Serializable
, Cloneable
public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements Cloneable
Modifier and Type | Field | Description |
---|---|---|
static String |
ASSEMBLY_TAG |
|
static String |
MD5_TAG |
|
static 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 String |
SEQUENCE_LENGTH_TAG |
|
static String |
SEQUENCE_NAME_TAG |
|
static long |
serialVersionUID |
|
static String |
SPECIES_TAG |
|
static Set<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 String |
URI_TAG |
Constructor | Description |
---|---|
SAMSequenceRecord(String name) |
Deprecated.
Use
SAMSequenceRecord(String, int) instead. |
SAMSequenceRecord(String name,
int sequenceLength) |
Modifier and Type | Method | Description |
---|---|---|
SAMSequenceRecord |
clone() |
|
boolean |
equals(Object o) |
|
String |
getAssembly() |
|
String |
getMd5() |
|
String |
getSAMString() |
Returns the record in the SAM line-based text format.
|
int |
getSequenceIndex() |
|
int |
getSequenceLength() |
|
String |
getSequenceName() |
|
String |
getSpecies() |
|
int |
hashCode() |
|
boolean |
isSameSequence(SAMSequenceRecord that) |
Looser comparison than equals().
|
void |
setAssembly(String value) |
|
void |
setMd5(String value) |
|
void |
setSequenceIndex(int value) |
|
void |
setSequenceLength(int value) |
|
void |
setSpecies(String value) |
|
String |
toString() |
Simple to String that outputs the concrete class name and the set of attributes stored.
|
static String |
truncateSequenceName(String sequenceName) |
Truncate sequence name at first whitespace.
|
static void |
validateSequenceName(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 String SEQUENCE_NAME_TAG
public static final String SEQUENCE_LENGTH_TAG
public static final String MD5_TAG
public static final String ASSEMBLY_TAG
public static final String URI_TAG
public static final String SPECIES_TAG
public static final int UNKNOWN_SEQUENCE_LENGTH
public static final String RESERVED_MRNM_SEQUENCE_NAME
@Deprecated public SAMSequenceRecord(String name)
SAMSequenceRecord(String, int)
instead.
sequenceLength is required for the object to be considered valid.public SAMSequenceRecord(String name, int sequenceLength)
public String getSequenceName()
public int getSequenceLength()
public void setSequenceLength(int value)
public String getAssembly()
public void setAssembly(String value)
public String getSpecies()
public void setSpecies(String value)
public String getMd5()
public void setMd5(String value)
public int getSequenceIndex()
public void setSequenceIndex(int value)
public boolean isSameSequence(SAMSequenceRecord that)
public final SAMSequenceRecord clone()
public static String truncateSequenceName(String sequenceName)
public static void validateSequenceName(String name)
public String toString()
AbstractSAMHeaderRecord
toString
in class AbstractSAMHeaderRecord
public String getSAMString()
AbstractSAMHeaderRecord
getSAMString
in class AbstractSAMHeaderRecord