org.fhcrc.cpl.viewer.align
Class Aligner

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

Direct Known Subclasses:

QuantileRegressionAligner, SplineAligner

public abstract class Aligner
extends java.lang.Object

Created by IntelliJ IDEA. User: migra Date: Mar 1, 2005 Time: 10:10:36 AM dhmay, 5/7/08. Making this class abstract. Alignment can be performed via two different algorithms: a spline-based regression, or a quantile regression similar to what's used in AMT. The two algorithms perform very similarly on data that are tightly filtered, but the quantile regression performs much better on noisy data.

Nested Class Summary

static interface	Aligner.FeaturePairSelector Interface for classes that provide a way of selecting pairs of features.
static class	Aligner.HybridFeaturePairSelector Select pairs of features based on peptide agreement, and also mass tolerance
static class	Aligner.MassFeaturePairSelector
static class	Aligner.MassOrMzFeaturePairSelector This class selects pairs of features purely based on m/z -- it pairs up features that are within a given m/z tolerance.
static class	Aligner.MzFeaturePairSelector
static class	Aligner.PeptideFeaturePairSelector Selecte pairs of features based on peptide agreement

Field Summary

protected PanelWithChart	alignmentChart
protected boolean	buildCharts
static Aligner.FeaturePairSelector	DEFAULT_FEATURE_PAIR_SELECTOR
protected Aligner.FeaturePairSelector	featurePairSelector
protected double	maxLeverageNumerator
protected double	maxStudRes
protected java.util.List<int[]>	warpingMaps

Constructor Summary

Aligner()

Method Summary

java.util.List<FeatureSet>	alignFeatureSets(java.util.List<FeatureSet> sets, boolean showCharts) Perform the non-linear mapping between feature sets
double[]	alignPairs(Pair<java.lang.Integer,java.lang.Double>[] pairs, int maxValueToWarp) Cover method.
abstract double[]	alignPairs(Pair<java.lang.Integer,java.lang.Double>[] pairs, int maxValueToWarp, java.lang.String tempFileNameStart) Generic method for creating a warping based on pairs of values.
protected PanelWithChart	createChart(Pair<java.lang.Integer,java.lang.Double>[] allPairedScans, Pair<java.lang.Integer,java.lang.Double>[] restrictedPairs, double[] warpedValues)
protected java.lang.String	getAlignedFileName(java.util.List featureSets, int i) Return a filename with an "align" in it.
PanelWithChart	getAlignmentChart()
Aligner.FeaturePairSelector	getFeaturePairSelector()
double	getMaxLeverageNumerator()
static int	getMaxScan(Feature[] features) Calculate the maximum scan number of any of these features
double	getMaxStudRes()
static float	getMaxTime(Feature[] features) Calculate the maximum time of any of these features
java.util.List<int[]>	getWarpingMaps() Provide access to the scan maps created for individual feature sets.
boolean	isBuildCharts()
void	plotWarping(double[] warping)
void	plotWarpings()
void	plotWarpings(double[][] warpings)
protected Pair<java.lang.Integer,java.lang.Double>[]	restrictPairsForRegression(Pair<java.lang.Integer,java.lang.Double>[] allPairs)
void	setAlignmentChart(PanelWithChart alignmentChart)
void	setBuildCharts(boolean buildCharts)
void	setFeaturePairSelector(Aligner.FeaturePairSelector featurePairSelector)
void	setMaxLeverageNumerator(double maxLeverageNumerator)
void	setMaxStudRes(double maxStudRes)
protected java.io.File	writePairsFile(Pair<java.lang.Integer,java.lang.Double>[] pairs, java.lang.String fileName) Write a file containing pairs

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_FEATURE_PAIR_SELECTOR

public static final Aligner.FeaturePairSelector DEFAULT_FEATURE_PAIR_SELECTOR

featurePairSelector

protected Aligner.FeaturePairSelector featurePairSelector

warpingMaps

protected java.util.List<int[]> warpingMaps

buildCharts

protected boolean buildCharts

alignmentChart

protected PanelWithChart alignmentChart

maxStudRes

protected double maxStudRes

maxLeverageNumerator

protected double maxLeverageNumerator

Constructor Detail

Aligner

public Aligner()

Method Detail

getMaxScan

public static int getMaxScan(Feature[] features)

Calculate the maximum scan number of any of these features

Parameters:

features -

Returns:

getMaxTime

public static float getMaxTime(Feature[] features)

Calculate the maximum time of any of these features

Parameters:

features -

Returns:

alignFeatureSets

public java.util.List<FeatureSet> alignFeatureSets(java.util.List<FeatureSet> sets,
                                                   boolean showCharts)

Perform the non-linear mapping between feature sets

restrictPairsForRegression

protected Pair<java.lang.Integer,java.lang.Double>[] restrictPairsForRegression(Pair<java.lang.Integer,java.lang.Double>[] allPairs)

alignPairs

public double[] alignPairs(Pair<java.lang.Integer,java.lang.Double>[] pairs,
                           int maxValueToWarp)

Cover method. In the absence of filename information, use a filename that's likely to be unique

Parameters:

pairs -

maxValueToWarp -

Returns:

alignPairs

public abstract double[] alignPairs(Pair<java.lang.Integer,java.lang.Double>[] pairs,
                                    int maxValueToWarp,
                                    java.lang.String tempFileNameStart)

Generic method for creating a warping based on pairs of values. Create temp files with names based on tempFileNameStart, in case the user wants to peruse them

Parameters:

pairs -

maxValueToWarp -

Returns:

createChart

protected PanelWithChart createChart(Pair<java.lang.Integer,java.lang.Double>[] allPairedScans,
                                     Pair<java.lang.Integer,java.lang.Double>[] restrictedPairs,
                                     double[] warpedValues)

writePairsFile

protected java.io.File writePairsFile(Pair<java.lang.Integer,java.lang.Double>[] pairs,
                                      java.lang.String fileName)
                               throws java.io.FileNotFoundException

Write a file containing pairs

Parameters:

fileName -

Throws:

java.io.FileNotFoundException

getAlignedFileName

protected java.lang.String getAlignedFileName(java.util.List featureSets,
                                              int i)

Return a filename with an "align" in it. If there's a source file for the featureset, use that name to start with. If not, index.

Parameters:

featureSets -

i -

Returns:

getWarpingMaps

public java.util.List<int[]> getWarpingMaps()

Provide access to the scan maps created for individual feature sets. Obviously, only applicable if you've just done alignment on a bunch of feature sets

Returns:

plotWarpings

public void plotWarpings()

plotWarpings

public void plotWarpings(double[][] warpings)

plotWarping

public void plotWarping(double[] warping)

getFeaturePairSelector

public Aligner.FeaturePairSelector getFeaturePairSelector()

setFeaturePairSelector

public void setFeaturePairSelector(Aligner.FeaturePairSelector featurePairSelector)

isBuildCharts

public boolean isBuildCharts()

setBuildCharts

public void setBuildCharts(boolean buildCharts)

getAlignmentChart

public PanelWithChart getAlignmentChart()

setAlignmentChart

public void setAlignmentChart(PanelWithChart alignmentChart)

getMaxStudRes

public double getMaxStudRes()

setMaxStudRes

public void setMaxStudRes(double maxStudRes)

getMaxLeverageNumerator

public double getMaxLeverageNumerator()

setMaxLeverageNumerator

public void setMaxLeverageNumerator(double maxLeverageNumerator)