Class: CalculatePrefixAndSuffixMass

CalculatePrefixAndSuffixMass()

Class to calculate prefix and suffix mass

Constructor

new CalculatePrefixAndSuffixMass()

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Methods

addMassShift(position, massShiftList, mass)

Add mass shifts to massShift list
Parameters:
Name Type Description
position int position of the mass list
massShiftList Array Contains the list of all the mass shifts
mass Float Mass shift to be added to the list
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getFixedPTMMassList(massShiftList, prsm)

Get all the Fixed Ptms and add the corresponding mass shits to mass shift list
Parameters:
Name Type Description
massShiftList Array Contains all the mass shifts
prsm Object Contains the data of the prsm(Attribute inside prsm_data global variable from data file)
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getIonTypeMass(ionType)

Check for ionType and return the corresponding mass shift value
Parameters:
Name Type Description
ionType String String with Corresponding iontype
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getMassofFixedPtm(abbrevation)

Returns Fixed Mass for certain abbrivation
Parameters:
Name Type Description
abbrevation String Contains abbrevation to get corresponding fixed mass
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getPrefixMassList(sequence, massShiftList, ionType_massShift)

Calculate and generate Prefix mass list
Parameters:
Name Type Description
sequence String Contains sequence of the protein
massShiftList Array Contains the Mass shift which are to be added in the corresponding positions
ionType_massShift Float Contains the mass based on the ion Type
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getSequence(prsm_data)

Get the sequence from the prsm_data global variable from data file
Parameters:
Name Type Description
prsm_data Object This is a global object from data file which contains all the prsm information
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getSuffixMassList(sequence, massShiftList, ionType_massShift)

Generate Suffix mass list
Parameters:
Name Type Description
sequence String Contains sequence of the protein
massShiftList Array Contains the Mass shift which are to be added in the corresponding positions
ionType_massShift Float Contains the mass based on the ion Type
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getUnknownMassList()

Get unknow mass list
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