Class: MatchedPeaks

MatchedPeaks()

Class to calculate Matched Peaks and distribution of the Amoino Acids

Constructor

new MatchedPeaks()

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Methods

getDistribution(peakDataList, sequence, matchedUnMatchedList)

Get the envelopes/distribution for the sequence
Parameters:
Name Type Description
peakDataList Array Contains peak list information
sequence String Contains protein sequence
matchedUnMatchedList Array Contains all matched and unmatched list
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getMatchedAndUnMatchedList(monoMassList, matchedList)

Set matched indicator to complete data and Seperate matched and unmatched list of data with matchedInd attribute
Parameters:
Name Type Description
monoMassList Array Contains mono Mass list data
matchedList Array Contains all the data of both matched and unmatched data
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getMatchedAndUnmatchedPrefixAndSuffixMassList(prefixOrSuffixMassList, monoMassList, massErrorthVal, ppmErrorthVal, prefixInd)

Get All the matched positions and mass list seperated with a matched indicator
Parameters:
Name Type Description
prefixOrSuffixMassList Array List of prefix and suffix masses
monoMassList Array Contains Mono Mass list
massErrorthVal Float Mass Error Threshold value entered by user
ppmErrorthVal Float PPM Error Threshold value entered by user
prefixInd String contains if the complete data is of prefix/suffix mass list
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getMatchedPeakList(prefixOrSuffixMassList, monoMassList, sequence, massErrorthVal, ppmErrorthVal, ionType, preOrSufInd)

Returns Complete list with matched Indication
Parameters:
Name Type Description
prefixOrSuffixMassList Array List with either prefix or suffix mass list
monoMassList Array Contains Mono Mass list from html page
sequence String Protein sequence
massErrorthVal Float Threshhold value entered by user to determine the mass error and matched peaks
ppmErrorthVal Float Threshhold value entered by user to determine the mass error and matched peaks in ppm units
ionType String Contains either y/b
preOrSufInd String Contains information of either PREFIX/SUFFIX
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matchedPeakAttributes(monoMassList_temp, id, ion, position, massDiff, mass, matchedInd)

Function to form object with necessary attributes at each amino acid position
Parameters:
Name Type Description
monoMassList_temp Object Single element from mono Mass List
id String Unique Id for each peak
ion String Contains matched type(b/y) appended with charge
position Integer Position of the amino acid
massDiff Float Mass difference at particular position
mass Float Mass at the position of the acid
matchedInd Char Indicator indicating matched/not matched. If matched containd "Y"
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