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java.lang.Objectuk.ac.sanger.cgp.standalonecsa.beans.CdsBean
public class CdsBean
A CdsBean holds information regarding the name, dna sequence, protein sequence and coding orientation of the CDS.
Constructor Summary | |
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CdsBean(java.lang.String name,
java.lang.String seq)
Creates a new instance of CdsBean from it's name and DNA sequence. |
Method Summary | |
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java.lang.String |
getCdsSeq()
Gets the unformatted CDS DNA sequence. |
java.lang.String |
getCdsSeq(int lineSize)
Gets the CDS DNA sequence formatted to the width provided. |
java.lang.String |
getName()
Get the name of this CDS. |
java.lang.String |
getProteinSeq()
Get the unformatted protein sequence of the provided CDS. |
java.lang.String |
getProteinSeq(int lineSize)
Get the protein sequence of the provided CDS formatted to the specified width in characters. |
boolean |
isSenseTranslated()
Indicates that the CDS DNA sequence translated best in the provided orientation. |
void |
setCdsSeq(java.lang.String cdsSeq)
Set the CDS DNA sequence to the provided string. |
void |
setProteinSeq(java.lang.String proteinSeq)
Set the protein sequence to the provided string. |
void |
setSenseTranslated(boolean senseTranslated)
Sets the senseTranslated boolean to the provided value. |
java.lang.String |
toString()
String representation of this object. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public CdsBean(java.lang.String name, java.lang.String seq)
name
- the name of this CDSseq
- the DNA sequence for this CDSMethod Detail |
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public java.lang.String getName()
public java.lang.String getCdsSeq(int lineSize)
lineSize
- number of characters per line
public java.lang.String getCdsSeq()
public boolean isSenseTranslated()
public void setSenseTranslated(boolean senseTranslated)
senseTranslated
- booleanpublic java.lang.String getProteinSeq(int lineSize)
lineSize
- number of characters per line
public java.lang.String getProteinSeq()
public void setProteinSeq(java.lang.String proteinSeq)
proteinSeq
- protein sequence to be setpublic void setCdsSeq(java.lang.String cdsSeq)
cdsSeq
- the CDS DNA sequencepublic java.lang.String toString()
toString
in class java.lang.Object
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