htsjdk.samtools

Class SAMProgramRecord

java.lang.Object

htsjdk.samtools.AbstractSAMHeaderRecord

htsjdk.samtools.SAMProgramRecord

All Implemented Interfaces:

java.io.Serializable

public class SAMProgramRecord
extends AbstractSAMHeaderRecord

In-memory representation of @PG SAM header record.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	COMMAND_LINE_TAG
static java.lang.String	PREVIOUS_PROGRAM_GROUP_ID_TAG
static java.lang.String	PROGRAM_GROUP_ID_TAG
static java.lang.String	PROGRAM_NAME_TAG
static java.lang.String	PROGRAM_VERSION_TAG
static java.util.Set<java.lang.String>	STANDARD_TAGS

Fields inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

serialVersionUID

Constructor Summary

Constructors

Constructor and Description
SAMProgramRecord(java.lang.String programGroupId)
SAMProgramRecord(java.lang.String id, SAMProgramRecord srcProgramRecord)

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
boolean	equivalent(SAMProgramRecord that)
java.lang.String	getCommandLine()
java.lang.String	getId() Returns the ID tag (or equivalent) for this header record.
java.lang.String	getPreviousProgramGroupId()
java.lang.String	getProgramGroupId()
java.lang.String	getProgramName()
java.lang.String	getProgramVersion()
int	hashCode()
void	setCommandLine(java.lang.String commandLine)
void	setPreviousProgramGroupId(java.lang.String id)
void	setProgramName(java.lang.String name)
void	setProgramVersion(java.lang.String version)

Methods inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

attributesEqual, attributesHashCode, getAttribute, getAttributes, setAttribute, setAttribute, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

PROGRAM_GROUP_ID_TAG

public static final java.lang.String PROGRAM_GROUP_ID_TAG

See Also:

Constant Field Values

PROGRAM_NAME_TAG

public static final java.lang.String PROGRAM_NAME_TAG

See Also:

Constant Field Values

PROGRAM_VERSION_TAG

public static final java.lang.String PROGRAM_VERSION_TAG

See Also:

Constant Field Values

COMMAND_LINE_TAG

public static final java.lang.String COMMAND_LINE_TAG

See Also:

Constant Field Values

PREVIOUS_PROGRAM_GROUP_ID_TAG

public static final java.lang.String PREVIOUS_PROGRAM_GROUP_ID_TAG

See Also:

Constant Field Values

STANDARD_TAGS

public static final java.util.Set<java.lang.String> STANDARD_TAGS

Constructor Detail

SAMProgramRecord

public SAMProgramRecord(java.lang.String programGroupId)

SAMProgramRecord

public SAMProgramRecord(java.lang.String id,
                        SAMProgramRecord srcProgramRecord)

Method Detail

getId

public java.lang.String getId()

Description copied from class: AbstractSAMHeaderRecord

Returns the ID tag (or equivalent) for this header record. The default implementation throws a SAMException to indicate "not implemented".

Overrides:

getId in class AbstractSAMHeaderRecord

getProgramGroupId

public java.lang.String getProgramGroupId()

getProgramName

public java.lang.String getProgramName()

setProgramName

public void setProgramName(java.lang.String name)

getProgramVersion

public java.lang.String getProgramVersion()

setProgramVersion

public void setProgramVersion(java.lang.String version)

getCommandLine

public java.lang.String getCommandLine()

setCommandLine

public void setCommandLine(java.lang.String commandLine)

getPreviousProgramGroupId

public java.lang.String getPreviousProgramGroupId()

setPreviousProgramGroupId

public void setPreviousProgramGroupId(java.lang.String id)

equivalent

public boolean equivalent(SAMProgramRecord that)

Returns:

true if this == that except for the program group ID, which is arbitrary

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object