symbol
Class PatternDemo
java.lang.Object
symbol.PatternDemo
public class PatternDemo
- extends Object
Constructor Summary |
PatternDemo(org.biojava.bio.seq.Sequence fileSeq,
org.biojava.bio.symbol.SymbolList motif,
String sub,
String ins,
String del)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ONEMILLION
public static final int ONEMILLION
- See Also:
- Constant Field Values
X_AXIS
public static final int X_AXIS
- See Also:
- Constant Field Values
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
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