SAMSequenceRecord (htsjdk 3.0.5 API)

java.lang.Object
- htsjdk.samtools.AbstractSAMHeaderRecord
- - htsjdk.samtools.SAMSequenceRecord

All Implemented Interfaces:

Locatable, java.io.Serializable, java.lang.Cloneable
```
public class SAMSequenceRecord
extends AbstractSAMHeaderRecord
implements java.lang.Cloneable, Locatable
```
Header information about a reference sequence. Corresponds to @SQ header record in SAM text header.

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`ALTERNATIVE_SEQUENCE_NAME_TAG`
`static java.lang.String`	`ASSEMBLY_TAG`
`static java.lang.String`	`DESCRIPTION_TAG`
`static java.lang.String`	`MD5_TAG`
`static java.lang.String`	`RESERVED_MRNM_SEQUENCE_NAME` Deprecated.
`static java.lang.String`	`RESERVED_RNEXT_SEQUENCE_NAME` This is not a valid sequence name, because it is reserved in the RNEXT 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 long`	`serialVersionUID`
`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`	`UNAVAILABLE_SEQUENCE_INDEX`
`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`

Constructor Summary

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAlternativeSequenceName(java.lang.String name)` Adds an alternative sequence name if it is not the same as the sequence name or it is not present already.
`SAMSequenceRecord`	`clone()`
`boolean`	`equals(java.lang.Object o)`
`java.util.Set<java.lang.String>`	`getAlternativeSequenceNames()` Returns unmodifiable set with alternative sequence names.
`java.lang.String`	`getAssembly()`
`java.lang.String`	`getContig()` always returns `getSequenceName()`
`java.lang.String`	`getDescription()`
`int`	`getEnd()` always returns `getSequenceLength()`
`java.lang.String`	`getMd5()`
`java.lang.String`	`getSAMString()` Returns the record in the SAM line-based text format.
`int`	`getSequenceIndex()`
`int`	`getSequenceLength()`
`java.lang.String`	`getSequenceName()`
`java.lang.String`	`getSpecies()`
`int`	`getStart()` always returns 1
`boolean`	`hasAlternativeSequenceNames()` Returns `true` if there are alternative sequence names; `false` otherwise.
`int`	`hashCode()`
`boolean`	`isSameSequence(SAMSequenceRecord that)` Looser comparison than equals().
`SAMSequenceRecord`	`setAlternativeSequenceName(java.util.Collection<java.lang.String> alternativeSequences)` Sets the alternative sequence names in the order provided by iteration, removing the previous values.
`SAMSequenceRecord`	`setAssembly(java.lang.String value)`
`SAMSequenceRecord`	`setDescription(java.lang.String value)`
`SAMSequenceRecord`	`setMd5(java.lang.String value)`
`SAMSequenceRecord`	`setSequenceIndex(int value)`
`SAMSequenceRecord`	`setSequenceLength(int value)`
`SAMSequenceRecord`	`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, setAttribute

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.Locatable
contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

- Field Detail
  - serialVersionUID
```
public static final long serialVersionUID
```
    See Also:
    
    Constant Field Values
  - UNAVAILABLE_SEQUENCE_INDEX
```
public static final int UNAVAILABLE_SEQUENCE_INDEX
```
    See Also:
    
    Constant Field Values
  - SEQUENCE_NAME_TAG
```
public static final java.lang.String SEQUENCE_NAME_TAG
```
    See Also:
    
    Constant Field Values
  - ALTERNATIVE_SEQUENCE_NAME_TAG
```
public static final java.lang.String ALTERNATIVE_SEQUENCE_NAME_TAG
```
    See Also:
    
    Constant Field Values
  - SEQUENCE_LENGTH_TAG
```
public static final java.lang.String SEQUENCE_LENGTH_TAG
```
    See Also:
    
    Constant Field Values
  - MD5_TAG
```
public static final java.lang.String MD5_TAG
```
    See Also:
    
    Constant Field Values
  - ASSEMBLY_TAG
```
public static final java.lang.String ASSEMBLY_TAG
```
    See Also:
    
    Constant Field Values
  - URI_TAG
```
public static final java.lang.String URI_TAG
```
    See Also:
    
    Constant Field Values
  - SPECIES_TAG
```
public static final java.lang.String SPECIES_TAG
```
    See Also:
    
    Constant Field Values
  - DESCRIPTION_TAG
```
public static final java.lang.String DESCRIPTION_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_RNEXT_SEQUENCE_NAME
```
public static final java.lang.String RESERVED_RNEXT_SEQUENCE_NAME
```
    This is not a valid sequence name, because it is reserved in the RNEXT field of SAM text format to mean "same reference as RNAME field."
    
    See Also:
    
    Constant Field Values
  - RESERVED_MRNM_SEQUENCE_NAME
```
@Deprecated
public static final java.lang.String RESERVED_MRNM_SEQUENCE_NAME
```
    Deprecated.
    
    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
```
@Deprecated
public SAMSequenceRecord(java.lang.String name)
```
    Deprecated. Use SAMSequenceRecord(String, int) 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 SAMSequenceRecord setSequenceLength(int value)
```
  - getAssembly
```
public java.lang.String getAssembly()
```
  - setAssembly
```
public SAMSequenceRecord setAssembly(java.lang.String value)
```
  - getSpecies
```
public java.lang.String getSpecies()
```
  - setSpecies
```
public SAMSequenceRecord setSpecies(java.lang.String value)
```
  - getMd5
```
public java.lang.String getMd5()
```
  - setMd5
```
public SAMSequenceRecord setMd5(java.lang.String value)
```
  - getDescription
```
public java.lang.String getDescription()
```
  - setDescription
```
public SAMSequenceRecord setDescription(java.lang.String value)
```
  - getSequenceIndex
```
public int getSequenceIndex()
```
    Returns:
    
    Index of this record in the sequence dictionary it lives in.
  - setSequenceIndex
```
public SAMSequenceRecord setSequenceIndex(int value)
```
  - getAlternativeSequenceNames
```
public java.util.Set<java.lang.String> getAlternativeSequenceNames()
```
    Returns unmodifiable set with alternative sequence names.
  - addAlternativeSequenceName
```
public void addAlternativeSequenceName(java.lang.String name)
```
    Adds an alternative sequence name if it is not the same as the sequence name or it is not present already.
  - setAlternativeSequenceName
```
public SAMSequenceRecord setAlternativeSequenceName(java.util.Collection<java.lang.String> alternativeSequences)
```
    Sets the alternative sequence names in the order provided by iteration, removing the previous values.
  - hasAlternativeSequenceNames
```
public boolean hasAlternativeSequenceNames()
```
    Returns true if there are alternative sequence names; false otherwise.
  - 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
  - getSAMString
```
public java.lang.String getSAMString()
```
    Description copied from class: AbstractSAMHeaderRecord
    
    Returns the record in the SAM line-based text format. Fields are separated by '\t' characters. The String is NOT terminated by '\n'.
    
    Specified by:
    
    getSAMString in class AbstractSAMHeaderRecord
  - getContig
```
public final java.lang.String getContig()
```
    always returns getSequenceName()
    
    Specified by:
    
    getContig in interface Locatable
    
    Returns:
    
    name of the contig this is mapped to, potentially null
    
    See Also:
    
    getSequenceName()
  - getStart
```
public final int getStart()
```
    always returns 1
    
    Specified by:
    
    getStart in interface Locatable
    
    Returns:
    
    1-based start position, undefined if getContig() == null
  - getEnd
```
public final int getEnd()
```
    always returns getSequenceLength()
    
    Specified by:
    
    getEnd in interface Locatable
    
    Returns:
    
    1-based closed-ended position, undefined if getContig() == null
    
    See Also:
    
    getSequenceLength()

Class SAMSequenceRecord

Field Summary

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.samtools.util.Locatable

Field Detail

serialVersionUID

UNAVAILABLE_SEQUENCE_INDEX

SEQUENCE_NAME_TAG

ALTERNATIVE_SEQUENCE_NAME_TAG

SEQUENCE_LENGTH_TAG

MD5_TAG

ASSEMBLY_TAG

URI_TAG

SPECIES_TAG

DESCRIPTION_TAG

UNKNOWN_SEQUENCE_LENGTH

RESERVED_RNEXT_SEQUENCE_NAME

RESERVED_MRNM_SEQUENCE_NAME

STANDARD_TAGS

Constructor Detail

SAMSequenceRecord

SAMSequenceRecord

Method Detail

getSequenceName

getSequenceLength

setSequenceLength

getAssembly

setAssembly

getSpecies

setSpecies

getMd5

setMd5

getDescription

setDescription

getSequenceIndex

setSequenceIndex

getAlternativeSequenceNames

addAlternativeSequenceName

setAlternativeSequenceName

hasAlternativeSequenceNames

isSameSequence

equals

hashCode

clone

truncateSequenceName

validateSequenceName

toString

getSAMString

getContig

getStart

getEnd