Class HMM
java.lang.Object
HMM
class HMM
- extends java.lang.Object
Constructor Summary |
HMM(java.lang.String name)
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Method Summary |
void |
addDistributionGroup(java.util.LinkedList group)
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void |
addPriorfile(int nr,
java.lang.String s)
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void |
addPriorfile(java.lang.String s)
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void |
addTransPriorfile(java.lang.String s)
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void |
addTransTieGroup(java.util.LinkedList group)
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int |
createModule(java.lang.String name,
int moduleType,
int distribType,
int intervalStart,
int intervalEnd,
java.lang.String label)
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int |
createModule(java.lang.String name,
int moduleType,
int distribType,
int size,
java.lang.String label,
boolean global)
CREATE and ADD methods |
java.lang.String |
getAlphabet()
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java.lang.String |
getAlphabet2()
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java.lang.String |
getAlphabet3()
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java.lang.String |
getAlphabet4()
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int |
getAlphabetSize()
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int |
getAlphabetSize2()
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int |
getAlphabetSize3()
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int |
getAlphabetSize4()
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java.util.ListIterator |
getDistributionGroups()
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java.lang.String |
getFileName()
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Module |
getModule(java.lang.String name)
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java.util.Enumeration |
getModuleKeys()
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java.util.ListIterator |
getModules()
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java.lang.String |
getName()
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int |
getNrModules()
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int |
getNrOfAlphabets()
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int |
getNrOfDistributionGroups()
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int |
getNrOfDistributionGroupVertices()
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int |
getNrOfPriorfiles()
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int |
getNrOfPriorfiles(int nr)
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int |
getNrOfTransitions()
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int |
getNrOfTransPriorfiles()
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int |
getNrOfTransTieGroups()
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int |
getNrOfTransTieGroupVertices()
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int |
getNrVertices()
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static int |
GETNUMBER()
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java.util.Iterator |
getPriorfiles()
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java.util.Iterator |
getPriorfiles(int nr)
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java.util.Iterator |
getTransPriorfiles()
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java.util.ListIterator |
getTransTieGroups()
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Vertex |
getVertex(int nr)
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boolean |
identicalModules(java.lang.String moduleA,
java.lang.String moduleB)
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void |
initializeTransitionProbabilities(java.lang.String name)
MISC methods |
static void |
resetStatics()
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void |
setAlphabet(int alphabet)
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void |
setAlphabet(int nr,
int alphabet)
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void |
setAlphabet(int nr,
java.lang.String[] alphabet)
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void |
setAlphabet(java.lang.String[] alphabet)
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void |
setFileName(java.lang.String filename)
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void |
setInternalInitDistrib(java.lang.String name,
InternalInitDistrib iid)
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void |
setNrOfAlphabets(int nr)
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void |
setTransition(java.lang.String fromModule,
java.lang.String toModule)
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boolean |
transitionExists(int fromNr,
int toNr)
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boolean |
writeModule(java.lang.String moduleName,
java.io.BufferedWriter writer)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AMINO
public static final int AMINO
- See Also:
- Constant Field Values
DNA
public static final int DNA
- See Also:
- Constant Field Values
AMINO_GAP
public static final int AMINO_GAP
- See Also:
- Constant Field Values
AMINO_DOUBLE_GAP
public static final int AMINO_DOUBLE_GAP
- See Also:
- Constant Field Values
OWN
public static final int OWN
- See Also:
- Constant Field Values
A
public static final java.lang.String[] A
D
public static final java.lang.String[] D
A_gap
public static final java.lang.String[] A_gap
A_double_gap
public static final java.lang.String[] A_double_gap
NOTYPE
public static final int NOTYPE
- See Also:
- Constant Field Values
SINGLENODE
public static final int SINGLENODE
- See Also:
- Constant Field Values
CLUSTER
public static final int CLUSTER
- See Also:
- Constant Field Values
HIGHWAY
public static final int HIGHWAY
- See Also:
- Constant Field Values
PROFILE7
public static final int PROFILE7
- See Also:
- Constant Field Values
PROFILE9
public static final int PROFILE9
- See Also:
- Constant Field Values
SINGLELOOP
public static final int SINGLELOOP
- See Also:
- Constant Field Values
FORWARD_STD
public static final int FORWARD_STD
- See Also:
- Constant Field Values
FORWARD_ALT
public static final int FORWARD_ALT
- See Also:
- Constant Field Values
U_TURN
public static final int U_TURN
- See Also:
- Constant Field Values
STARTNODE
public static final int STARTNODE
- See Also:
- Constant Field Values
ENDNODE
public static final int ENDNODE
- See Also:
- Constant Field Values
EVEN
public static final int EVEN
- See Also:
- Constant Field Values
ZERO
public static final int ZERO
- See Also:
- Constant Field Values
RANDOM
public static final int RANDOM
- See Also:
- Constant Field Values
MANUAL
public static final int MANUAL
- See Also:
- Constant Field Values
LOCKED_EVEN
public static final int LOCKED_EVEN
- See Also:
- Constant Field Values
LOCKED_MANUAL
public static final int LOCKED_MANUAL
- See Also:
- Constant Field Values
STANDARD
public static final int STANDARD
- See Also:
- Constant Field Values
SILENT
public static final int SILENT
- See Also:
- Constant Field Values
LOCKED
public static final int LOCKED
- See Also:
- Constant Field Values
INSERT
public static final int INSERT
- See Also:
- Constant Field Values
DELETE
public static final int DELETE
- See Also:
- Constant Field Values
START
public static final int START
- See Also:
- Constant Field Values
END
public static final int END
- See Also:
- Constant Field Values
alphabet
public static java.lang.String[] alphabet
alphabet_2
public static java.lang.String[] alphabet_2
alphabet_3
public static java.lang.String[] alphabet_3
alphabet_4
public static java.lang.String[] alphabet_4
nrOfDistributionGroups
int nrOfDistributionGroups
nrOfDistributionGroupVertices
int nrOfDistributionGroupVertices
nrOfTransTieGroups
int nrOfTransTieGroups
nrOfTransTieGroupVertices
int nrOfTransTieGroupVertices
nrOfAlphabets
int nrOfAlphabets
HMM
public HMM(java.lang.String name)
GETNUMBER
public static int GETNUMBER()
resetStatics
public static void resetStatics()
transitionExists
public boolean transitionExists(int fromNr,
int toNr)
getNrModules
public int getNrModules()
getNrOfDistributionGroups
public int getNrOfDistributionGroups()
getNrOfDistributionGroupVertices
public int getNrOfDistributionGroupVertices()
getNrOfTransTieGroups
public int getNrOfTransTieGroups()
getNrOfTransTieGroupVertices
public int getNrOfTransTieGroupVertices()
getNrVertices
public int getNrVertices()
getNrOfTransitions
public int getNrOfTransitions()
getName
public java.lang.String getName()
getFileName
public java.lang.String getFileName()
getNrOfAlphabets
public int getNrOfAlphabets()
getAlphabet
public java.lang.String getAlphabet()
getAlphabetSize
public int getAlphabetSize()
getAlphabet2
public java.lang.String getAlphabet2()
getAlphabetSize2
public int getAlphabetSize2()
getAlphabet3
public java.lang.String getAlphabet3()
getAlphabetSize3
public int getAlphabetSize3()
getAlphabet4
public java.lang.String getAlphabet4()
getAlphabetSize4
public int getAlphabetSize4()
getModuleKeys
public java.util.Enumeration getModuleKeys()
getModule
public Module getModule(java.lang.String name)
getVertex
public Vertex getVertex(int nr)
getModules
public java.util.ListIterator getModules()
getDistributionGroups
public java.util.ListIterator getDistributionGroups()
getTransTieGroups
public java.util.ListIterator getTransTieGroups()
getNrOfPriorfiles
public int getNrOfPriorfiles()
getNrOfPriorfiles
public int getNrOfPriorfiles(int nr)
getNrOfTransPriorfiles
public int getNrOfTransPriorfiles()
getPriorfiles
public java.util.Iterator getPriorfiles()
getPriorfiles
public java.util.Iterator getPriorfiles(int nr)
getTransPriorfiles
public java.util.Iterator getTransPriorfiles()
setFileName
public void setFileName(java.lang.String filename)
setNrOfAlphabets
public void setNrOfAlphabets(int nr)
setAlphabet
public void setAlphabet(int alphabet)
setAlphabet
public void setAlphabet(int nr,
int alphabet)
setAlphabet
public void setAlphabet(java.lang.String[] alphabet)
setAlphabet
public void setAlphabet(int nr,
java.lang.String[] alphabet)
setTransition
public void setTransition(java.lang.String fromModule,
java.lang.String toModule)
setInternalInitDistrib
public void setInternalInitDistrib(java.lang.String name,
InternalInitDistrib iid)
createModule
public int createModule(java.lang.String name,
int moduleType,
int distribType,
int size,
java.lang.String label,
boolean global)
- CREATE and ADD methods
createModule
public int createModule(java.lang.String name,
int moduleType,
int distribType,
int intervalStart,
int intervalEnd,
java.lang.String label)
addDistributionGroup
public void addDistributionGroup(java.util.LinkedList group)
addPriorfile
public void addPriorfile(java.lang.String s)
addPriorfile
public void addPriorfile(int nr,
java.lang.String s)
addTransPriorfile
public void addTransPriorfile(java.lang.String s)
addTransTieGroup
public void addTransTieGroup(java.util.LinkedList group)
initializeTransitionProbabilities
public void initializeTransitionProbabilities(java.lang.String name)
- MISC methods
writeModule
public boolean writeModule(java.lang.String moduleName,
java.io.BufferedWriter writer)
identicalModules
public boolean identicalModules(java.lang.String moduleA,
java.lang.String moduleB)