Package pal.datatype
Class SimpleDataType
- java.lang.Object
-
- pal.datatype.SimpleDataType
-
- All Implemented Interfaces:
java.io.Serializable
,DataType
- Direct Known Subclasses:
AminoAcids
,Codons
,GapBalanced
,IUPACNucleotides
,Nucleotides
,NumericDataType
,StateRemover
,TwoStates
public abstract class SimpleDataType extends java.lang.Object implements DataType
interface for sequence data types- Version:
- $Id: SimpleDataType.java,v 1.14 2003/11/30 05:29:22 matt Exp $
- Author:
- Alexei Drummond
- See Also:
- Serialized Form
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from interface pal.datatype.DataType
DataType.Utils
-
-
Field Summary
-
Fields inherited from interface pal.datatype.DataType
AMINO_ACID_DESCRIPTION, AMINOACIDS, CODON_DESCRIPTION, CODONS, GAP_BALANCED, GAP_BALANCED_DESCRIPTION, IUPAC_NUCELOTIDES_DESCRIPTION, IUPACNUCLEOTIDES, NUCLEOTIDE_DESCRIPTION, NUCLEOTIDES, NUMERIC, PRIMARY_SUGGESTED_GAP_CHARACTER, SUGGESTED_GAP_CHARACTERS, SUGGESTED_GAP_STATE, SUGGESTED_UNKNOWN_STATE, TWO_STATE_DESCRIPTION, TWOSTATES, UNKNOWN, UNKNOWN_CHARACTER, UNKNOWN_TLA
-
-
Constructor Summary
Constructors Constructor Description SimpleDataType()
-
Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description AmbiguousDataType
getAmbiguousVersion()
char
getChar(int state)
Handles gap state and then passes on to getStateImplprotected abstract char
getCharImpl(int state)
char
getPreferredChar(char c)
Automatically handles Gaps for sub classesprotected char
getPreferredCharImpl(char c)
Can be overidden by subclasses.int
getRecommendedGapState()
int
getRecommendedUnknownState()
int
getState(char c)
Handles gap char and then passes on to getStateImplprotected abstract int
getStateImpl(char c)
For sub classes to implement main functionality of getState.boolean
hasGap()
boolean
isAmbiguous()
boolean
isGapChar(char c)
boolean
isGapState(int state)
boolean
isUnknownChar(char c)
boolean
isUnknownState(int state)
Checks if state is a gap state (then returns true), otherwise passes on to isUnknownStateImplprotected abstract boolean
isUnknownStateImpl(int state)
For subclasses to handle, without regard for gapsjava.lang.String
toString()
-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
-
Methods inherited from interface pal.datatype.DataType
getDescription, getNumStates, getTypeID
-
-
-
-
Method Detail
-
getState
public final int getState(char c)
Handles gap char and then passes on to getStateImpl
-
getChar
public final char getChar(int state)
Handles gap state and then passes on to getStateImpl
-
getStateImpl
protected abstract int getStateImpl(char c)
For sub classes to implement main functionality of getState. Gaps do not need to be considered
-
getCharImpl
protected abstract char getCharImpl(int state)
-
getPreferredChar
public final char getPreferredChar(char c)
Automatically handles Gaps for sub classes- Specified by:
getPreferredChar
in interfaceDataType
-
getPreferredCharImpl
protected char getPreferredCharImpl(char c)
Can be overidden by subclasses. Default implementation get's character's state and that get's the character for that state
-
isUnknownChar
public final boolean isUnknownChar(char c)
- Specified by:
isUnknownChar
in interfaceDataType
- Returns:
- true if this state is unknown (or a gap)
-
isUnknownState
public final boolean isUnknownState(int state)
Checks if state is a gap state (then returns true), otherwise passes on to isUnknownStateImpl- Specified by:
isUnknownState
in interfaceDataType
- Returns:
- true if this state is an unknown state (the same as check if a state is >= the number of states... but neater)
-
isUnknownStateImpl
protected abstract boolean isUnknownStateImpl(int state)
For subclasses to handle, without regard for gaps
-
toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
-
getRecommendedUnknownState
public int getRecommendedUnknownState()
- Specified by:
getRecommendedUnknownState
in interfaceDataType
- Returns:
- -1 (not getNumStates())
-
isAmbiguous
public boolean isAmbiguous()
- Specified by:
isAmbiguous
in interfaceDataType
- Returns:
- false
-
getAmbiguousVersion
public AmbiguousDataType getAmbiguousVersion()
- Specified by:
getAmbiguousVersion
in interfaceDataType
- Returns:
- null
-
isGapChar
public final boolean isGapChar(char c)
-
isGapState
public final boolean isGapState(int state)
- Specified by:
isGapState
in interfaceDataType
- Returns:
- true if state is gap state (-2), false other wise
-
getRecommendedGapState
public final int getRecommendedGapState()
- Specified by:
getRecommendedGapState
in interfaceDataType
- Returns:
- GAP_STATE (-2)
-
-