public class ReferenceSequence extends Object
Constructor | Description |
---|---|
ReferenceSequence(String name,
int index,
byte[] bases) |
creates a fully formed ReferenceSequence
|
Modifier and Type | Method | Description |
---|---|---|
byte[] |
getBases() |
Gets the array of bases that define this sequence.
|
String |
getBaseString() |
Returns the bases represented by this ReferenceSequence as a String.
|
int |
getContigIndex() |
Gets the 0-based index of this contig in the source file from which it came.
|
String |
getName() |
Gets the set of names given to this sequence in the source file.
|
int |
length() |
Gets the length of this reference sequence in bases.
|
String |
toString() |
public ReferenceSequence(String name, int index, byte[] bases)
name
- the name of the sequence from the source fileindex
- the zero based index of this contig in the source filebases
- the bases themselves stored as one-byte characterspublic String getName()
public byte[] getBases()
public String getBaseString()
ReferenceSequenceFile.getSubsequenceAt(String, long, long)
public int getContigIndex()
public int length()