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java.lang.Objectedu.unc.csbio.data.Feature
edu.unc.csbio.data.Transcript
public class Transcript
The class Transcript
inherits abstract class
Feature
and contains information of transcript.
Field Summary | |
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private java.util.ArrayList<Exon> |
exons
An ArrayList of exons in the gene |
private java.lang.String |
id
The name and id of the transcript. |
private java.lang.String |
name
The name and id of the transcript. |
Fields inherited from class edu.unc.csbio.data.Feature |
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chrom, end, start |
Constructor Summary | |
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Transcript(java.lang.String _id,
java.lang.String _name,
Exon _e)
A constructor for Transcript object |
Method Summary | |
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void |
addExon(Exon e)
The method to add a new exon |
java.lang.String |
getId()
the method to get id of transcript |
int |
getLength()
The method to get the exon part length of the transcript |
java.lang.String |
getSequence(SequenceBuffer motherSequence)
The method to get a transcript sequence from a sequence buffer. |
int |
refPos(int seqPos)
The method to convert a position in transcript sequence coordinate to the reference coordinate |
java.lang.String |
toString()
A method to get transcript information |
Methods inherited from class edu.unc.csbio.data.Feature |
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compareTo, getChromosome, getEnd, getRange, getStart |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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private java.lang.String name
private java.lang.String id
private java.util.ArrayList<Exon> exons
Constructor Detail |
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public Transcript(java.lang.String _id, java.lang.String _name, Exon _e)
Transcript
object
_id
- id of the transcript_name
- name of the transcript_e
- the first exon in the transcriptMethod Detail |
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public java.lang.String getId()
public void addExon(Exon e)
public int refPos(int seqPos)
public java.lang.String getSequence(SequenceBuffer motherSequence)
motherSequence
- a sequence buffer
public int getLength()
getLength
in class Feature
public java.lang.String toString()
toString
in class Feature
Object.toString()
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