  const yOfAsTexts = 7 * baseRadius;
+  const yOfComment = asExists ? 11 * baseRadius : 8.5 * baseRadius;
+  const yOfSsCircles = 3.5 * baseRadius;
+  const yOfAsCircles = 6.5 * baseRadius;
+  const yOfCirclesInLegends = asExists ? 9 * baseRadius : 6 * baseRadius;
+  const yOfTextLegend = asExists ? 9.5 * baseRadius - 3 : yOfAsCircles - 3;
+
+  const image = svg.render(width, height);
 
   image.append(
     svg.text(ssLeftText, xOfLeftTexts, yOfSsTexts, baseFontSize, fontColor),
@@ -162,31 +178,40 @@ export function drawAxolabsPattern(patternName: string, asExists: boolean, ssBas
     asExists ? svg.text(asFiveModification, xOfAsRightModifications, yOfAsTexts, baseFontSize, modificationsColor) : '',
     svg.text(comment, xOfLeftTexts, yOfComment, legendFontSize, fontColor),
     isPtoExist ? svg.star(baseRadius, yOfCirclesInLegends, psLinkageColor) : '',
-    isPtoExist ? svg.text('ps linkage', 2 * baseRadius - 8, yOfTextLegend, legendFontSize, fontColor) : ''
+    isPtoExist ? svg.text('ps linkage', 2 * baseRadius - 8, yOfTextLegend, legendFontSize, fontColor) : '',
   );
 
   let numberOfSsNucleotides = 0;
-  for (let i = 0; i < ssBases.length; i++)
+  for (let i = 0; i < ssBases.length; i++) {
     if (ssBases[i].slice(-3) != '(o)')
       numberOfSsNucleotides++;
+  }
   let nucleotideCounter = numberOfSsNucleotides;
   for (let i = ssBases.length - 1; i > -1; i--) {
     if (ssBases[i].slice(-3) != '(o)')
       nucleotideCounter--;
     image.append(
       svg.circle(getXOfBaseCircles(i, ssRightOverhangs), yOfSsCircles, baseRadius, getBaseColor(ssBases[i])),
-      svg.text(getTextInsideCircle(ssBases, i, nucleotideCounter, numberOfSsNucleotides, enumerateModifications), getXOfBaseCircles(i, ssRightOverhangs) + getShiftToAlignNumberInsideCircle(ssBases, ssBases.length - i, numberOfSsNucleotides - nucleotideCounter), yOfSsTexts, baseFontSize, getFontColorVisibleOnBackground(axolabsMap[ssBases[i]]["color"])),
-      ssPtoStatuses[i] ? svg.star(getXOfBaseCircles(i, ssRightOverhangs) + baseRadius, yOfSsTexts + psLinkageRadius, psLinkageColor) : ''
+      svg.text(getTextInsideCircle(ssBases, i, nucleotideCounter, numberOfSsNucleotides, enumerateModifications),
+        getXOfBaseCircles(i, ssRightOverhangs) +
+        getShiftToAlignNumberInsideCircle(ssBases, ssBases.length - i, numberOfSsNucleotides - nucleotideCounter),
+        yOfSsTexts, baseFontSize, getFontColorVisibleOnBackground(axolabsMap[ssBases[i]]['color'])),
+      ssPtoStatuses[i] ?
+        svg.star(getXOfBaseCircles(i, ssRightOverhangs) + baseRadius, yOfSsTexts + psLinkageRadius, psLinkageColor) :
+        '',
     );
   }
   image.append(
-    ssPtoStatuses[ssBases.length] ? svg.star(getXOfBaseCircles(ssBases.length, ssRightOverhangs) + baseRadius, yOfSsTexts + psLinkageRadius, psLinkageColor) : ''
+    ssPtoStatuses[ssBases.length] ?
+      svg.star(getXOfBaseCircles(ssBases.length, ssRightOverhangs) +
+      baseRadius, yOfSsTexts + psLinkageRadius, psLinkageColor) : '',
   );
 
   let numberOfAsNucleotides = 0;
-  for (let i = 0; i < asBases.length; i++)
+  for (let i = 0; i < asBases.length; i++) {
     if (asBases[i].slice(-3) != '(o)')
       numberOfAsNucleotides++;
+  }
   if (asExists) {
     let nucleotideCounter = numberOfAsNucleotides;
     for (let i = asBases.length - 1; i > -1; i--) {
@@ -194,21 +219,31 @@ export function drawAxolabsPattern(patternName: string, asExists: boolean, ssBas
         nucleotideCounter--;
       image.append(
         svg.circle(getXOfBaseCircles(i, asRightOverhangs), yOfAsCircles, baseRadius, getBaseColor(asBases[i])),
-        svg.text(getTextInsideCircle(asBases, i, numberOfAsNucleotides - nucleotideCounter - 1, numberOfAsNucleotides, enumerateModifications), getXOfBaseCircles(i, asRightOverhangs) + getShiftToAlignNumberInsideCircle(asBases, i, nucleotideCounter + 1), yOfAsTexts, baseFontSize, getFontColorVisibleOnBackground(axolabsMap[asBases[i]]["color"])),
-        asPtoStatuses[i] ? svg.star(getXOfBaseCircles(i, asRightOverhangs) + baseRadius, yOfAsTexts + psLinkageRadius, psLinkageColor) : ''
+        svg.text(getTextInsideCircle(
+          asBases, i, numberOfAsNucleotides - nucleotideCounter - 1, numberOfAsNucleotides, enumerateModifications),
+        getXOfBaseCircles(i, asRightOverhangs) +
+          getShiftToAlignNumberInsideCircle(asBases, i, nucleotideCounter + 1),
+        yOfAsTexts, baseFontSize, getFontColorVisibleOnBackground(axolabsMap[asBases[i]]['color'])),
+        asPtoStatuses[i] ? svg.star(getXOfBaseCircles(i, asRightOverhangs) +
+          baseRadius, yOfAsTexts + psLinkageRadius, psLinkageColor) : '',
       );
     }
     image.append(
-      asPtoStatuses[asBases.length] ? svg.star(getXOfBaseCircles(asBases.length, asRightOverhangs) + baseRadius, yOfAsTexts + psLinkageRadius, psLinkageColor) : ''
+      asPtoStatuses[asBases.length] ?
+        svg.star(getXOfBaseCircles(asBases.length, asRightOverhangs) +
+         baseRadius, yOfAsTexts + psLinkageRadius, psLinkageColor) : '',
     );
   }
 
-  let title = patternName + ' for ' + String(numberOfSsNucleotides) + (asExists ? '/' + String(numberOfAsNucleotides) : '') + 'mer';
+  const title = patternName + ' for ' +
+    String(numberOfSsNucleotides) + (asExists ? '/' + String(numberOfAsNucleotides) : '') + 'mer';
   image.append(svg.text(title, xOfTitle, yOfTitle, baseFontSize, titleFontColor));
-  for (let i = 0; i < uniqueBases.length; i++)
+  for (let i = 0; i < uniqueBases.length; i++) {
     image.append(
       svg.circle(getEquidistantXForLegend(i), yOfCirclesInLegends, legendRadius, getBaseColor(uniqueBases[i])),
-      svg.text(uniqueBases[i], getEquidistantXForLegend(i) + legendRadius + 4, yOfTextLegend, legendFontSize, fontColor)
+      svg.text(uniqueBases[i], getEquidistantXForLegend(i) +
+        legendRadius + 4, yOfTextLegend, legendFontSize, fontColor),
     );
+  }
   return image;
-}
+}