public class AbstractLocusInfo<E extends AbstractRecordAndOffset> extends java.lang.Object implements Locus
RecordAndOffset
class is used, one object represents one aligned read that overlaps the locus.
If TypedRecordAndOffset
class is used, one object represents one aligned read,
that starts or ends at the locus.Constructor and Description |
---|
AbstractLocusInfo(SAMSequenceRecord referenceSequence,
int position) |
Modifier and Type | Method and Description |
---|---|
void |
add(E recordAndOffset)
Accumulates info for one read aligned to the locus.
|
int |
getPosition() |
java.util.List<E> |
getRecordAndOffsets() |
java.util.List<E> |
getRecordAndPositions()
Deprecated.
since name of the method can be confusing, new implementation should be used
getRecordAndOffsets() |
int |
getSequenceIndex() |
int |
getSequenceLength() |
java.lang.String |
getSequenceName() |
boolean |
isEmpty() |
int |
size() |
java.lang.String |
toString() |
public AbstractLocusInfo(SAMSequenceRecord referenceSequence, int position)
referenceSequence
- reference sequence to which the reads are alignedposition
- position in the sequence to which the reads are alignedpublic void add(E recordAndOffset)
recordAndOffset
is really aligned to current reference position, so it must have valid reference sequence and
position or further processing can go wrong.recordAndOffset
- object to add to current locuspublic int getSequenceIndex()
getSequenceIndex
in interface Locus
public int getPosition()
getPosition
in interface Locus
@Deprecated public java.util.List<E> getRecordAndPositions()
getRecordAndOffsets()
recordsAndOffsets
public java.util.List<E> getRecordAndOffsets()
recordsAndOffsets
public java.lang.String getSequenceName()
public java.lang.String toString()
toString
in class java.lang.Object
public int getSequenceLength()
public int size()
public boolean isEmpty()
true
if RecordAndOffset list is empty;