symbol

Class PatternDemo

java.lang.Object

symbol.PatternDemo

public class PatternDemo
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	ONEMILLION
static int	X_AXIS

Constructor Summary

Constructors

Constructor and Description
PatternDemo(org.biojava.bio.seq.Sequence fileSeq, org.biojava.bio.symbol.SymbolList motif, String sub, String ins, String del)

Method Summary

Methods

Modifier and Type	Method and Description
void	arrangeSBs()
boolean	backtrack(int x, int y)
void	fillMatrix()
int	getTotalHits()
boolean	initialVector(int x, int y)
static void	main(String[] args)
void	printAlignment()
void	printHit()
void	printMatrix(int s)
void	printPath()
void	printScores()
boolean	probePaths(int x, int y)
void	resetPath(Collection c)
void	resetScores()
void	setFileSeqIndices()
boolean	sidFailure()
void	startBacktrack()
void	startSearch()
void	updateScores()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ONEMILLION

public static final int ONEMILLION

See Also:

Constant Field Values

X_AXIS

public static final int X_AXIS

See Also:

Constant Field Values

Constructor Detail

PatternDemo

public PatternDemo(org.biojava.bio.seq.Sequence fileSeq,
           org.biojava.bio.symbol.SymbolList motif,
           String sub,
           String ins,
           String del)
            throws Exception

Throws:

Exception

Method Detail

fillMatrix

public void fillMatrix()
                throws org.biojava.bio.BioException

Throws:

org.biojava.bio.BioException

printMatrix

public void printMatrix(int s)

backtrack

public boolean backtrack(int x,
                int y)

resetPath

public void resetPath(Collection c)

sidFailure

public boolean sidFailure()

initialVector

public boolean initialVector(int x,
                    int y)

probePaths

public boolean probePaths(int x,
                 int y)

resetScores

public void resetScores()

printScores

public void printScores()

getTotalHits

public int getTotalHits()

startBacktrack

public void startBacktrack()

startSearch

public void startSearch()
                 throws Exception

Throws:

Exception

setFileSeqIndices

public void setFileSeqIndices()

printAlignment

public void printAlignment()

arrangeSBs

public void arrangeSBs()

printPath

public void printPath()

printHit

public void printHit()

updateScores

public void updateScores()

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception