AFLPcore
Class HighestPeakLocate

java.lang.Object
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  +--AFLPcore.Operation
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        +--AFLPcore.PeakLocate
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              +--AFLPcore.HighestPeakLocate

public class HighestPeakLocate

extends PeakLocate

This class can be used to find peaks in lanes. It will simply find the highest value in the specified range. It will then add this value to the list of peaks in the given lane. However, it the peak already exists, same locaton, then it will not be added. The highest value is found using methods in the lane. No existing peaks will be cleared if a new peak is found in the region. Also, the area of the peak is NOT calculated and is instead set to 0.

Fields inherited from class AFLPcore.PeakLocate

MAX, MIN

Fields inherited from class AFLPcore.Operation

descript, helpFile, name, options

Constructor Summary

HighestPeakLocate()
Creats a new peak locating class that finds the highest value in a range and calls it a peak.

Method Summary

void	findPeak(DataList lanes, double minSize, double maxSize) Finds a peak in each lane and saves it in the lane.
java.lang.String	getDescription() Gives a brief description of the peak location function/algorithm.
java.lang.String	getHelpFile() Gives the help file for the Highest peak location function
java.lang.String	getName() Gives the name of this peak location function
Option[]	getOptions() Gives the options, but since there aren't any, this is always null.
void	setOptions(Option[] opts) Since this operations does not have any options, the method does not do anything.

Methods inherited from class java.lang.Object

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

Constructor Detail

HighestPeakLocate

public HighestPeakLocate()

Creats a new peak locating class that finds the highest value in a range and calls it a peak.

Method Detail

getName

public java.lang.String getName()

Gives the name of this peak location function

Overrides:

getName in class Operation

Returns:

the name

getDescription

public java.lang.String getDescription()

Gives a brief description of the peak location function/algorithm.

Overrides:

getDescription in class Operation

Returns:

a sentence description

getHelpFile

public java.lang.String getHelpFile()

Gives the help file for the Highest peak location function

Overrides:

getHelpFile in class Operation

Returns:

an html or plaintest file with help info. null if this file does not exist.

getOptions

public Option[] getOptions()

Gives the options, but since there aren't any, this is always null. All of the information that is needed is passed into the findPeaks method. These are merely implemented to satisfy the requirements of the parent class.

Overrides:

getOptions in class Operation

Returns:

null, always

setOptions

public void setOptions(Option[] opts)

Since this operations does not have any options, the method does not do anything. It is implemented merely to satisfy the requirements of the abstarct parent class that it is inheretid from.

Overrides:

setOptions in class Operation

Following copied from class: AFLPcore.Operation

Parameters:

opts - the values for the options that this operation understands.

findPeak

public void findPeak(DataList lanes,
                     double minSize,
                     double maxSize)

Finds a peak in each lane and saves it in the lane. The peak will be between (inclusive) minSize and maxSize. The list of peaks will not be cleared. Instead, peaks will simply be added to whatever already exists, with the exception of duplicate peaks, which will not be added. The algorithm used is described above in the class description.

Overrides:

findPeak in class PeakLocate

Parameters:

lanes - the list of lanes that the algorithm should look for peaks in.

minSize - the minimum size of any peak. If the value MIN is given, then the smallest size in the lane will be used.

maxSize - the maximum size of any peak. If the value MAX is given, then the largest size in the lane will be used.