Class NucleicAcidAbstract

constructor

• new NucleicAcid(nucleicAcidType): NucleicAcid

• Parameters

  • nucleicAcidType: NucleicAcidType

    The type of NucleicAcid

  Returns NucleicAcid

Readonly nucleicAcidType

contains

• contains(subsequence): boolean

• Checks if the sequence contains the specified subsequence

  Parameters

  • subsequence: string | NucleicAcid

    The subsequence to search for (string or same nucleic acid type)

  Returns boolean

  True if the subsequence is found, false otherwise

  Example

  const dna = new DNA('ATCGATCG');
  console.log(dna.contains('TCG')); // true
  console.log(dna.contains('AAA')); // false
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endsWith

• endsWith(suffix): boolean

• Checks if the sequence ends with the specified suffix

  Parameters

  • suffix: string | NucleicAcid

    The suffix to check for (string or same nucleic acid type)

  Returns boolean

  True if the sequence ends with the suffix, false otherwise

  Example

  const dna = new DNA('ATCGATCG');
  console.log(dna.endsWith('TCG')); // true
  console.log(dna.endsWith('ATC')); // false
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equals

• equals(nucleicAcid): boolean

• Checks if the given NucleicAcid is equal

  Parameters

  • nucleicAcid: NucleicAcid

    The NucleicAcid to compare

  Returns boolean

  True if the NucleicAcids are equal, false otherwise

Abstract getComplement

• getComplement(): NucleicAcid

• Returns the complement as a new nucleic acid instance of the same type This is the object-oriented API for getting complements

  Returns NucleicAcid

  A new nucleic acid instance containing the complement sequence

  Example

  const dna = new DNA('ATCG');
  const complement = dna.getComplement(); // Returns new DNA('TAGC')
  
  const rna = new RNA('AUCG');
  const complement = rna.getComplement(); // Returns new RNA('UAGC')
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getComplementSequence

• getComplementSequence(): string

• Returns the complement of the sequence

  Returns string

  String representing the complement of the sequence

Abstract getReverseComplement

• getReverseComplement(): NucleicAcid

• Returns the reverse complement as a new nucleic acid instance of the same type This represents the opposite strand of double-stranded nucleic acids

  Returns NucleicAcid

  A new nucleic acid instance containing the reverse complement sequence

  Example

  const dna = new DNA('ATCG');
  const reverseComplement = dna.getReverseComplement(); // Returns new DNA('CGAT')
  
  // Chainable operations
  const result = dna.getReverseComplement().getComplement(); // Returns new DNA('ATCG')
  
  const rna = new RNA('AUCG');
  const reverseComplement = rna.getReverseComplement(); // Returns new RNA('CGAU')
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getReverseComplementSequence

• getReverseComplementSequence(): string

• Returns the reverse complement of the sequence This represents the opposite strand of double-stranded nucleic acids

  Returns string

  String representing the reverse complement of the sequence

  Example

  const dna = new DNA('ATCG');
  console.log(dna.getReverseComplementSequence()); // 'CGAT'
  
  const rna = new RNA('AUCG');
  console.log(rna.getReverseComplementSequence()); // 'CGAU'
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Abstract getSequence

• getSequence(): string

• Returns string

Abstract getSubsequence

• getSubsequence(start, end?): NucleicAcid

• Returns a subsequence from the specified start position to the end position

  Parameters

  • start: number

    The starting position (inclusive, 0-based)
  • Optional end: number

    The ending position (exclusive, 0-based). If not specified, goes to end of sequence

  Returns NucleicAcid

  A new instance of the same nucleic acid type containing the subsequence

  Example

  const dna = new DNA('ATCGATCG');
  const sub = dna.getSubsequence(2, 5); // Creates new DNA with 'CGA'
  console.log(sub.getSequence()); // 'CGA'
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indexOf

• indexOf(subsequence, startPosition?): number

• Returns the index of the first occurrence of the specified subsequence

  Parameters

  • subsequence: string | NucleicAcid

    The subsequence to search for (string or same nucleic acid type)
  • startPosition: number = 0

    The position to start searching from (default: 0)

  Returns number

  The index of the first occurrence, or -1 if not found

  Example

  const dna = new DNA('ATCGATCG');
  console.log(dna.indexOf('TCG')); // 1
  console.log(dna.indexOf('TCG', 2)); // 5
  console.log(dna.indexOf('AAA')); // -1
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length

• length(): number

• Returns the length of the nucleic acid sequence

  Returns number

  The length of the sequence in nucleotides/base pairs

  Example

  const dna = new DNA('ATCG');
  console.log(dna.length()); // 4
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startsWith

• startsWith(prefix): boolean

• Checks if the sequence starts with the specified prefix

  Parameters

  • prefix: string | NucleicAcid

    The prefix to check for (string or same nucleic acid type)

  Returns boolean

  True if the sequence starts with the prefix, false otherwise

  Example

  const dna = new DNA('ATCGATCG');
  console.log(dna.startsWith('ATC')); // true
  console.log(dna.startsWith('GTC')); // false
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