symbol
Class PatternDemo

java.lang.Object
  extended by symbol.PatternDemo

public class PatternDemo
extends Object


Field Summary
static int ONEMILLION
           
static int X_AXIS
           
 
Constructor Summary
PatternDemo(org.biojava.bio.seq.Sequence fileSeq, org.biojava.bio.symbol.SymbolList motif, String sub, String ins, String del)
           
 
Method Summary
 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