htsjdk.samtools

Class SAMSequenceRecord

java.lang.Object

htsjdk.samtools.AbstractSAMHeaderRecord

htsjdk.samtools.SAMSequenceRecord

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public class SAMSequenceRecord
extends AbstractSAMHeaderRecord
implements java.lang.Cloneable

Header information about a reference sequence. Corresponds to @SQ header record in SAM text header.

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Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ASSEMBLY_TAG
static java.lang.String	MD5_TAG
static java.lang.String	RESERVED_MRNM_SEQUENCE_NAME This is not a valid sequence name, because it is reserved in the MRNM field of SAM text format to mean "same reference as RNAME field."
static java.lang.String	SEQUENCE_LENGTH_TAG
static java.lang.String	SEQUENCE_NAME_TAG
static java.lang.String	SPECIES_TAG
static java.util.Set<java.lang.String>	STANDARD_TAGS The standard tags are stored in text header without type information, because the type of these tags is known.
static int	UNKNOWN_SEQUENCE_LENGTH If one sequence has this length, and another sequence had a different length, isSameSequence will not complain that they are different sequences.
static java.lang.String	URI_TAG

Fields inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

serialVersionUID

Constructor Summary

Constructors

Constructor and Description
SAMSequenceRecord(java.lang.String name) Deprecated. Use SAMSequenceRecord(final String name, final int sequenceLength) instead. sequenceLength is required for the object to be considered valid.
SAMSequenceRecord(java.lang.String name, int sequenceLength)

Method Summary

Methods

Modifier and Type	Method and Description
SAMSequenceRecord	clone()
boolean	equals(java.lang.Object o)
java.lang.String	getAssembly()
int	getSequenceIndex()
int	getSequenceLength()
java.lang.String	getSequenceName()
java.lang.String	getSpecies()
int	hashCode()
boolean	isSameSequence(SAMSequenceRecord that) Looser comparison than equals().
void	setAssembly(java.lang.String value)
void	setSequenceIndex(int value)
void	setSequenceLength(int value)
void	setSpecies(java.lang.String value)
java.lang.String	toString() Simple to String that outputs the concrete class name and the set of attributes stored.
static java.lang.String	truncateSequenceName(java.lang.String sequenceName) Truncate sequence name at first whitespace.
static void	validateSequenceName(java.lang.String name) Throw an exception if the sequence name is not valid.

Methods inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

attributesEqual, attributesHashCode, getAttribute, getAttributes, getId, setAttribute, setAttribute

Methods inherited from class java.lang.Object

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

Field Detail

SEQUENCE_NAME_TAG

public static final java.lang.String SEQUENCE_NAME_TAG

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Constant Field Values

SEQUENCE_LENGTH_TAG

public static final java.lang.String SEQUENCE_LENGTH_TAG

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Constant Field Values

MD5_TAG

public static final java.lang.String MD5_TAG

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Constant Field Values

ASSEMBLY_TAG

public static final java.lang.String ASSEMBLY_TAG

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Constant Field Values

URI_TAG

public static final java.lang.String URI_TAG

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Constant Field Values

SPECIES_TAG

public static final java.lang.String SPECIES_TAG

See Also:

Constant Field Values

UNKNOWN_SEQUENCE_LENGTH

public static final int UNKNOWN_SEQUENCE_LENGTH

If one sequence has this length, and another sequence had a different length, isSameSequence will not complain that they are different sequences.

See Also:

Constant Field Values

RESERVED_MRNM_SEQUENCE_NAME

public static final java.lang.String RESERVED_MRNM_SEQUENCE_NAME

This is not a valid sequence name, because it is reserved in the MRNM field of SAM text format to mean "same reference as RNAME field."

See Also:

Constant Field Values

STANDARD_TAGS

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

The standard tags are stored in text header without type information, because the type of these tags is known.

Constructor Detail

SAMSequenceRecord

public SAMSequenceRecord(java.lang.String name)

Deprecated. Use SAMSequenceRecord(final String name, final int sequenceLength) instead. sequenceLength is required for the object to be considered valid.

SAMSequenceRecord

public SAMSequenceRecord(java.lang.String name,
                 int sequenceLength)

Method Detail

getSequenceName

public java.lang.String getSequenceName()

getSequenceLength

public int getSequenceLength()

setSequenceLength

public void setSequenceLength(int value)

getAssembly

public java.lang.String getAssembly()

setAssembly

public void setAssembly(java.lang.String value)

getSpecies

public java.lang.String getSpecies()

setSpecies

public void setSpecies(java.lang.String value)

getSequenceIndex

public int getSequenceIndex()

Returns:

Index of this record in the sequence dictionary it lives in.

setSequenceIndex

public void setSequenceIndex(int value)

isSameSequence

public boolean isSameSequence(SAMSequenceRecord that)

Looser comparison than equals(). We look only at sequence index, sequence length, and MD5 tag value (or sequence names, if there is no MD5 tag in either record.

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

clone

public final SAMSequenceRecord clone()

Overrides:

clone in class java.lang.Object

truncateSequenceName

public static java.lang.String truncateSequenceName(java.lang.String sequenceName)

Truncate sequence name at first whitespace.

validateSequenceName

public static void validateSequenceName(java.lang.String name)

Throw an exception if the sequence name is not valid.

toString

public java.lang.String toString()

Description copied from class: AbstractSAMHeaderRecord

Simple to String that outputs the concrete class name and the set of attributes stored.

Overrides:

toString in class AbstractSAMHeaderRecord