peakml.util.rjava
Class Project

java.lang.Object
  peakml.util.rjava.Project

public class Project
extends java.lang.Object

Constructor Summary

Project()

Project(java.lang.String[] measurements, java.lang.String[] filenames, java.lang.String[] sets)

Method Summary

void	addAnnotation(int index, java.lang.String label, java.lang.String value)
void	addGroupAnnotation(int groupid, java.lang.String label, java.lang.String value)
void	addHeaderAnnotation(java.lang.String label, java.lang.String value)
void	addMassChromatogram(int measurementid, int[] scanids, double[] retentiontimes, double[] masses, double[] intensities, java.lang.String ionisation)
void	addPeakSet(int indices)
void	addPeakSet(int[] indices)
void	addScanAnnotation(int measurementid, int scanid, java.lang.String label, java.lang.String value)
void	addScanInfo(int measurementid, double retentiontime, java.lang.String polarity)
java.lang.String	getAnnotation(int index, java.lang.String name)
java.lang.String[]	getAnnotationLabels(int index)
java.lang.String[]	getFileNames()
java.lang.String	getGroupAnnotation(int groupid, java.lang.String name)
java.lang.String[]	getGroupAnnotationLabels(int groupid)
java.lang.String	getHeaderAnnotation(java.lang.String label)
double[]	getIntensities(int index)
java.lang.String	getIonisation(int measurementid, int scanid)
double[][]	getMassChromatograms()
double[]	getMasses(int index)
int	getMeasurementID(int index)
java.lang.String[]	getMeasurementNames()
double[]	getMeasurementRetentionTimes(int measurementid)
double[]	getMeasurementRetentionTimes(java.lang.String measurementname)
int	getNrMassChromatograms()
int	getNrPeaksets()
int	getNrScans(int measurementid)
double[]	getRetentionTimes(int index)
java.lang.String	getScanAnnotation(int measurementid, int scanid, java.lang.String label)
int[]	getScanIDs(int index)
java.lang.String[]	getSetNames()
void	load(java.lang.String filename)
java.lang.String	toString()
void	write(java.lang.String filename)
void	writeMeasurements(java.lang.String path)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Project

public Project()

Project

public Project(java.lang.String[] measurements,
               java.lang.String[] filenames,
               java.lang.String[] sets)

Method Detail

addHeaderAnnotation

public void addHeaderAnnotation(java.lang.String label,
                                java.lang.String value)

getHeaderAnnotation

public java.lang.String getHeaderAnnotation(java.lang.String label)

addScanInfo

public void addScanInfo(int measurementid,
                        double retentiontime,
                        java.lang.String polarity)

addScanAnnotation

public void addScanAnnotation(int measurementid,
                              int scanid,
                              java.lang.String label,
                              java.lang.String value)

getScanAnnotation

public java.lang.String getScanAnnotation(int measurementid,
                                          int scanid,
                                          java.lang.String label)

getNrScans

public int getNrScans(int measurementid)

getIonisation

public java.lang.String getIonisation(int measurementid,
                                      int scanid)

addMassChromatogram

public void addMassChromatogram(int measurementid,
                                int[] scanids,
                                double[] retentiontimes,
                                double[] masses,
                                double[] intensities,
                                java.lang.String ionisation)

Parameters:

measurementid -

scanids -

retentiontimes -

masses -

intensities -

ionisation -

getNrMassChromatograms

public int getNrMassChromatograms()

addPeakSet

public void addPeakSet(int indices)

addPeakSet

public void addPeakSet(int[] indices)

getNrPeaksets

public int getNrPeaksets()

write

public void write(java.lang.String filename)
           throws java.io.IOException

Throws:

java.io.IOException

writeMeasurements

public void writeMeasurements(java.lang.String path)
                       throws java.io.IOException

Throws:

java.io.IOException

getSetNames

public java.lang.String[] getSetNames()

getFileNames

public java.lang.String[] getFileNames()

getMeasurementNames

public java.lang.String[] getMeasurementNames()

getMeasurementRetentionTimes

public double[] getMeasurementRetentionTimes(int measurementid)

getMeasurementRetentionTimes

public double[] getMeasurementRetentionTimes(java.lang.String measurementname)

getMassChromatograms

public double[][] getMassChromatograms()

getMeasurementID

public int getMeasurementID(int index)

getScanIDs

public int[] getScanIDs(int index)

getRetentionTimes

public double[] getRetentionTimes(int index)

getMasses

public double[] getMasses(int index)

getIntensities

public double[] getIntensities(int index)

getAnnotationLabels

public java.lang.String[] getAnnotationLabels(int index)

getAnnotation

public java.lang.String getAnnotation(int index,
                                      java.lang.String name)

addAnnotation

public void addAnnotation(int index,
                          java.lang.String label,
                          java.lang.String value)

getGroupAnnotationLabels

public java.lang.String[] getGroupAnnotationLabels(int groupid)

getGroupAnnotation

public java.lang.String getGroupAnnotation(int groupid,
                                           java.lang.String name)

addGroupAnnotation

public void addGroupAnnotation(int groupid,
                               java.lang.String label,
                               java.lang.String value)

load

public void load(java.lang.String filename)
          throws java.io.IOException,
                 domsax.XmlParserException

Throws:

java.io.IOException

domsax.XmlParserException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object