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

java.lang.Object
  org.biojava.bio.chromatogram.AbstractChromatogram
      org.biojava.bio.program.abi.ABIFChromatogram
          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)