io.github.msdk.featuredetection.adap3d.algorithms

Class SliceSparseMatrix

java.lang.Object

io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix

public class SliceSparseMatrix
extends Object

SliceSparseMatrix class is used for slicing the sparse matrix of raw data as per given mz value. slice contains intensities for one mz value for different scans. In this class sparse matrix has been implemented in the form of multikey map. Mz and scan number are keys and object containing Intensities along information like retention time and whether the value is still in matrix or not is the value. Consider Scan numbers as column index and mz values as row index. cell values as object containing Intensities along with other information like retention time and whether the value is still in matrix or not.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SliceSparseMatrix.Triplet Triplet is used for representing elements of sparse matrix.
static class	SliceSparseMatrix.VerticalSliceDataPoint This is the data model for getting vertical slice from sparse matrix.

Field Summary

Fields

Modifier and Type	Field and Description
List<Integer>	mzValues mzValues is used to store all the mz values from raw file.

Constructor Summary

Constructors

Constructor and Description
SliceSparseMatrix(RawDataFile rawFile) This constructor takes raw data file and create the triplet map which contains information such as mz,intensity,rt,scan number
SliceSparseMatrix(RawDataFile rawFile, Predicate<MsScan> msScanPredicate) This constructor takes raw data file and create the triplet map which contains information such as mz,intensity,rt,scan number

Method Summary

Modifier and Type	Method and Description
SliceSparseMatrix.Triplet	findNextMaxIntensity() This method finds next maximum intensity from filterListOfTriplet
List<ContinuousWaveletTransform.DataPoint>	getCWTDataPoint(List<SliceSparseMatrix.Triplet> slice) This method returns sorted list of ContinuousWaveletTransform.DataPoint object.Object contain retention time and intensity values.
float	getFinishedPercent(SliceSparseMatrix.Triplet maxIntensityTriplet) This method tracks progress of algorithm
List<SliceSparseMatrix.Triplet>	getHorizontalSlice(double mz, int lowerScanBound, int upperScanBound) This method returns the MultiKeyMap slice of data for given mz,lowerScanBound,upperScanBound
List<SliceSparseMatrix.Triplet>	getHorizontalSlice(int roundedMZ, int lowerScanBound, int upperScanBound) This method returns the MultiKeyMap slice of data for rounded mz,lowerScanBound,upperScanBound
float[]	getIntensities(ADAP3DPeakDetectionAlgorithm.GoodPeakInfo peak) This method returns intensity array for detected peak
double	getRetentionTime(int scanNumber) This method returns retention time for given scan number.
float[]	getRetentionTimeArray(int lowerScanBound, int upperScanbound) This method returns retention time array for given upper and lower scan bounds.
int	getSizeOfRawDataFile() This method returns size of raw data file in terms of total scans.
List<SliceSparseMatrix.VerticalSliceDataPoint>	getVerticalSlice(int scanNumber) This method returns the List of type VerticalSliceDataPoint for given Scan Number.
double	numOfScans()
List<SliceSparseMatrix.Triplet>	removeDataPoints(int roundedmz, int lowerScanBound, int upperScanBound) This method removes data points from whole data set for given mz,lowerscanbound and upperscanbound
List<SliceSparseMatrix.Triplet>	restoreDataPoints(int roundedmz, int lowerScanBound, int upperScanBound) This method restores data points from whole data set for given mz,lowerscanbound and upperscanbound
int	roundMZ(double mz) This method rounds mz value based on roundMz variable
void	setMaxIntensityIndexZero() This method sets maxIntensityIndex to 0

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

mzValues

public final List<Integer> mzValues

mzValues is used to store all the mz values from raw file.

Constructor Detail

SliceSparseMatrix

public SliceSparseMatrix(RawDataFile rawFile)

This constructor takes raw data file and create the triplet map which contains information such as mz,intensity,rt,scan number

Parameters:

rawFile - a RawDataFile object. This is raw data file object by which we can pass raw file.

SliceSparseMatrix

public SliceSparseMatrix(RawDataFile rawFile,
                         Predicate<MsScan> msScanPredicate)

This constructor takes raw data file and create the triplet map which contains information such as mz,intensity,rt,scan number

Parameters:

rawFile - a RawDataFile object. This is raw data file object by which we can pass raw file.

msScanPredicate - a Predicate object. Only MsScan which pass this predicate will be processed.

Method Detail

getHorizontalSlice

public List<SliceSparseMatrix.Triplet> getHorizontalSlice(double mz,
                                                          int lowerScanBound,
                                                          int upperScanBound)

This method returns the MultiKeyMap slice of data for given mz,lowerScanBound,upperScanBound

Parameters:

mz - a Double object. This is original m/z value from raw file.

lowerScanBound - a Integer object. This is lowest scan number in the horizontal matrix slice.

upperScanBound - a Integer object. This is highest scan number in the horizontal matrix slice.

Returns:

sliceMap a org.apache.commons.collections4.map.MultiKeyMap object. This object contains horizontal slice with single m/z value,different scan numbers and different intensities along with retention time.

getHorizontalSlice

public List<SliceSparseMatrix.Triplet> getHorizontalSlice(int roundedMZ,
                                                          int lowerScanBound,
                                                          int upperScanBound)

This method returns the MultiKeyMap slice of data for rounded mz,lowerScanBound,upperScanBound

Parameters:

roundedMZ - a Double object. This is rounded m/z value which is already multiplied by 10000.

lowerScanBound - a Integer object. This is lowest scan number in the horizontal matrix slice.

upperScanBound - a Integer object. This is highest scan number in the horizontal matrix slice.

Returns:

sliceMap a org.apache.commons.collections4.map.MultiKeyMap object. This object contains horizontal slice with single m/z value,different scan numbers and different intensities along with retention time.

getVerticalSlice

public List<SliceSparseMatrix.VerticalSliceDataPoint> getVerticalSlice(int scanNumber)

This method returns the List of type VerticalSliceDataPoint for given Scan Number.

Parameters:

scanNumber - a int.

Returns:

datapointList a SliceSparseMatrix.VerticalSliceDataPoint list. This is list containing m/z and intensities for one scan number.

findNextMaxIntensity

public SliceSparseMatrix.Triplet findNextMaxIntensity()

This method finds next maximum intensity from filterListOfTriplet

Returns:

tripletObject a SliceSparseMatrix.Triplet object. This is element of sparse matrix.

getCWTDataPoint

public List<ContinuousWaveletTransform.DataPoint> getCWTDataPoint(List<SliceSparseMatrix.Triplet> slice)

This method returns sorted list of ContinuousWaveletTransform.DataPoint object.Object contain retention time and intensity values.

Parameters:

slice - a org.apache.commons.collections4.map.MultiKeyMap object. This is horizontal slice from sparse matrix.

Returns:

listOfDataPoint a SliceSparseMatrix.Triplet list. This returns list of retention time and intensities.

removeDataPoints

public List<SliceSparseMatrix.Triplet> removeDataPoints(int roundedmz,
                                                        int lowerScanBound,
                                                        int upperScanBound)

This method removes data points from whole data set for given mz,lowerscanbound and upperscanbound

Parameters:

lowerScanBound - a Integer object.This is lowest scan number.

upperScanBound - a Integer object.This is highest scan number.

roundedmz - a int.

Returns:

tripletMap a org.apache.commons.collections4.map.MultiKeyMap object. This is whole sparse matrix.

restoreDataPoints

public List<SliceSparseMatrix.Triplet> restoreDataPoints(int roundedmz,
                                                         int lowerScanBound,
                                                         int upperScanBound)

This method restores data points from whole data set for given mz,lowerscanbound and upperscanbound

Parameters:

lowerScanBound - a Integer object.This is lowest scan number.

upperScanBound - a Integer object.This is highest scan number.

roundedmz - a int.

Returns:

tripletMap a org.apache.commons.collections4.map.MultiKeyMap object. This is whole sparse matrix.

roundMZ

public int roundMZ(double mz)

This method rounds mz value based on roundMz variable

Parameters:

mz - a Double object. This takes original m/z value from raw file.

Returns:

roundedmz a Integer object. This value is rounded by multiplying 10000.

setMaxIntensityIndexZero

public void setMaxIntensityIndexZero()

This method sets maxIntensityIndex to 0

getSizeOfRawDataFile

public int getSizeOfRawDataFile()

This method returns size of raw data file in terms of total scans.

Returns:

size a Integer object. This is total number of scans in raw file.

getRetentionTimeArray

public float[] getRetentionTimeArray(int lowerScanBound,
                                     int upperScanbound)

This method returns retention time array for given upper and lower scan bounds.

Parameters:

lowerScanBound - a int.

upperScanbound - a int.

Returns:

retentionTime a Float array.

getIntensities

public float[] getIntensities(ADAP3DPeakDetectionAlgorithm.GoodPeakInfo peak)

This method returns intensity array for detected peak

Parameters:

peak - a ADAP3DPeakDetectionAlgorithm.GoodPeakInfo object.

Returns:

intensities a Float array.

getRetentionTime

public double getRetentionTime(int scanNumber)

This method returns retention time for given scan number.

Parameters:

scanNumber - a int.

Returns:

Double object.

getFinishedPercent

public float getFinishedPercent(SliceSparseMatrix.Triplet maxIntensityTriplet)

This method tracks progress of algorithm

Parameters:

maxIntensityTriplet - a SliceSparseMatrix.Triplet object.

Returns:

progress a Float object.

numOfScans

public double numOfScans()