org.fhcrc.cpl.viewer.align
Class SplineAligner

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

public class SplineAligner
extends Aligner

Spline-based alignment algorithm

Nested Class Summary

Nested classes/interfaces inherited from class org.fhcrc.cpl.viewer.align.Aligner

Aligner.FeaturePairSelector, Aligner.HybridFeaturePairSelector, Aligner.MassFeaturePairSelector, Aligner.MassOrMzFeaturePairSelector, Aligner.MzFeaturePairSelector, Aligner.PeptideFeaturePairSelector

Field Summary

protected boolean	copiedRCode
static int	DEFAULT_DEGREES_OF_FREEDOM
protected int	degreesOfFreedom

Fields inherited from class org.fhcrc.cpl.viewer.align.Aligner

alignmentChart, buildCharts, DEFAULT_FEATURE_PAIR_SELECTOR, featurePairSelector, maxLeverageNumerator, maxStudRes, warpingMaps

Constructor Summary

SplineAligner()

Method Summary

double[]	alignPairs(Pair<java.lang.Integer,java.lang.Double>[] pairs, int maxValueToWarp) Cover method.
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 void	copyRCode() copy warp_scans.R to the temp directory
int	getDegreesOfFreedom()
double[]	parseWarpingMap(java.io.File mapFile, int maxValueToWarp) Generic code for parsing a map of integers to doubles
void	setDegreesOfFreedom(int degreesOfFreedom)
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 org.fhcrc.cpl.viewer.align.Aligner

alignFeatureSets, createChart, getAlignedFileName, getAlignmentChart, getFeaturePairSelector, getMaxLeverageNumerator, getMaxScan, getMaxStudRes, getMaxTime, getWarpingMaps, isBuildCharts, plotWarping, plotWarpings, plotWarpings, restrictPairsForRegression, setAlignmentChart, setBuildCharts, setFeaturePairSelector, setMaxLeverageNumerator, setMaxStudRes

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_DEGREES_OF_FREEDOM

public static final int DEFAULT_DEGREES_OF_FREEDOM

See Also:

Constant Field Values

degreesOfFreedom

protected int degreesOfFreedom

copiedRCode

protected boolean copiedRCode

Constructor Detail

SplineAligner

public SplineAligner()

Method Detail

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

Overrides:

alignPairs in class Aligner

Parameters:

pairs -

maxValueToWarp -

Returns:

alignPairs

public 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

Specified by:

alignPairs in class Aligner

Parameters:

pairs -

maxValueToWarp -

Returns:

copyRCode

protected void copyRCode()
                  throws java.io.IOException,
                         java.io.FileNotFoundException

copy warp_scans.R to the temp directory

Throws:

java.io.IOException

java.io.FileNotFoundException

parseWarpingMap

public double[] parseWarpingMap(java.io.File mapFile,
                                int maxValueToWarp)
                         throws java.io.IOException,
                                java.io.FileNotFoundException

Generic code for parsing a map of integers to doubles

Parameters:

mapFile -

Returns:

Throws:

java.io.IOException

java.io.FileNotFoundException

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

Overrides:

writePairsFile in class Aligner

Parameters:

fileName -

Throws:

java.io.FileNotFoundException

getDegreesOfFreedom

public int getDegreesOfFreedom()

setDegreesOfFreedom

public void setDegreesOfFreedom(int degreesOfFreedom)