public class BasePair
extends java.lang.Object
Constructor and Description |
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BasePair(int pos)
To create a BasePair, we need to give the position in the sequence where starts the String TopAcid or BottomAcid.
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Modifier and Type | Method and Description |
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java.lang.String |
getBottomAcid()
This method is called to get the nucleic acid "BottomAcid" of BasePair..
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static java.util.ArrayList<java.lang.String> |
getExistingNucleicAcids()
This method is called to get the existingNucleicAcids of BasePair.
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int |
getLengthAcid()
This method is called to get the length of the nucleic acid.
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int |
getPosition()
This method is called to get the position of BasePair in the duplex.
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java.lang.String |
getTopAcid()
This method is called to get the nucleic acid "TopAcid" of BasePair.
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static void |
initialiseNucleicAcidList()
initialises the existingNucleicAcids of BasePair.
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boolean |
isBasePairEqualTo(java.lang.String base1,
java.lang.String base2)
Check if the two nucleic acids of the base pair are (base1, base2) or (base2, base1).
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boolean |
isBasePairStrictlyEqualTo(java.lang.String base1,
java.lang.String base2)
Check if the two nucleic acids of the base pair are (base1, base2).
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boolean |
isBottomBasePyrimidine()
Check if the nucleic acid represented by BottomAcid is a pyrimidine.
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boolean |
isComplementaryBasePair()
To check if the two nucleic acids in the base pair are complementary.
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boolean |
isComplementaryLockedPair()
To check if the two nucleic acids in the base pair are complementary when one of them is a locked nucleic acid.
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boolean |
isFrequentNucleicAcidTopBase()
Check if the Nucleic acid TopAcid is a frequent nucleic acid.
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boolean |
isTopBasePyrimidine()
Check if the nucleic acid represented by TopAcid is a pyrimidine.
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boolean |
isUnpaired()
To check if the nucleic acids in the base pair are paired.
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boolean |
isWatsonCrickBottomBase()
Check if the Nucleic acid BottomAcid is a frequent nucleic acid.
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void |
setBottomAcid(java.lang.String bottomAcid)
To change the BottomAcid Value of BasePair.
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void |
setTopAcid(java.lang.String topAcid)
To change the TopAcid Value of BasePair..
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public BasePair(int pos)
pos
- : the position of the base pair in the sequence. It is the starting position of the String
TopAcid or BottomAcid in the String sequence.public java.lang.String getTopAcid()
public void setTopAcid(java.lang.String topAcid)
public java.lang.String getBottomAcid()
public void setBottomAcid(java.lang.String bottomAcid)
public boolean isComplementaryBasePair()
public boolean isComplementaryLockedPair()
public boolean isFrequentNucleicAcidTopBase()
public boolean isWatsonCrickBottomBase()
public boolean isTopBasePyrimidine()
public boolean isBottomBasePyrimidine()
public boolean isBasePairEqualTo(java.lang.String base1, java.lang.String base2)
base1
- : first base (the nucleic acid is represented by a String)base2
- : second base (the nucleic acid is represented by a String)public boolean isBasePairStrictlyEqualTo(java.lang.String base1, java.lang.String base2)
base1
- : first base (the nucleic acid is represented by a String)base2
- : second base (the nucleic acid is represented by a String)public int getLengthAcid()
public boolean isUnpaired()
public static void initialiseNucleicAcidList()
public static java.util.ArrayList<java.lang.String> getExistingNucleicAcids()
public int getPosition()