@datagrok/sequence-translator 1.0.17 → 1.1.4

package/src/sdf-tab/sequence-codes-tools.ts

@@ -1,347 +0,0 @@
-import {
-  map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, DELIMITER, gcrsCodesWithoutSmiles, NUCLEOTIDES
-} from '../hardcode-to-be-eliminated/map';
-import {sortByStringLengthInDescendingOrder} from '../utils/helpers';
-import {
-  asoGapmersNucleotidesToBioSpring, asoGapmersNucleotidesToGcrs,
-  asoGapmersBioSpringToNucleotides, asoGapmersBioSpringToGcrs, gcrsToMermade12, siRnaNucleotideToBioSpringSenseStrand,
-  siRnaNucleotideToAxolabsSenseStrand, siRnaNucleotidesToGcrs, siRnaBioSpringToNucleotides,
-  siRnaBioSpringToAxolabs, siRnaBioSpringToGcrs, siRnaAxolabsToNucleotides,
-  siRnaAxolabsToBioSpring, siRnaAxolabsToGcrs, siRnaGcrsToNucleotides,
-  siRnaGcrsToBioSpring, siRnaGcrsToAxolabs, gcrsToNucleotides, gcrsToLcms
-} from '../hardcode-to-be-eliminated/converters';
-
-const noTranslationTableAvailable = 'No translation table available';
-export const undefinedInputSequence = 'Type of input sequence is undefined';
-
-export function getFormat(sequence: string): string | null {
-  const possibleSynthesizers = getListOfPossibleSynthesizersByFirstMatchedCode(sequence);
-
-  if (possibleSynthesizers.length == 0)
-    return null;
-
-  let outputIndex = 0;
-
-  const firstUniqueCharacters = ['r', 'd'];
-
-  possibleSynthesizers.forEach((synthesizer) => {
-    const codes = getAllCodesOfSynthesizer(synthesizer);
-    while (outputIndex < sequence.length) {
-      const matchedCode = codes.find((c) => c == sequence.slice(outputIndex, outputIndex + c.length));
-
-      if (matchedCode == null)
-        break;
-
-      if ( // for mistake pattern 'rAA'
-        outputIndex > 1 &&
-        NUCLEOTIDES.includes(sequence[outputIndex]) &&
-        firstUniqueCharacters.includes(sequence[outputIndex - 2])
-      ) break;
-
-      if ( // for mistake pattern 'ArA'
-        firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
-        NUCLEOTIDES.includes(sequence[outputIndex])
-      ) {
-        outputIndex++;
-        break;
-      }
-
-      outputIndex += matchedCode.length;
-    }
-  });
-
-  const indexOfFirstNotValidChar = (outputIndex == sequence.length) ? -1 : outputIndex;
-  if (indexOfFirstNotValidChar != -1)
-    return possibleSynthesizers[0];
-
-  const possibleTechnologies = getListOfPossibleTechnologiesByFirstMatchedCode(sequence, possibleSynthesizers[0]);
-
-  if (possibleTechnologies.length == 0)
-    return null;
-
-  outputIndex = 0;
-
-  possibleTechnologies.forEach((technology: string) => {
-    const codes = Object.keys(map[possibleSynthesizers[0]][technology]);
-    while (outputIndex < sequence.length) {
-      const matchedCode = codes.find((c) => c == sequence.slice(outputIndex, outputIndex + c.length));
-
-      if (matchedCode == null)
-        break;
-
-      if ( // for mistake pattern 'rAA'
-        outputIndex > 1 &&
-        NUCLEOTIDES.includes(sequence[outputIndex]) &&
-        firstUniqueCharacters.includes(sequence[outputIndex - 2])
-      ) break;
-
-      if ( // for mistake pattern 'ArA'
-        firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
-        NUCLEOTIDES.includes(sequence[outputIndex])
-      ) {
-        outputIndex++;
-        break;
-      }
-
-      outputIndex += matchedCode.length;
-    }
-  });
-
-  return possibleSynthesizers[0];
-}
-
-
-export function isValidSequence(sequence: string, format: string | null): {
-  indexOfFirstNotValidChar: number,
-  synthesizer: string[] | null,
-  // technology: string[] | null
-} {
-  const possibleSynthesizers = format == null ?
-    getListOfPossibleSynthesizersByFirstMatchedCode(sequence) :
-    [format];
-
-  // if (possibleSynthesizers.length > 1) {
-  //   const synthesizer = ui.choiceInput('Choose synthesizer from list: ', possibleSynthesizers[0],
-  //  possibleSynthesizers);
-  //   ui.dialog('Choose Synthesizer')
-  //     .add(ui.panel([synthesizer.root], {style: {fontWeight: 'bold'}}))
-  //     .onOK(() => possibleSynthesizers = [synthesizer.value])
-  //     .onCancel(() => {
-  //       possibleSynthesizers = [possibleSynthesizers[0]];
-  //       grok.shell.warning('Input sequence is expected to be in format ' + possibleSynthesizers[0]);
-  //     })
-  //     .show();
-  // } else if (possibleSynthesizers.length == 0)
-  if (possibleSynthesizers.length == 0)
-    return {indexOfFirstNotValidChar: 0, synthesizer: null};//, technology: null};
-
-  const outputIndices = Array(possibleSynthesizers.length).fill(0);
-
-  const firstUniqueCharacters = ['r', 'd'];
-  possibleSynthesizers.forEach(function(synthesizer, i) {
-    const codes = sortByStringLengthInDescendingOrder(getAllCodesOfSynthesizer(synthesizer));
-    while (outputIndices[i] < sequence.length) {
-      const matchedCode = codes.find((c) => c == sequence.slice(outputIndices[i], outputIndices[i] + c.length));
-
-      if (matchedCode == null)
-        break;
-
-      if ( // for mistake pattern 'rAA'
-        outputIndices[i] > 1 &&
-        NUCLEOTIDES.includes(sequence[outputIndices[i]]) &&
-        firstUniqueCharacters.includes(sequence[outputIndices[i] - 2])
-      ) break;
-
-      if ( // for mistake pattern 'ArA'
-        firstUniqueCharacters.includes(sequence[outputIndices[i] + 1]) &&
-        NUCLEOTIDES.includes(sequence[outputIndices[i]])
-      ) {
-        outputIndices[i]++;
-        break;
-      }
-
-      outputIndices[i] += matchedCode.length;
-    }
-  });
-
-  const outputIndex = Math.max(...outputIndices);
-  const synthesizer = possibleSynthesizers[outputIndices.indexOf(outputIndex)];
-  const indexOfFirstNotValidChar = (outputIndex == sequence.length) ? -1 : outputIndex;
-  if (indexOfFirstNotValidChar != -1) {
-    return {
-      indexOfFirstNotValidChar: indexOfFirstNotValidChar,
-      synthesizer: [synthesizer],
-      // technology: null,
-    };
-  }
-
-  // const possibleTechnologies =
-  //   getListOfPossibleTechnologiesByFirstMatchedCode(sequence, possibleSynthesizers[outputIndex]);
-
-  // if (possibleTechnologies.length > 1) {
-  //   const technology = ui.choiceInput('Choose technology from list: ', possibleTechnologies[0],
-  // possibleTechnologies);
-  //   ui.dialog('Choose Technology')
-  //     .add(ui.panel([technology.root], {style: {fontWeight: 'bold'}}))
-  //     .onOK(() => possibleTechnologies = [technology.value])
-  //     .onCancel(() => {
-  //       possibleTechnologies = [possibleTechnologies[0]];
-  //       grok.shell.warning('Input sequence is expected to be in format ' + possibleTechnologies[0]);
-  //     })
-  //     .show();
-  // } else if (possibleTechnologies.length == 0)
-  // if (possibleTechnologies.length == 0)
-  //   return {indexOfFirstNotValidChar: 0, synthesizer: [possibleSynthesizers[3]], technology: null};
-
-  // outputIndex = 0;
-
-  // possibleTechnologies.forEach((technology: string) => {
-  //   const codes = Object.keys(map[possibleSynthesizers[0]][technology]);
-  //   while (outputIndex < sequence.length) {
-  //     const matchedCode = codes.find((c) => c == sequence.slice(outputIndex, outputIndex + c.length));
-
-  //     if (matchedCode == null)
-  //       break;
-
-  //     if ( // for mistake pattern 'rAA'
-  //       outputIndex > 1 &&
-  //       nucleotides.includes(sequence[outputIndex]) &&
-  //       firstUniqueCharacters.includes(sequence[outputIndex - 2])
-  //     ) break;
-
-  //     if ( // for mistake pattern 'ArA'
-  //       firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
-  //       nucleotides.includes(sequence[outputIndex])
-  //     ) {
-  //       outputIndex++;
-  //       break;
-  //     }
-
-  //     outputIndex += matchedCode.length;
-  //   }
-  // });
-
-  return {
-    indexOfFirstNotValidChar: indexOfFirstNotValidChar,
-    synthesizer: [synthesizer],
-    // technology: [possibleTechnologies[0]],
-  };
-}
-
-export function getAllCodesOfSynthesizer(synthesizer: string): string[] {
-  let codes: string[] = [];
-  for (const technology of Object.keys(map[synthesizer]))
-    codes = codes.concat(Object.keys(map[synthesizer][technology]));
-  return codes.concat(Object.keys(MODIFICATIONS)).concat(DELIMITER);
-}
-
-function getListOfPossibleSynthesizersByFirstMatchedCode(sequence: string): string[] {
-  let synthesizers: string[] = [];
-  Object.keys(map).forEach((synthesizer: string) => {
-    let codes = sortByStringLengthInDescendingOrder(getAllCodesOfSynthesizer(synthesizer));
-    if (synthesizer == 'Janssen GCRS Codes')
-      codes = codes.concat(gcrsCodesWithoutSmiles);
-    //TODO: get first non-dropdown code when there are two modifications
-    let start = 0;
-    for (let i = 0; i < sequence.length; i++) {
-      if (sequence[i] == ')' && i != sequence.length - 1) {
-        start = i + 1;
-        break;
-      }
-    }
-    if (gcrsCodesWithoutSmiles.some((s: string) => s == sequence.slice(start, start + s.length)))
-      synthesizers = ['Janssen GCRS Codes'];
-    if (codes.some((s: string) => s == sequence.slice(start, start + s.length)))
-      synthesizers.push(synthesizer);
-  });
-  return synthesizers;
-}
-
-function getListOfPossibleTechnologiesByFirstMatchedCode(sequence: string, synthesizer: string): string[] {
-  const technologies: string[] = [];
-  Object.keys(map[synthesizer]).forEach((technology: string) => {
-    const codes = Object.keys(map[synthesizer][technology]).concat(Object.keys(MODIFICATIONS));
-    if (codes.some((s) => s == sequence.slice(0, s.length)))
-      technologies.push(technology);
-  });
-  return technologies;
-}
-
-export function convertSequence(sequence: string, output: {
-  indexOfFirstNotValidChar: number, synthesizer: string[] | null}) {//, technology: string[] | null}) {
-  if (output.indexOfFirstNotValidChar != -1) {
-    return {
-      // type: '',
-      indexOfFirstNotValidChar: JSON.stringify(output),
-      Error: undefinedInputSequence,
-    };
-  }
-  if (output.synthesizer!.includes(SYNTHESIZERS.RAW_NUCLEOTIDES)) {//&& output.technology!.includes(TECHNOLOGIES.DNA)) {
-    return {
-      type: SYNTHESIZERS.RAW_NUCLEOTIDES, // + ' ' + TECHNOLOGIES.DNA,
-      Nucleotides: sequence,
-      BioSpring: asoGapmersNucleotidesToBioSpring(sequence),
-      GCRS: asoGapmersNucleotidesToGcrs(sequence),
-    };
-  }
-  if (output.synthesizer!.includes(SYNTHESIZERS.BIOSPRING)) {
-    // && output.technology!.includes(TECHNOLOGIES.ASO_GAPMERS)) {
-    return {
-      type: SYNTHESIZERS.BIOSPRING + ' ' + TECHNOLOGIES.ASO_GAPMERS,
-      Nucleotides: asoGapmersBioSpringToNucleotides(sequence),
-      BioSpring: sequence,
-      GCRS: asoGapmersBioSpringToGcrs(sequence),
-    };
-  }
-  if (output.synthesizer!.includes(SYNTHESIZERS.GCRS)) { // && output.technology!.includes(TECHNOLOGIES.ASO_GAPMERS)) {
-    return {
-      type: SYNTHESIZERS.GCRS + ' ' + TECHNOLOGIES.ASO_GAPMERS,
-      Nucleotides: gcrsToNucleotides(sequence),
-      BioSpring: siRnaGcrsToBioSpring(sequence),
-      Axolabs: siRnaGcrsToAxolabs(sequence),
-      Mermade12: gcrsToMermade12(sequence),
-      GCRS: sequence,
-      LCMS: gcrsToLcms(sequence),
-    };
-  }
-  if (output.synthesizer!.includes(SYNTHESIZERS.RAW_NUCLEOTIDES)) {
-    // && output.technology!.includes(TECHNOLOGIES.RNA)) {
-    return {
-      type: SYNTHESIZERS.RAW_NUCLEOTIDES + ' ' + TECHNOLOGIES.RNA,
-      Nucleotides: sequence,
-      BioSpring: siRnaNucleotideToBioSpringSenseStrand(sequence),
-      Axolabs: siRnaNucleotideToAxolabsSenseStrand(sequence),
-      GCRS: siRnaNucleotidesToGcrs(sequence),
-    };
-  }
-  if (output.synthesizer!.includes(SYNTHESIZERS.BIOSPRING)) { // && output.technology!.includes(TECHNOLOGIES.SI_RNA)) {
-    return {
-      type: SYNTHESIZERS.BIOSPRING + ' ' + TECHNOLOGIES.SI_RNA,
-      Nucleotides: siRnaBioSpringToNucleotides(sequence),
-      BioSpring: sequence,
-      Axolabs: siRnaBioSpringToAxolabs(sequence),
-      GCRS: siRnaBioSpringToGcrs(sequence),
-    };
-  }
-  if (output.synthesizer!.includes(SYNTHESIZERS.AXOLABS)) {
-    return {
-      type: SYNTHESIZERS.AXOLABS + ' ' + TECHNOLOGIES.SI_RNA,
-      Nucleotides: siRnaAxolabsToNucleotides(sequence),
-      BioSpring: siRnaAxolabsToBioSpring(sequence),
-      Axolabs: sequence,
-      GCRS: siRnaAxolabsToGcrs(sequence),
-    };
-  }
-  if (output.synthesizer!.includes(SYNTHESIZERS.GCRS)) { // && output.technology!.includes(TECHNOLOGIES.SI_RNA)) {
-    return {
-      type: SYNTHESIZERS.GCRS + ' ' + TECHNOLOGIES.SI_RNA,
-      Nucleotides: siRnaGcrsToNucleotides(sequence),
-      BioSpring: siRnaGcrsToBioSpring(sequence),
-      Axolabs: siRnaGcrsToAxolabs(sequence),
-      MM12: gcrsToMermade12(sequence),
-      GCRS: sequence,
-      LCMS: gcrsToLcms(sequence),
-    };
-  }
-  if (output.synthesizer!.includes(SYNTHESIZERS.GCRS)) {
-    return {
-      type: SYNTHESIZERS.GCRS,
-      Nucleotides: gcrsToNucleotides(sequence),
-      GCRS: sequence,
-      Mermade12: gcrsToMermade12(sequence),
-      LCMS: gcrsToLcms(sequence),
-    };
-  }
-  if (output.synthesizer!.includes(SYNTHESIZERS.MERMADE_12)) {
-    return {
-      type: SYNTHESIZERS.MERMADE_12,
-      Nucleotides: noTranslationTableAvailable,
-      GCRS: noTranslationTableAvailable,
-      Mermade12: sequence,
-    };
-  }
-  return {
-    type: undefinedInputSequence,
-    Nucleotides: undefinedInputSequence,
-  };
-}