# All files / src/sequence-utils sequence-processor.ts

96.29% Statements 26/27
75% Branches 9/12
100% Functions 3/3
96.15% Lines 25/26

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     import { commentLineRE, extractNameFromFASTAHeader } from '.';
    import { sequenceValidator } from './sequenceValidator';

    const whitespaceRE = /\s+/g;

    export type SequenceObject = {
      raw: string;
      name: string;
      header: string;
      sequence: string;
      likelyType?: 'aa' | 'na';
      valid?: boolean;
      message?: string;
    };

    const getNewSequenceObject = (): SequenceObject => ({
      raw: '',
      name: '',
      header: '',
      sequence: '',
    });

    const validate = (
      sequenceObject: SequenceObject,
      minimumLength?: number,
      strict?: boolean
    ): SequenceObject => {
      const validation = sequenceValidator(
        sequenceObject.sequence,
        minimumLength,
        strict
      );
      return { ...validation, ...sequenceObject };
    };

    const sequenceProcessor = (
      rawText: string,
      minimumLength?: number,
      strict?: boolean // Strict validates only conventional amino acids (no ambiguous amino acids)
    ): SequenceObject[] => {
      const sequences: SequenceObject[] = [];
      let currentSequence = getNewSequenceObject();
      for (const line of rawText.split('\n')) {
        // for each line

        if (commentLineRE.test(line)) {
          // if this is a comment line

          if (currentSequence.sequence) {
            // if we already have sequence data being processed
            // store current sequence
            sequences.push(validate(currentSequence, minimumLength, strict));

            // and start new sequence
            currentSequence = getNewSequenceObject();
          }

          Iif (currentSequence.header) {
            // multiline header
            currentSequence.header += '\n';
          } else {
            // first header line
            const name = extractNameFromFASTAHeader(line);
            Eif (name) {
              currentSequence.name = name;
            }
          }
          currentSequence.header += line;
        } else {
          // if this is a sequence line
          currentSequence.sequence += line.replace(whitespaceRE, '');
        }

        // store the raw string
        if (currentSequence.raw) {
          currentSequence.raw += '\n';
        }
        currentSequence.raw += line;
      }

      Eif (currentSequence.raw) {
        sequences.push(validate(currentSequence, minimumLength, strict));
      }

      return sequences;
    };

    export default sequenceProcessor;