htsjdk.samtools

Class SAMValidationError

java.lang.Object

htsjdk.samtools.SAMValidationError

All Implemented Interfaces:

java.io.Serializable

public class SAMValidationError
extends java.lang.Object
implements java.io.Serializable

Class that encapsulates a validation error message as well as a type code so that errors can be aggregated by type.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SAMValidationError.Severity
static class	SAMValidationError.Type

Field Summary

Fields

Modifier and Type	Field and Description
static long	serialVersionUID

Constructor Summary

Constructors

Constructor and Description
SAMValidationError(SAMValidationError.Type type, java.lang.String message, java.lang.String readName) Construct a SAMValidationError with unknown record number.
SAMValidationError(SAMValidationError.Type type, java.lang.String message, java.lang.String readName, long recordNumber) Construct a SAMValidationError with possibly-known record number.

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getMessage()
java.lang.String	getReadName() may be null
long	getRecordNumber() 1-based.
java.lang.String	getSource()
SAMValidationError.Type	getType()
void	setRecordNumber(long recordNumber)
void	setSource(java.lang.String source)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

Constructor Detail

SAMValidationError

public SAMValidationError(SAMValidationError.Type type,
                  java.lang.String message,
                  java.lang.String readName)

Construct a SAMValidationError with unknown record number.

Parameters:

type -

message -

readName - May be null if readName is not known.

SAMValidationError

public SAMValidationError(SAMValidationError.Type type,
                  java.lang.String message,
                  java.lang.String readName,
                  long recordNumber)

Construct a SAMValidationError with possibly-known record number.

Parameters:

type -

message -

readName - May be null if readName is not known.

recordNumber - Position of the record in the SAM file it has been read from. -1 if not known.

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getType

public SAMValidationError.Type getType()

getMessage

public java.lang.String getMessage()

getReadName

public java.lang.String getReadName()

may be null

getRecordNumber

public long getRecordNumber()

1-based. -1 if not known.

setRecordNumber

public void setRecordNumber(long recordNumber)

getSource

public java.lang.String getSource()

setSource

public void setSource(java.lang.String source)