gov.nih.nci.caarray.services.bioassaydata.reader
Class AgilentTxtReader

java.lang.Object
  extended by gov.nih.nci.caarray.services.bioassaydata.reader.AbstractDataFileReader
      extended by gov.nih.nci.caarray.services.bioassaydata.reader.AgilentTxtReader

public class AgilentTxtReader
extends AbstractDataFileReader

Reader for Agilent gene expression data files.

Author:
tavelae

Field Summary
protected  java.util.List<java.lang.String> dataRowValues
           
protected static java.util.HashMap<java.lang.String,QuantitationTypeDescriptor> map
          Represents a map of
 
Method Summary
 void close()
           
static AgilentTxtReader create(java.io.File dataFile)
           
 int getCol()
           
 int getFeatureNum()
           
protected  int getIndex(QuantitationTypeDescriptor descriptor)
           
 int getRow()
           
 java.lang.Object getValue(QuantitationTypeDescriptor descriptor)
           
 java.lang.Boolean getValueAsBoolean(int columnIndex)
           
protected  java.lang.Boolean getValueAsBoolean(java.lang.String stringValue, java.lang.String columnName)
           
 java.lang.Float getValueAsFloat(int columnIndex)
           
protected  java.lang.Float getValueAsFloat(java.lang.String stringValue, java.lang.String columnName)
           
 java.lang.Integer getValueAsInteger(int columnIndex)
           
protected  java.lang.Integer getValueAsInteger(java.lang.String stringValue, java.lang.String columnName)
           
 java.lang.String getValueAsString(int columnIndex)
           
protected  java.lang.String getValueAsString(java.lang.String stringValueTrimmed, java.lang.String columnName)
           
 java.lang.String getValueAsStringOrNull(int columnIndex)
           
 boolean next()
           
 void reset()
           
 
Methods inherited from class gov.nih.nci.caarray.services.bioassaydata.reader.AbstractDataFileReader
getErrors, getQuantitationTypeDescriptors
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

map

protected static java.util.HashMap<java.lang.String,QuantitationTypeDescriptor> map
Represents a map of


dataRowValues

protected java.util.List<java.lang.String> dataRowValues
Method Detail

next

public boolean next()
             throws DataFileParseException
Throws:
DataFileParseException

reset

public void reset()
           throws DataFileParseException
Throws:
DataFileParseException

create

public static AgilentTxtReader create(java.io.File dataFile)
                               throws DataFileParseException
Throws:
DataFileParseException

getRow

public int getRow()
           throws DataFileParseException
Throws:
DataFileParseException

getCol

public int getCol()
           throws DataFileParseException
Throws:
DataFileParseException

getFeatureNum

public int getFeatureNum()
                  throws DataFileParseException
Throws:
DataFileParseException

close

public void close()

getValue

public final java.lang.Object getValue(QuantitationTypeDescriptor descriptor)
                                throws DataFileParseException
Specified by:
getValue in class AbstractDataFileReader
Throws:
DataFileParseException

getValueAsString

public java.lang.String getValueAsString(int columnIndex)

getValueAsStringOrNull

public java.lang.String getValueAsStringOrNull(int columnIndex)

getValueAsFloat

public java.lang.Float getValueAsFloat(int columnIndex)
                                throws DataFileParseException
Throws:
DataFileParseException

getValueAsInteger

public java.lang.Integer getValueAsInteger(int columnIndex)
                                    throws DataFileParseException
Throws:
DataFileParseException

getValueAsBoolean

public java.lang.Boolean getValueAsBoolean(int columnIndex)

getValueAsString

protected java.lang.String getValueAsString(java.lang.String stringValueTrimmed,
                                            java.lang.String columnName)

getValueAsBoolean

protected java.lang.Boolean getValueAsBoolean(java.lang.String stringValue,
                                              java.lang.String columnName)

getValueAsFloat

protected java.lang.Float getValueAsFloat(java.lang.String stringValue,
                                          java.lang.String columnName)
                                   throws DataFileParseException
Throws:
DataFileParseException

getValueAsInteger

protected java.lang.Integer getValueAsInteger(java.lang.String stringValue,
                                              java.lang.String columnName)
                                       throws DataFileParseException
Throws:
DataFileParseException

getIndex

protected int getIndex(QuantitationTypeDescriptor descriptor)