io.github.msdk.featuredetection.adap3d.algorithms

Class Peak3DTest

java.lang.Object

io.github.msdk.featuredetection.adap3d.algorithms.Peak3DTest

public class Peak3DTest
extends Object

Peak3DTest is used for determining true or false peak by comparing adjacent m/z-slices in profile data.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Peak3DTest.Result Result class is used for returning lower and upper mz bound,boolean good peak value and list of similarity value.

Field Summary

Fields

Modifier and Type	Field and Description
static double	EPSILON Constant EPSILON=1E-8

Constructor Summary

Constructors

Constructor and Description
Peak3DTest() Constructor for Peak3DTest.
Peak3DTest(SliceSparseMatrix objsliceSparseMatrix, int fwhm) Constructor for Peak3DTest.

Method Summary

Modifier and Type	Method and Description
Peak3DTest.Result	execute(int roundedMz, int leftBound, int rightBound, double peakSimilarityThreshold) execute method is used for testing a peak with given m/z-value (variable mz) and left and right bounds (variables leftBound and rightBound).

Methods inherited from class java.lang.Object

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

Field Detail

EPSILON

public static final double EPSILON

Constant EPSILON=1E-8

See Also:

Constant Field Values

Constructor Detail

Peak3DTest

public Peak3DTest(SliceSparseMatrix objsliceSparseMatrix,
                  int fwhm)

Constructor for Peak3DTest.

Parameters:

objsliceSparseMatrix - a SliceSparseMatrix object.

fwhm - a int.

Peak3DTest

public Peak3DTest()

Constructor for Peak3DTest.

Method Detail

execute

public Peak3DTest.Result execute(int roundedMz,
                                 int leftBound,
                                 int rightBound,
                                 double peakSimilarityThreshold)

execute method is used for testing a peak with given m/z-value (variable mz) and left and right bounds (variables leftBound and rightBound). Peak is tested by comparing similarity between adjacent m/z slices. Let mzValues be a sorted list of all m/z values in the profile data. Let index be an integer such that mzValues[index] == mz We find similarities between the EIC corresponding to m/z value mzValues[index] and adjacent EICs corresponding to ..., mzValues[index-2], mzValues[index-1], mzValues[index+1], mzValues[index+2], ... as long as those similarities are higher than the similarity threshold. First, we check each m/z-value higher than mzValues[index], stop when the current similarity becomes lower than the similarity threshold, and save the last m/z-value (variable upperMZbound). Next, we check each m/z-value lower than mzValues[index], stop when the current similarity becomes lower than the similarity threshold, and save the last m/z-value (variable lowerMZbound) Peak is considered to be good if the differences upperMZbound - mzValues[index], mzValues[index] - lowerMZbound, upperMZbound - lowerMZbound exceed certain thresholds, which depend on FWHM-value.

Parameters:

roundedMz - a Double object. It's rounded m/z value. Original m/z value multiplied by 10000.

leftBound - a Integer object. This is lowest scan number from which peak determining starts.

rightBound - a Integer object. This is highest scan number on which peak determining ends.

peakSimilarityThreshold - a double.

Returns:

a Peak3DTest.Result object. Result object contains similarity values, lower and upper mz boundaries for adjacent similar peaks.