public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements java.lang.Cloneable
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 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 |
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 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) |
Modifier and Type | Method and Description |
---|---|
SAMSequenceRecord |
clone() |
boolean |
equals(java.lang.Object o) |
java.lang.String |
getAssembly() |
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 |
hashCode() |
boolean |
isSameSequence(SAMSequenceRecord that)
Looser comparison than equals().
|
void |
setAssembly(java.lang.String value) |
void |
setMd5(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.
|
attributesEqual, attributesHashCode, getAttribute, getAttributes, getId, setAttribute, setAttribute
public static final long serialVersionUID
public static final java.lang.String SEQUENCE_NAME_TAG
public static final java.lang.String SEQUENCE_LENGTH_TAG
public static final java.lang.String MD5_TAG
public static final java.lang.String ASSEMBLY_TAG
public static final java.lang.String URI_TAG
public static final java.lang.String SPECIES_TAG
public static final int UNKNOWN_SEQUENCE_LENGTH
public static final java.lang.String RESERVED_MRNM_SEQUENCE_NAME
public static final java.util.Set<java.lang.String> STANDARD_TAGS
@Deprecated public SAMSequenceRecord(java.lang.String name)
SAMSequenceRecord(String, int)
instead.
sequenceLength is required for the object to be considered valid.public SAMSequenceRecord(java.lang.String name, int sequenceLength)
public java.lang.String getSequenceName()
public int getSequenceLength()
public void setSequenceLength(int value)
public java.lang.String getAssembly()
public void setAssembly(java.lang.String value)
public java.lang.String getSpecies()
public void setSpecies(java.lang.String value)
public java.lang.String getMd5()
public void setMd5(java.lang.String value)
public int getSequenceIndex()
public void setSequenceIndex(int value)
public boolean isSameSequence(SAMSequenceRecord that)
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
public final SAMSequenceRecord clone()
clone
in class java.lang.Object
public static java.lang.String truncateSequenceName(java.lang.String sequenceName)
public static void validateSequenceName(java.lang.String name)
public java.lang.String toString()
AbstractSAMHeaderRecord
toString
in class AbstractSAMHeaderRecord
public java.lang.String getSAMString()
AbstractSAMHeaderRecord
getSAMString
in class AbstractSAMHeaderRecord