gov.nih.nci.caarray.services.fileparse2.arraydesign
Class ArrayDesignTextFileHeaderParser

java.lang.Object
  extended by gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
      extended by gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
          extended by gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignTextFileHeaderParser
All Implemented Interfaces:
ArrayDesignFileHeaderParserItf
Direct Known Subclasses:
GenePixGALFileHeaderParser, UCSFSpotFileHeaderParser

public abstract class ArrayDesignTextFileHeaderParser
extends MicroarrayTextFileHeaderParser
implements ArrayDesignFileHeaderParserItf

Author:
TranP

Field Summary
 
Fields inherited from class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
headerEndMarkerPattern_
 
Fields inherited from class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
dataSetMapper_, header_, logger_
 
Constructor Summary
ArrayDesignTextFileHeaderParser(DataSetMapper dataSetMapper)
           
ArrayDesignTextFileHeaderParser(DataSetMapper dataSetMapper, java.lang.String headerEndMarkerPattern)
           
 
Method Summary
 boolean addZoneLocation(java.lang.Integer row, java.lang.Integer column, java.lang.Float upperLeftX, java.lang.Float upperLeftY)
           
 void addZoneLocation(Zone zone)
           
 ZoneGroup getZoneGroup()
           
 boolean removeZoneLocation(java.lang.Integer row, java.lang.Integer column)
           
 void setZoneLayout(java.lang.Float spacingBetweenCols, java.lang.Float spacingBetweenRows, java.lang.Integer numFeaturesPerCol, java.lang.Integer numFeaturesPerRow)
           
 void setZoneLayout(ZoneLayout layout)
           
 
Methods inherited from class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
extractHeaderSection, getMatch, main, match, matchHeaderEndMarkerPattern, parse, validate
 
Methods inherited from class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
getDataSetMapper, getHeader
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParserItf
parse
 

Constructor Detail

ArrayDesignTextFileHeaderParser

public ArrayDesignTextFileHeaderParser(DataSetMapper dataSetMapper)

ArrayDesignTextFileHeaderParser

public ArrayDesignTextFileHeaderParser(DataSetMapper dataSetMapper,
                                       java.lang.String headerEndMarkerPattern)
Method Detail

getZoneGroup

public final ZoneGroup getZoneGroup()
Specified by:
getZoneGroup in interface ArrayDesignFileHeaderParserItf

setZoneLayout

public final void setZoneLayout(ZoneLayout layout)
Specified by:
setZoneLayout in interface ArrayDesignFileHeaderParserItf

setZoneLayout

public final void setZoneLayout(java.lang.Float spacingBetweenCols,
                                java.lang.Float spacingBetweenRows,
                                java.lang.Integer numFeaturesPerCol,
                                java.lang.Integer numFeaturesPerRow)
Specified by:
setZoneLayout in interface ArrayDesignFileHeaderParserItf

addZoneLocation

public final void addZoneLocation(Zone zone)
Specified by:
addZoneLocation in interface ArrayDesignFileHeaderParserItf

addZoneLocation

public final boolean addZoneLocation(java.lang.Integer row,
                                     java.lang.Integer column,
                                     java.lang.Float upperLeftX,
                                     java.lang.Float upperLeftY)
Specified by:
addZoneLocation in interface ArrayDesignFileHeaderParserItf

removeZoneLocation

public final boolean removeZoneLocation(java.lang.Integer row,
                                        java.lang.Integer column)
Specified by:
removeZoneLocation in interface ArrayDesignFileHeaderParserItf