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java.lang.Objectedu.unc.csbio.data.SequenceBuffer
edu.unc.csbio.data.ExtendedSequenceBuffer
public class ExtendedSequenceBuffer
The class extending SequenceBuffer
for handling structure
variants in the sequence.
Field Summary | |
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private java.util.ArrayList<Feature> |
sv
An ArrayList of Feature representing structure variants in
the sequence |
Constructor Summary | |
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ExtendedSequenceBuffer(java.lang.String _raw,
int _offset,
java.util.ArrayList<Feature> _sv)
A constructor for object ExtendedSequenceBuffer |
Method Summary | |
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private int |
findFirstOverlappedSV(int start,
int end)
Find the SV that has the position just before the given region |
java.lang.String |
get(int start,
int end)
Get the sequence for the region [start, end] including structure variants |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private final java.util.ArrayList<Feature> sv
Feature
representing structure variants in
the sequence
Constructor Detail |
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public ExtendedSequenceBuffer(java.lang.String _raw, int _offset, java.util.ArrayList<Feature> _sv)
ExtendedSequenceBuffer
_raw
- the sequence_offset
- the position difference between the start position of
sequence and the start position of the reference gene_sv
- an ArrayList of Feature
representing
structure variants in the sequenceMethod Detail |
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private int findFirstOverlappedSV(int start, int end)
start
- the start position of the region in reference coordinate.end
- the end position of the region in reference coordinate.
public java.lang.String get(int start, int end)
get
in class SequenceBuffer
start
- the start position of the region in reference coordinate.end
- the end position of the region in reference coordinate.
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