edu.cmu.cs.sb.drem
Class DREM_DataSet

java.lang.Object
  extended by edu.cmu.cs.sb.core.DataSetCore
      extended by edu.cmu.cs.sb.drem.DREM_DataSet

public class DREM_DataSet
extends DataSetCore

Class extends DataSetCore which contains the underlying data and parameters of the methods with an instance of DREM_GoAnnotations


Field Summary
 
Fields inherited from class edu.cmu.cs.sb.core.DataSetCore
badd0, bfullrepeat, bmaxminval, bspotincluded, btakelog, data, dmincorrelation, dsamplemins, dthresholdvalue, genenames, generepeatspottimedata, generepeatspottimepma, genespottimedata, genespottimepma, htFiltered, nmaxmissing, numcols, numrows, otherInputFiles, pmavalues, probenames, sortedcorrvals, szGeneHeader, szInputFile, szProbeHeader
 
Constructor Summary
DREM_DataSet(DataSetCore theDataSetCore, DREM_GoAnnotations tga)
          Constructor that does a simple copy the contents of theDataSetCore and tga
DREM_DataSet(java.lang.String szInputFile, int nmaxmissing, double dthresholdvalue, double dmincorrelation, boolean btakelog, boolean bspotincluded, boolean brepeatset, boolean badd0, boolean bmaxminval, boolean bfullrepeat)
          Constructor that takes input parameters and calls dataSetReader to read in the content of szInputFile
 
Method Summary
 
Methods inherited from class edu.cmu.cs.sb.core.DataSetCore
addExtraToFilter, averageAndFilterDuplicates, dataSetReader, filterdistprofiles, filterDuplicates, filtergenesgeneral, filtergenesthreshold1point, filtergenesthreshold2, filterMissing, filterMissing1point, logratio2, mergeDataSets
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

DREM_DataSet

public DREM_DataSet(DataSetCore theDataSetCore,
                    DREM_GoAnnotations tga)
Constructor that does a simple copy the contents of theDataSetCore and tga


DREM_DataSet

public DREM_DataSet(java.lang.String szInputFile,
                    int nmaxmissing,
                    double dthresholdvalue,
                    double dmincorrelation,
                    boolean btakelog,
                    boolean bspotincluded,
                    boolean brepeatset,
                    boolean badd0,
                    boolean bmaxminval,
                    boolean bfullrepeat)
             throws java.io.IOException,
                    java.io.FileNotFoundException,
                    java.lang.IllegalArgumentException
Constructor that takes input parameters and calls dataSetReader to read in the content of szInputFile

Throws:
java.io.IOException
java.io.FileNotFoundException
java.lang.IllegalArgumentException