public class AbstractLocusInfo<E extends AbstractRecordAndOffset> extends java.lang.Object implements Locus, Locatable
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.
|
java.lang.String |
getContig()
Gets the contig name for the contig this is mapped to.
|
int |
getEnd() |
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() |
int |
getStart() |
boolean |
isEmpty() |
int |
size() |
java.lang.String |
toString() |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitcontains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOfpublic 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 Locuspublic int getPosition()
getPosition in interface Locus@Deprecated public java.util.List<E> getRecordAndPositions()
getRecordAndOffsets()recordsAndOffsetspublic java.util.List<E> getRecordAndOffsets()
recordsAndOffsetspublic java.lang.String getSequenceName()
public java.lang.String toString()
toString in class java.lang.Objectpublic int getSequenceLength()
public int size()
public boolean isEmpty()
true if RecordAndOffset list is empty;public java.lang.String getContig()
Locatablepublic int getStart()