uk.ac.sanger.cgp.standalonecsa.util
Class FileHandler

java.lang.Object
  extended by org.biojava.bio.chromatogram.AbstractChromatogram
      extended by org.biojava.bio.program.abi.ABIFChromatogram
          extended by uk.ac.sanger.cgp.standalonecsa.util.FileHandler
All Implemented Interfaces:
org.biojava.bio.chromatogram.Chromatogram

public class FileHandler
extends org.biojava.bio.program.abi.ABIFChromatogram

Author:
Original: kr2, $Author: kr2 $

Nested Class Summary
 
Nested classes/interfaces inherited from class org.biojava.bio.program.abi.ABIFChromatogram
org.biojava.bio.program.abi.ABIFChromatogram.Parser
 
Field Summary
protected static FileProcessingInfoBean fileComponentBean
           
protected static org.apache.commons.logging.Log log
           
 
Fields inherited from interface org.biojava.bio.chromatogram.Chromatogram
DNA, OFFSETS
 
Constructor Summary
protected FileHandler()
          Creates a new instance of FileHandler
 
Method Summary
static boolean createOutputDirs(java.io.File outputLocation, boolean isPath)
           
static ExperimentBean experimentFromFile(java.io.File file, boolean loadChromatogram)
           
protected static void getChromatogram(ExperimentBean eb)
           
 
Methods inherited from class org.biojava.bio.program.abi.ABIFChromatogram
create, create, load, load, reverseComplementInstance
 
Methods inherited from class org.biojava.bio.chromatogram.AbstractChromatogram
clearTraces, createImmutableAlignment, createImmutableSymbolList, getBaseCalls, getMax, getMax, getSequenceLength, getSignificantBits, getTrace, getTraceLength, reverse, reverseComplement, reverseComplementBaseCallList, reverseComplementBaseCalls, setBaseCallAlignment, setBits, setTrace
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

fileComponentBean

protected static final FileProcessingInfoBean fileComponentBean

log

protected static final org.apache.commons.logging.Log log
Constructor Detail

FileHandler

protected FileHandler()
Creates a new instance of FileHandler

Method Detail

experimentFromFile

public static ExperimentBean experimentFromFile(java.io.File file,
                                                boolean loadChromatogram)

getChromatogram

protected static void getChromatogram(ExperimentBean eb)

createOutputDirs

public static boolean createOutputDirs(java.io.File outputLocation,
                                       boolean isPath)