com.hfg.bio.seq.format.abi

Class ABIF

java.lang.Object

com.hfg.bio.seq.format.abi.ABIF

public class ABIF
extends Object

Extracts data from ABIF (ab1) format sequencing chromatographic trace files.

Constructor Summary

Constructors

Constructor and Description
ABIF(byte[] inBytes)
ABIF(File inFile)

Method Summary

Modifier and Type	Method and Description
int	getABIF_FormatVersionNum()
short[]	getBasecallerPeakLocations()
short[]	getBasecallerQualityScores()
String	getBasecallerSeq()
String	getInstrumentClass()
String	getInstrumentFamily()
String	getInstrumentName()
Integer	getLane()
String	getMachineName()
Integer	getMaxQualityScore()
short	getMaxTraceValue() Returns the largest trace intensity value - helpful for scaling.
String	getQC_Errors() 3500/3500xl specific: Returns any QC errors as a concatenated comma-separated string.
String	getQC_Warnings() 3500/3500xl specific: Returns any QC warnings as a concatenated comma-separated string.
Long	getQV20_Score() 3500/3500xl specific: Returns the QV20+ value.
String	getQV20_Status() 3500/3500xl specific: Returns the QV20 status as one of 'Pass', 'Fail', or 'Check'.
Date	getRunDate()
String	getSampleComment()
String	getSampleName()
String	getSampleTrackingID()
short[]	getTraceValues(Nucleotide inNucleotide)
short[]	getUserPeakLocations()
short[]	getUserQualityScores()
String	getUserSeq()
NucleicAcid	toNucleicAcid()
SVG	toSVG()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ABIF

public ABIF(File inFile)
     throws IOException

Throws:

IOException

ABIF

public ABIF(byte[] inBytes)
     throws IOException

Throws:

IOException

Method Detail

getABIF_FormatVersionNum

public int getABIF_FormatVersionNum()

getLane

public Integer getLane()

getInstrumentClass

public String getInstrumentClass()

getInstrumentFamily

public String getInstrumentFamily()

getInstrumentName

public String getInstrumentName()

getMachineName

public String getMachineName()

getRunDate

public Date getRunDate()

getSampleName

public String getSampleName()

getSampleTrackingID

public String getSampleTrackingID()

getSampleComment

public String getSampleComment()

getBasecallerSeq

public String getBasecallerSeq()

getBasecallerPeakLocations

public short[] getBasecallerPeakLocations()

getBasecallerQualityScores

public short[] getBasecallerQualityScores()

getUserSeq

public String getUserSeq()

getUserQualityScores

public short[] getUserQualityScores()

getMaxQualityScore

public Integer getMaxQualityScore()

getUserPeakLocations

public short[] getUserPeakLocations()

getTraceValues

public short[] getTraceValues(Nucleotide inNucleotide)

getQC_Warnings

public String getQC_Warnings()

3500/3500xl specific: Returns any QC warnings as a concatenated comma-separated string.

Returns:

QC warnings

getQC_Errors

public String getQC_Errors()

3500/3500xl specific: Returns any QC errors as a concatenated comma-separated string.

Returns:

QC errors or null

getQV20_Score

public Long getQV20_Score()

3500/3500xl specific: Returns the QV20+ value.

Returns:

QV20+ score or null

getQV20_Status

public String getQV20_Status()

3500/3500xl specific: Returns the QV20 status as one of 'Pass', 'Fail', or 'Check'.

Returns:

QV20 status or null

toNucleicAcid

public NucleicAcid toNucleicAcid()

getMaxTraceValue

public short getMaxTraceValue()

Returns the largest trace intensity value - helpful for scaling.

Returns:

the largest trace intensity value

toSVG

public SVG toSVG()