pal.datatype
Class Nucleotides
java.lang.Object
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+--pal.datatype.SimpleDataType
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+--pal.datatype.Nucleotides
- All Implemented Interfaces:
- DataType, java.io.Serializable
- public class Nucleotides
- extends SimpleDataType
implements DataType for nucleotides
- See Also:
- Serialized Form
Fields inherited from interface pal.datatype.DataType |
AMINO_ACID_DESCRIPTION, AMINOACIDS, CODON_DESCRIPTION, CODONS, GENERALIZED_CODONS_DESCRIPTION, GENERALIZEDCODONS, IUPAC_NUCELOTIDES_DESCRIPTION, IUPACNUCLEOTIDES, NUCLEOTIDE_DESCRIPTION, NUCLEOTIDES, TWO_STATE_DESCRIPTION, TWOSTATES, UNKNOWN_CHARACTER |
Constructor Summary |
Nucleotides()
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Nucleotides(boolean isRNA)
If isRNA is true than getChar(state) will return a U instead of a T |
Method Summary |
char |
getChar(int state)
Get character corresponding to a given state |
java.lang.String |
getDescription()
description of data type |
int |
getNumStates()
get number of unique states |
int |
getState(char c)
Get state corresponding to character c
NOTE: IF YOU CHANGE THIS IT MAY STOP THE NUCLEOTIDE TRANSLATOR FROM WORKING!
|
int |
getTypeID()
get numerical code describing the data type |
boolean |
isTransistionByChar(char firstChar,
char secondChar)
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boolean |
isTransistionByState(int firstState,
int secondState)
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boolean |
isUnknownState(int state)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
A_STATE
public static final int A_STATE
C_STATE
public static final int C_STATE
G_STATE
public static final int G_STATE
UT_STATE
public static final int UT_STATE
DEFAULT_INSTANCE
public static final Nucleotides DEFAULT_INSTANCE
Nucleotides
public Nucleotides()
Nucleotides
public Nucleotides(boolean isRNA)
- If isRNA is true than getChar(state) will return a U instead of a T
getNumStates
public int getNumStates()
- Description copied from interface:
DataType
- get number of unique states
- Following copied from interface:
pal.datatype.DataType
- Returns:
- number of unique states
isUnknownState
public boolean isUnknownState(int state)
- Overrides:
isUnknownState
in class SimpleDataType
- Returns:
- true if this state is an unknown state
getState
public int getState(char c)
- Get state corresponding to character c
NOTE: IF YOU CHANGE THIS IT MAY STOP THE NUCLEOTIDE TRANSLATOR FROM WORKING!
- It relies on the fact that all the states for 'ACGTU' are between [0, 3]- Following copied from interface:
pal.datatype.DataType
- Parameters:
c
- character- Returns:
- state
getChar
public char getChar(int state)
- Get character corresponding to a given state
- Following copied from interface:
pal.datatype.DataType
- Parameters:
state
- state
return corresponding character
getDescription
public java.lang.String getDescription()
- Description copied from interface:
DataType
- description of data type
- Returns:
- a string describing the data type
getTypeID
public int getTypeID()
- Description copied from interface:
DataType
- get numerical code describing the data type
- Returns:
- the unique numerical code describing the data type
isTransistionByState
public final boolean isTransistionByState(int firstState,
int secondState)
- Returns:
- true if A->G, G->A, C->T, or T->C
if firstState equals secondState returns FALSE!
isTransistionByChar
public final boolean isTransistionByChar(char firstChar,
char secondChar)
- Returns:
- true if A->G, G->A, C->T, or T->C
if firstState equals secondState returns FALSE!
(I've renamed things to avoid confusion between java typing of ints and chars)