SvbDecompressRawSignal decompresses raw signal back to a []int16. It requires not only the mask array and data array returned by SvbCompressRawSignal,

ToXML converts an Entry back to its XML representation

Alignment_Validate validates an alignment as valid, given the REGEXP/range defined in the SAM document. Not implemented yet.

WriteCodonJSON writes a codonTable struct out to JSON.

boothLeastRotation gets the least rotation of a circular string.

Captures any logged output from running func `f` and returns it as a string

contains is a helper function to check if errStr contains the expected substring

Convert Location

parameters: nucs[i], nucs[j-1], nucs[j]

decodeFromBase58 decodes a Base58 string to a byte slice

evaluteSecondaryStructure returns the total minimum free energy of the given `secondaryStructure` and sets the energy fields of all the loops in the s

extractCodingRegion loops through genbank data to find all CDS (coding sequences)

findProblems is a helper function in FixCDS that concurrently runs each sequence check and returns a list of all the suggested changes.

getSuggestions gets suggestions from the suggestions channel. This removes the need for a magic number.

hairpin sets the required single stranded hairpin nucleotides of a `parseCompound`'s annotatedStructure and returns `Hairpin` closed by (`closingFiveP

parameters: nucs[i], nucs[i+1], nucs[j-1], nucs[j]

parameters: nucs[i], nucs[j]

leaf0x80000004 looks at the Processor Brand String in leaves 0x80000002 through 0x80000004

** * Logs energy contributions in the same format as ViennaRNA does. This is used * to compare output to ViennaRNA in test cases. * Note: 1 is added t

minInt returns the minimum of two ints

Compute the energy of a multi-loop. A multi-loop has this structure: · · · · · · A - B ·

multiLoop sets the nucleotides present in a multi-loops's single stranded region in a `parseCompound`'s annotatedStructure and returns the `MultiLoop`

The main function where the parsing of energy param files starts from. Note that the `RNAfold parameter file v2.0` file format has a flaw. Since the

** * Returns a slice `pairTableFromDotBracketStructure` where `pairTableFromDotBracketStructure[i]` returns the index of the * nucleotide that that th

pairedMinimumFreeEnergyV returns the minimum free energy of a subsequence of paired bases and end. From Figure 2B of Zuker, 1981: let V(i,j) be the mi

in-place quick-select

readUncommentedLine continues reading until a line without comments is read

rescaleDgFloat64 is the same as rescaleDg, but for float64

scaleByTemperature scales energy paramaters according to the specificed temperatue. See `rescaleDg` for more information of how energy values are resc