@teselagen/sequence-utils 0.1.1

package/getAminoAcidDataForEachBaseOfDna.d.ts

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+/**
+ * @private
+ * Gets aminoAcid data, including position in string and position in codon
+ * from the sequenceString and the direction of the translation
+ * @param  {String} sequenceString The dna sequenceString.
+ * @param  {boolean} forward Should we find forward facing orfs or reverse facing orfs
+ * @param  {boolean} isProteinSequence We're passing in a sequence of AA chars instead of DNA chars (slightly confusing but we'll still use the dna indexing for rendering in OVE)
+ * @return [{
+        aminoAcid:
+        positionInCodon:
+      }]
+ */
+export default function getAminoAcidDataForEachBaseOfDna(originalSequenceString: any, forward: boolean, optionalSubrangeRange: any, isProteinSequence: boolean): {
+    aminoAcid: any;
+    positionInCodon: number;
+    aminoAcidIndex: number;
+    sequenceIndex: any;
+    codonRange: any;
+    fullCodon: boolean;
+}[];

package/getAminoAcidFromSequenceTriplet.d.ts

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+export default function getAminoAcidFromSequenceTriplet(sequenceString: any): any;

package/getAminoAcidStringFromSequenceString.d.ts

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+export default function getAminoAcidStringFromSequenceString(sequenceString: any): string;

package/getCodonRangeForAASliver.d.ts

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+export default function getCodonRangeForAASliver(aminoAcidPositionInSequence: any, aminoAcidSliver: any, AARepresentationOfTranslation: any, relativeAAPositionInTranslation: any): {
+    start: any;
+    end: any;
+};

package/getComplementAminoAcidStringFromSequenceString.d.ts

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+export default function getComplementAminoAcidStringFromSequenceString(sequenceString: any): string;

package/getComplementSequenceAndAnnotations.d.ts

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+export default function getComplementSequenceAndAnnotations(pSeqObj: any, options?: {}): any;

package/getComplementSequenceString.d.ts

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+export default function getComplementSequenceString(sequence: any): string;

package/getCutsiteType.d.ts

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+export default function getCutsiteType(restrictionEnzyme: any): "blunt" | "5' overhang" | "3' overhang";

package/getCutsitesFromSequence.d.ts

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+export default function getCutsitesFromSequence(sequence: any, circular: any, restrictionEnzymes: any): {};

package/getDegenerateDnaStringFromAAString.d.ts

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+export default function getDegenerateDnaStringFromAAString(aaString: any): any;

package/getDegenerateRnaStringFromAAString.d.ts

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+export default function getDegenerateRnaStringFromAAString(aaString: any): any;

package/getDigestFragmentsForCutsites.d.ts

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+export default function getDigestFragmentsForCutsites(sequenceLength: any, circular: any, cutsites: any, opts?: {}): any[];

package/getDigestFragmentsForRestrictionEnzymes.d.ts

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+export default function getDigestFragmentsForRestrictionEnzymes(sequence: any, circular: any, restrictionEnzymeOrEnzymes: any, opts: any): any[];

package/getInsertBetweenVals.d.ts

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+export default function getInsertBetweenVals(caretPosition: any, selectionLayer: any, sequenceLength: any): any[];

package/getLeftAndRightOfSequenceInRangeGivenPosition.d.ts

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+export default function getLeftAndRightOfSequenceInRangeGivenPosition(range: any, position: any, sequence: any): {
+    leftHandSide: string;
+    rightHandSide: string;
+};

package/getMassOfAaString.d.ts

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+/**
+ * @param {string} aaString A string of amino acid characters
+ * @param {number} numsAfterDecimal the number of digits to round to after the decimal point, must be greater than 0
+ * @param {boolean} divideByThree divide the final mass by three,
+ *  this is useful in situtations where nucelotides are converted to
+ *  amino acids in a way that the amino acid appears three times
+ * @returns The sum of the mass of all amino acids in the string
+ */
+export default function getMassOfAaString(aaString: string, numsAfterDecimal?: number, divideByThree?: boolean): number;

package/getOrfsFromSequence.d.ts

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+/**
+ * @private
+ * Finds ORFs in a given DNA forward in a given frame.
+ * @param  {Int} frame The frame to look in.
+ * @param  {String}sequence The dna sequence.
+ * @param  {Int} minimumOrfSize The minimum length of ORF to return.
+ * @param  {boolean} forward Should we find forward facing orfs or reverse facing orfs
+ * @return {Teselagen.bio.orf.ORF[]} The list of ORFs found.
+ */
+export default function getOrfsFromSequence(options: any): Teselagen.bio.orf.ORF[];

package/getOverlapBetweenTwoSequences.d.ts

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+/**
+ * This function gets the overlapping of one sequence to another based on sequence equality.
+ *
+ * @param  {string} sequenceToFind
+ * @param  {string} sequenceToSearchIn
+ * @param  {object} options            optional
+ * @return {object || null}            null if no overlap exists or a range object with .start and .end properties
+ */
+export default function getOverlapBetweenTwoSequences(sequenceToFind: string, sequenceToSearchIn: string, options: object): object;

package/getPossiblePartsFromSequenceAndEnzymes.d.ts

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+export default function getPossiblePartsFromSequenceAndEnzyme(seqData: any, restrictionEnzymes: any): any[];

package/getReverseAminoAcidStringFromSequenceString.d.ts

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+export default function getReverseAminoAcidStringFromSequenceString(sequenceString: any): string;

package/getReverseComplementAminoAcidStringFromSequenceString.d.ts

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+export default function getReverseComplementAminoAcidStringFromSequenceString(sequenceString: any): string;

package/getReverseComplementAnnotation.d.ts

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+export default function getReverseComplementAnnotation(annotation: any, sequenceLength: any): any;

package/getReverseComplementSequenceAndAnnotations.d.ts

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+export default function getReverseComplementSequenceAndAnnoations(pSeqObj: any, options?: {}): any;

package/getReverseComplementSequenceString.d.ts

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+export default function getReverseComplementSequenceString(sequence: any): string;

package/getReverseSequenceString.d.ts

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+export default function getReverseSequenceString(sequence: any): string;

package/getSequenceDataBetweenRange.d.ts

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+export default function getSequenceDataBetweenRange(seqData: any, range: any, options?: {}): any;

package/getVirtualDigest.d.ts

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+export default function getVirtualDigest({ cutsites, sequenceLength, isCircular, computePartialDigest, computePartialDigestDisabled, computeDigestDisabled }: {
+    cutsites: any;
+    sequenceLength: any;
+    isCircular: any;
+    computePartialDigest: any;
+    computePartialDigestDisabled: any;
+    computeDigestDisabled: any;
+}): {
+    computePartialDigestDisabled: any;
+    computeDigestDisabled: any;
+    fragments: any[];
+    overlappingEnzymes: any[];
+};

package/guessIfSequenceIsDnaAndNotProtein.d.ts

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+export default function guessIfSequenceIsDnaAndNotProtein(seq: any, options?: {}): boolean;

package/index.d.ts

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+export * from "./computeDigestFragments";
+export * from "./diffUtils";
+export * as bioData from "./bioData";
+export { default as getAllInsertionsInSeqReads } from "./getAllInsertionsInSeqReads";
+export { default as annotateSingleSeq } from "./annotateSingleSeq";
+export { default as getDegenerateDnaStringFromAAString } from "./getDegenerateDnaStringFromAAString";
+export { default as getDegenerateRnaStringFromAAString } from "./getDegenerateRnaStringFromAAString";
+export { default as getVirtualDigest } from "./getVirtualDigest";
+export { default as isEnzymeType2S } from "./isEnzymeType2S";
+export { default as insertGapsIntoRefSeq } from "./insertGapsIntoRefSeq";
+export { default as adjustBpsToReplaceOrInsert } from "./adjustBpsToReplaceOrInsert";
+export { default as annotationTypes } from "./annotationTypes";
+export { default as calculatePercentGC } from "./calculatePercentGC";
+export { default as calculateTm } from "./calculateTm";
+export { default as cutSequenceByRestrictionEnzyme } from "./cutSequenceByRestrictionEnzyme";
+export { default as deleteSequenceDataAtRange } from "./deleteSequenceDataAtRange";
+export { default as DNAComplementMap } from "./DNAComplementMap";
+export { default as doesEnzymeChopOutsideOfRecognitionSite } from "./doesEnzymeChopOutsideOfRecognitionSite";
+export { default as aliasedEnzymesByName } from "./aliasedEnzymesByName";
+export { default as defaultEnzymesByName } from "./defaultEnzymesByName";
+export { default as generateSequenceData } from "./generateSequenceData";
+export { default as generateAnnotations } from "./generateAnnotations";
+export { default as filterAminoAcidSequenceString } from "./filterAminoAcidSequenceString";
+export { default as filterSequenceString } from "./filterSequenceString";
+export { default as findNearestRangeOfSequenceOverlapToPosition } from "./findNearestRangeOfSequenceOverlapToPosition";
+export { default as findOrfsInPlasmid } from "./findOrfsInPlasmid";
+export { default as findSequenceMatches } from "./findSequenceMatches";
+export { default as getAminoAcidDataForEachBaseOfDna } from "./getAminoAcidDataForEachBaseOfDna";
+export { default as getAminoAcidFromSequenceTriplet } from "./getAminoAcidFromSequenceTriplet";
+export { default as getAminoAcidStringFromSequenceString } from "./getAminoAcidStringFromSequenceString";
+export { default as getCodonRangeForAASliver } from "./getCodonRangeForAASliver";
+export { default as getComplementAminoAcidStringFromSequenceString } from "./getComplementAminoAcidStringFromSequenceString";
+export { default as getComplementSequenceAndAnnotations } from "./getComplementSequenceAndAnnotations";
+export { default as getComplementSequenceString } from "./getComplementSequenceString";
+export { default as getCutsitesFromSequence } from "./getCutsitesFromSequence";
+export { default as getCutsiteType } from "./getCutsiteType";
+export { default as getInsertBetweenVals } from "./getInsertBetweenVals";
+export { default as getLeftAndRightOfSequenceInRangeGivenPosition } from "./getLeftAndRightOfSequenceInRangeGivenPosition";
+export { default as getOrfsFromSequence } from "./getOrfsFromSequence";
+export { default as getOverlapBetweenTwoSequences } from "./getOverlapBetweenTwoSequences";
+export { default as getPossiblePartsFromSequenceAndEnzymes } from "./getPossiblePartsFromSequenceAndEnzymes";
+export { default as getReverseAminoAcidStringFromSequenceString } from "./getReverseAminoAcidStringFromSequenceString";
+export { default as getReverseComplementAminoAcidStringFromSequenceString } from "./getReverseComplementAminoAcidStringFromSequenceString";
+export { default as getReverseComplementAnnotation } from "./getReverseComplementAnnotation";
+export { default as getReverseComplementSequenceAndAnnotations } from "./getReverseComplementSequenceAndAnnotations";
+export { default as getReverseComplementSequenceString } from "./getReverseComplementSequenceString";
+export { default as getReverseSequenceString } from "./getReverseSequenceString";
+export { default as getSequenceDataBetweenRange } from "./getSequenceDataBetweenRange";
+export { default as guessIfSequenceIsDnaAndNotProtein } from "./guessIfSequenceIsDnaAndNotProtein";
+export { default as insertSequenceDataAtPosition } from "./insertSequenceDataAtPosition";
+export { default as insertSequenceDataAtPositionOrRange } from "./insertSequenceDataAtPositionOrRange";
+export { default as mapAnnotationsToRows } from "./mapAnnotationsToRows";
+export { default as prepareCircularViewData } from "./prepareCircularViewData";
+export { default as prepareRowData } from "./prepareRowData";
+export { default as proteinAlphabet } from "./proteinAlphabet";
+export { default as rotateSequenceDataToPosition } from "./rotateSequenceDataToPosition";
+export { default as rotateBpsToPosition } from "./rotateBpsToPosition";
+export { default as threeLetterSequenceStringToAminoAcidMap } from "./threeLetterSequenceStringToAminoAcidMap";
+export { default as tidyUpSequenceData } from "./tidyUpSequenceData";
+export { default as tidyUpAnnotation } from "./tidyUpAnnotation";
+export { default as condensePairwiseAlignmentDifferences } from "./condensePairwiseAlignmentDifferences";
+export { default as addGapsToSeqReads } from "./addGapsToSeqReads";
+export { default as calculateNebTm } from "./calculateNebTm";
+export { default as calculateNebTa } from "./calculateNebTa";
+export { default as getDigestFragmentsForCutsites } from "./getDigestFragmentsForCutsites";
+export { default as getDigestFragmentsForRestrictionEnzymes } from "./getDigestFragmentsForRestrictionEnzymes";
+export { default as convertDnaCaretPositionOrRangeToAA } from "./convertDnaCaretPositionOrRangeToAA";
+export { default as convertAACaretPositionOrRangeToDna } from "./convertAACaretPositionOrRangeToDna";
+export { default as aminoAcidToDegenerateDnaMap } from "./aminoAcidToDegenerateDnaMap";
+export { default as aminoAcidToDegenerateRnaMap } from "./aminoAcidToDegenerateRnaMap";
+export { default as degenerateDnaToAminoAcidMap } from "./degenerateDnaToAminoAcidMap";
+export { default as degenerateRnaToAminoAcidMap } from "./degenerateRnaToAminoAcidMap";
+export { default as getMassOfAaString } from "./getMassOfAaString";
+export { default as shiftAnnotationsByLen } from "./shiftAnnotationsByLen";
+export { default as adjustAnnotationsToInsert } from "./adjustAnnotationsToInsert";
+import { getFeatureToColorMap } from "./featureTypesAndColors";
+import { getFeatureTypes } from "./featureTypesAndColors";
+import { genbankFeatureTypes } from "./featureTypesAndColors";
+import { getMergedFeatureMap } from "./featureTypesAndColors";
+export const FeatureTypes: any[];
+export const featureColors: {};
+import { autoAnnotate } from "./autoAnnotate";
+import { convertApELikeRegexToRegex } from "./autoAnnotate";
+import { convertProteinSeqToDNAIupac } from "./autoAnnotate";
+export { getFeatureToColorMap, getFeatureTypes, genbankFeatureTypes, getMergedFeatureMap, autoAnnotate, convertApELikeRegexToRegex, convertProteinSeqToDNAIupac };