public class ReferenceSequence
extends java.lang.Object
Constructor and Description |
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ReferenceSequence(java.lang.String name,
int index,
byte[] bases)
creates a fully formed ReferenceSequence
|
Modifier and Type | Method and Description |
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byte[] |
getBases()
Gets the array of bases that define this sequence.
|
java.lang.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.
|
java.lang.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.
|
java.lang.String |
toString() |
public ReferenceSequence(java.lang.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 java.lang.String getName()
public byte[] getBases()
public java.lang.String getBaseString()
ReferenceSequenceFile.getSubsequenceAt(String, long, long)
public int getContigIndex()
public int length()
public java.lang.String toString()
toString
in class java.lang.Object