org.fhcrc.cpl.viewer.ms2
Class Fractionation2DUtilities

java.lang.Object
  org.fhcrc.cpl.viewer.ms2.Fractionation2DUtilities

public class Fractionation2DUtilities
extends java.lang.Object

Utilities for working with 2D-fractionated MS/MS experiments

Nested Class Summary

static class	Fractionation2DUtilities.FractionatedAMTDatabaseStructure Describes the structure of an AMT database containing one or more fractionated experiments
static class	Fractionation2DUtilities.FractionatedExperimentStructure

Field Summary

protected static org.apache.log4j.Logger	_log
static int	BY_COLUMN
static int	BY_ROW

Constructor Summary

Fractionation2DUtilities()

Method Summary

static Fractionation2DUtilities.FractionatedAMTDatabaseStructure	digestAmtStructureArgument(java.lang.String structureArgument) num rows, num columns, fraction order, number of experiments
static Fractionation2DUtilities.FractionatedExperimentStructure	digestDimensionArgument(java.lang.String dimensionArgument) Takes a String argument defining the structure of an MS/MS experiment (number of rows, number of columns, and whether the runs appear in the order of rows or columns) and parses it
static void	showHeatMapChart(Fractionation2DUtilities.FractionatedAMTDatabaseStructure amtDatabaseStructure, double[] dataForChart, java.lang.String chartName, boolean showLegend)

Methods inherited from class java.lang.Object

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

Field Detail

_log

protected static org.apache.log4j.Logger _log

BY_ROW

public static final int BY_ROW

See Also:

Constant Field Values

BY_COLUMN

public static final int BY_COLUMN

See Also:

Constant Field Values

Constructor Detail

Fractionation2DUtilities

public Fractionation2DUtilities()

Method Detail

digestAmtStructureArgument

public static Fractionation2DUtilities.FractionatedAMTDatabaseStructure digestAmtStructureArgument(java.lang.String structureArgument)
                                                                                            throws ArgumentValidationException

num rows, num columns, fraction order, number of experiments

Parameters:

structureArgument -

Returns:

Throws:

ArgumentValidationException

digestDimensionArgument

public static Fractionation2DUtilities.FractionatedExperimentStructure digestDimensionArgument(java.lang.String dimensionArgument)
                                                                                        throws ArgumentValidationException

Takes a String argument defining the structure of an MS/MS experiment (number of rows, number of columns, and whether the runs appear in the order of rows or columns) and parses it

Parameters:

dimensionArgument -

Returns:

Throws:

ArgumentValidationException

showHeatMapChart

public static void showHeatMapChart(Fractionation2DUtilities.FractionatedAMTDatabaseStructure amtDatabaseStructure,
                                    double[] dataForChart,
                                    java.lang.String chartName,
                                    boolean showLegend)