gov.nih.nci.caarray.services.bioassaydata.reader
Class AgilentTxtReader
java.lang.Object
gov.nih.nci.caarray.services.bioassaydata.reader.AbstractDataFileReader
gov.nih.nci.caarray.services.bioassaydata.reader.AgilentTxtReader
public class AgilentTxtReader
- extends AbstractDataFileReader
Reader for Agilent gene expression data files.
- Author:
- tavelae
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
map
protected static java.util.HashMap<java.lang.String,QuantitationTypeDescriptor> map
- Represents a map of
dataRowValues
protected java.util.List<java.lang.String> dataRowValues
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)