org.cybertory.MSS
Class IntensitiesFileReader

java.lang.Object
  extended byorg.cybertory.MSS.IntensitiesFileReader
All Implemented Interfaces:
IntensitiesReader

public class IntensitiesFileReader
extends java.lang.Object
implements IntensitiesReader

A flexible class to read feature intensities data from a flat file. Input data includes: zone index and/or metarow/metacol, row, column, and intensities values.


Field Summary
static int ID_Col
           
static int ID_Ignore
           
static int ID_Metacol
           
static int ID_Metarow
           
static int ID_Row
           
static int ID_ZoneIndex
           
 
Constructor Summary
IntensitiesFileReader(java.io.Reader rdr)
           
IntensitiesFileReader(java.io.Reader rdr, int[] columnIDs)
           
IntensitiesFileReader(java.io.Reader rdr, int[] columnIDs, java.util.regex.Pattern pattern, boolean onlyOneZone)
           
 
Method Summary
 RawIntensitiesRecord[] getData()
           
 boolean includesMetaCoords()
           
 boolean includesZoneIndex()
           
 RawIntensitiesRecord[] readData()
           
 void setCommentLinePattern(java.util.regex.Pattern commentLinePattern)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

ID_Ignore

public static final int ID_Ignore
See Also:
Constant Field Values

ID_ZoneIndex

public static final int ID_ZoneIndex
See Also:
Constant Field Values

ID_Metarow

public static final int ID_Metarow
See Also:
Constant Field Values

ID_Metacol

public static final int ID_Metacol
See Also:
Constant Field Values

ID_Row

public static final int ID_Row
See Also:
Constant Field Values

ID_Col

public static final int ID_Col
See Also:
Constant Field Values
Constructor Detail

IntensitiesFileReader

public IntensitiesFileReader(java.io.Reader rdr)
                      throws DatMissingColumn

IntensitiesFileReader

public IntensitiesFileReader(java.io.Reader rdr,
                             int[] columnIDs)
                      throws DatMissingColumn

IntensitiesFileReader

public IntensitiesFileReader(java.io.Reader rdr,
                             int[] columnIDs,
                             java.util.regex.Pattern pattern,
                             boolean onlyOneZone)
                      throws DatMissingColumn
Method Detail

includesMetaCoords

public boolean includesMetaCoords()
Specified by:
includesMetaCoords in interface IntensitiesReader

includesZoneIndex

public boolean includesZoneIndex()
Specified by:
includesZoneIndex in interface IntensitiesReader

setCommentLinePattern

public void setCommentLinePattern(java.util.regex.Pattern commentLinePattern)

readData

public RawIntensitiesRecord[] readData()
                                throws DatException
Throws:
DatException

getData

public RawIntensitiesRecord[] getData()
                               throws DatException
Specified by:
getData in interface IntensitiesReader
Throws:
DatException