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java.lang.Objectpal.datatype.SimpleDataType
public abstract class SimpleDataType
interface for sequence data types
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.datatype.DataType |
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DataType.Utils |
Field Summary |
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Constructor Summary | |
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SimpleDataType()
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Method Summary | |
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AmbiguousDataType |
getAmbiguousVersion()
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char |
getChar(int state)
Handles gap state and then passes on to getStateImpl |
protected abstract char |
getCharImpl(int state)
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char |
getPreferredChar(char c)
Automatically handles Gaps for sub classes |
protected char |
getPreferredCharImpl(char c)
Can be overidden by subclasses. |
int |
getRecommendedGapState()
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int |
getRecommendedUnknownState()
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int |
getState(char c)
Handles gap char and then passes on to getStateImpl |
protected abstract int |
getStateImpl(char c)
For sub classes to implement main functionality of getState. |
boolean |
hasGap()
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boolean |
isAmbiguous()
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boolean |
isGapChar(char c)
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boolean |
isGapState(int state)
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boolean |
isUnknownChar(char c)
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boolean |
isUnknownState(int state)
Checks if state is a gap state (then returns true), otherwise passes on to isUnknownStateImpl |
protected abstract boolean |
isUnknownStateImpl(int state)
For subclasses to handle, without regard for gaps |
java.lang.String |
toString()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface pal.datatype.DataType |
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getDescription, getNumStates, getTypeID |
Constructor Detail |
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public SimpleDataType()
Method Detail |
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public final int getState(char c)
getState
in interface DataType
c
- character
public final char getChar(int state)
getChar
in interface DataType
state
- state
return corresponding characterprotected abstract int getStateImpl(char c)
protected abstract char getCharImpl(int state)
public final char getPreferredChar(char c)
getPreferredChar
in interface DataType
protected char getPreferredCharImpl(char c)
public final boolean isUnknownChar(char c)
isUnknownChar
in interface DataType
public final boolean isUnknownState(int state)
isUnknownState
in interface DataType
protected abstract boolean isUnknownStateImpl(int state)
public java.lang.String toString()
toString
in class java.lang.Object
public int getRecommendedUnknownState()
getRecommendedUnknownState
in interface DataType
public boolean isAmbiguous()
isAmbiguous
in interface DataType
public AmbiguousDataType getAmbiguousVersion()
getAmbiguousVersion
in interface DataType
public final boolean hasGap()
hasGap
in interface DataType
public final boolean isGapChar(char c)
isGapChar
in interface DataType
public final boolean isGapState(int state)
isGapState
in interface DataType
public final int getRecommendedGapState()
getRecommendedGapState
in interface DataType
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