# Class: MatchedPeaks

## MatchedPeaks()

Class to calculate Matched Peaks and distribution of the Amoino Acids

## Constructor

#### new MatchedPeaks()

Source:
  - matchedpeaks.js, line 17

### 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

Source:
  - matchedpeaks.js, line 159

#### 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

Source:
  - matchedpeaks.js, line 126

#### 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

Source:
  - matchedpeaks.js, line 224

#### 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

Source:
  - matchedpeaks.js, line 65

#### 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"

Source:
  - matchedpeaks.js, line 32