org.fhcrc.cpl.viewer.align
Class BucketedPeptideArray

java.lang.Object
  org.fhcrc.cpl.viewer.align.BucketedPeptideArray

All Implemented Interfaces:

java.lang.Runnable

public class BucketedPeptideArray
extends java.lang.Object
implements java.lang.Runnable

User: migra Date: Mar 9, 2005 Time: 11:06:52 AM

Field Summary

protected Aligner	_aligner
protected FeatureGrouper	_featureGrouper
protected Aligner.FeaturePairSelector	_featurePairSelector
protected double[]	_massBuckets
protected int[]	_scanBuckets
protected boolean	_shouldWriteUndeconvolutedDetails

Constructor Summary

BucketedPeptideArray(java.util.List<?> sets)

BucketedPeptideArray(java.util.List<?> sets, FeatureSet.FeatureSelector sel)

BucketedPeptideArray(java.util.List<?> sets, FeatureSet.FeatureSelector sel, int scanBucket, double massBucket, java.lang.String outFileName, boolean align)

Method Summary

void	alignByGroup(java.util.Map<java.lang.String,java.lang.String> tags, boolean strict) Group feature sets by tag.
static java.lang.String	calcDetailsFilepath(java.lang.String arrayFilepath, boolean undeconvoluted) Figure out the filepath for the details file related to an array file
FeatureSet.FeatureSelector	get_sel()
Aligner	getAligner()
int	getConflictResolver()
double	getDeconvoluteMassWindow()
int	getDeconvoluteScanWindow()
FeatureGrouper	getFeatureGrouper()
Aligner.FeaturePairSelector	getFeaturePairSelector()
java.util.List<?>	getFiles()
double	getMassBucket()
double[]	getMassBuckets()
boolean	getNormalize()
java.lang.String	getOutFileName()
int	getScanBucket()
int[]	getScanBuckets()
boolean	isAlign()
boolean	isShouldWriteUndeconvolutedDetails()
boolean	isSumDeconvolutedIntensities()
void	run()
void	run(boolean optimize)
void	run(boolean optimize, int optimizationMode)
void	run(boolean optimize, int optimizationMode, boolean showCharts)
void	set_sel(FeatureSet.FeatureSelector _sel)
void	setAlign(boolean align)
void	setAligner(Aligner _aligner)
void	setConflictResolver(int conflictResolver)
void	setDeconvoluteMassWindow(double deconvoluteMassWindow)
void	setDeconvoluteScanWindow(int deconvoluteScanWindow)
void	setFeatureGrouper(FeatureGrouper _featureGrouper)
void	setFeaturePairSelector(Aligner.FeaturePairSelector featurePairSelector)
void	setFiles(java.util.List<?> files)
void	setMassBucket(double massBucket)
void	setMassBuckets(double[] _massBuckets)
void	setNormalize(boolean normalize)
void	setOutFileName(java.lang.String outFileName)
void	setScanBucket(int scanBucket)
void	setScanBuckets(int[] _scanBuckets)
void	setShouldWriteUndeconvolutedDetails(boolean _shouldWriteUndeconvolutedDetails)
void	setSumDeconvolutedIntensities(boolean sumDeconvolutedIntensities)

Methods inherited from class java.lang.Object

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

Field Detail

_aligner

protected Aligner _aligner

_scanBuckets

protected int[] _scanBuckets

_massBuckets

protected double[] _massBuckets

_featureGrouper

protected FeatureGrouper _featureGrouper

_featurePairSelector

protected Aligner.FeaturePairSelector _featurePairSelector

_shouldWriteUndeconvolutedDetails

protected boolean _shouldWriteUndeconvolutedDetails

Constructor Detail

BucketedPeptideArray

public BucketedPeptideArray(java.util.List<?> sets)

BucketedPeptideArray

public BucketedPeptideArray(java.util.List<?> sets,
                            FeatureSet.FeatureSelector sel)

BucketedPeptideArray

public BucketedPeptideArray(java.util.List<?> sets,
                            FeatureSet.FeatureSelector sel,
                            int scanBucket,
                            double massBucket,
                            java.lang.String outFileName,
                            boolean align)

Method Detail

run

public void run()

Specified by:

run in interface java.lang.Runnable

run

public void run(boolean optimize)

run

public void run(boolean optimize,
                int optimizationMode)

run

public void run(boolean optimize,
                int optimizationMode,
                boolean showCharts)

calcDetailsFilepath

public static java.lang.String calcDetailsFilepath(java.lang.String arrayFilepath,
                                                   boolean undeconvoluted)

Figure out the filepath for the details file related to an array file

Parameters:

arrayFilepath -

undeconvoluted -

Returns:

alignByGroup

public void alignByGroup(java.util.Map<java.lang.String,java.lang.String> tags,
                         boolean strict)

Group feature sets by tag. Align within group to generate a representative FeatureSet for each. Then align the representatives.

getFiles

public java.util.List<?> getFiles()

setFiles

public void setFiles(java.util.List<?> files)

get_sel

public FeatureSet.FeatureSelector get_sel()

set_sel

public void set_sel(FeatureSet.FeatureSelector _sel)

isAlign

public boolean isAlign()

setAlign

public void setAlign(boolean align)

getNormalize

public boolean getNormalize()

setNormalize

public void setNormalize(boolean normalize)

getDeconvoluteScanWindow

public int getDeconvoluteScanWindow()

setDeconvoluteScanWindow

public void setDeconvoluteScanWindow(int deconvoluteScanWindow)

getDeconvoluteMassWindow

public double getDeconvoluteMassWindow()

setDeconvoluteMassWindow

public void setDeconvoluteMassWindow(double deconvoluteMassWindow)

getMassBucket

public double getMassBucket()

setMassBucket

public void setMassBucket(double massBucket)

getScanBucket

public int getScanBucket()

setScanBucket

public void setScanBucket(int scanBucket)

getOutFileName

public java.lang.String getOutFileName()

setOutFileName

public void setOutFileName(java.lang.String outFileName)

getScanBuckets

public int[] getScanBuckets()

setScanBuckets

public void setScanBuckets(int[] _scanBuckets)

getMassBuckets

public double[] getMassBuckets()

setMassBuckets

public void setMassBuckets(double[] _massBuckets)

getConflictResolver

public int getConflictResolver()

setConflictResolver

public void setConflictResolver(int conflictResolver)

getFeatureGrouper

public FeatureGrouper getFeatureGrouper()

setFeatureGrouper

public void setFeatureGrouper(FeatureGrouper _featureGrouper)

getFeaturePairSelector

public Aligner.FeaturePairSelector getFeaturePairSelector()

setFeaturePairSelector

public void setFeaturePairSelector(Aligner.FeaturePairSelector featurePairSelector)

getAligner

public Aligner getAligner()

setAligner

public void setAligner(Aligner _aligner)

isSumDeconvolutedIntensities

public boolean isSumDeconvolutedIntensities()

setSumDeconvolutedIntensities

public void setSumDeconvolutedIntensities(boolean sumDeconvolutedIntensities)

isShouldWriteUndeconvolutedDetails

public boolean isShouldWriteUndeconvolutedDetails()

setShouldWriteUndeconvolutedDetails

public void setShouldWriteUndeconvolutedDetails(boolean _shouldWriteUndeconvolutedDetails)