seq.engine
Class Engine

java.lang.Object
  |
  +--seq.engine.Engine

public final class Engine
extends java.lang.Object

Alignment engine.

Version:
1.1.0 (2002.06.23)
Author:
wegra (Bok-Youn, Lee)

Field Summary
static char[] VALID_CHARS_AMINO_ACID
          Default valid characters of amino acid {'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'}
static char[] VALID_CHARS_DNA_BASE
          Default valid characters of DNA base {'A', 'G', 'T', 'C'}.
static char[] VALID_CHARS_RNA_BASE
          Default valid characters of RNA base {'A', 'G', 'U', 'C'}.
 
Constructor Summary
Engine()
           
 
Method Summary
 int getGapCount()
          Return founded gap count during alignment.
 int getMatchCount()
          Return founded matched elements count during alignment.
 java.lang.String getMatchLine()
          Returns match/mismatch info line.
 int[][] getMatrix()
          Returns working matrix.
 int getMismatchCount()
          Return founded mismatched elements count during alignment.
 java.lang.String getResultSequenceA()
          Returns aligned characters of input sequence A.
 java.lang.String getResultSequenceB()
          Returns aligned characters of input sequence B.
 int getScore()
          Return final score.
 int[][] getTraceResult()
          Returns result of best path tracing.
 java.lang.String getValidChars()
          Valid character that recognizable to (Align) Engine.
 char[] getValidInputSequenceA()
          Returns valid input sequence that recognizable to (Align) Engine.
 char[] getValidInputSequenceB()
          Returns valid input sequence that recognizable to (Align) Engine.
 boolean isCaseSentitive()
          Returns case sentitiviness.
 void process(java.lang.String seqA, java.lang.String seqB, int match, int mismatch, int gap, boolean global)
          Aligns two input sequences.
 void setCaseSentitive(boolean caseSentitive)
          Sets case sentitive of not.
 void setValidChars(java.lang.String validChars)
          Sets valid character that recognizable to (Align) Engine.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

VALID_CHARS_AMINO_ACID

public static final char[] VALID_CHARS_AMINO_ACID
Default valid characters of amino acid {'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'}


VALID_CHARS_DNA_BASE

public static final char[] VALID_CHARS_DNA_BASE
Default valid characters of DNA base {'A', 'G', 'T', 'C'}.


VALID_CHARS_RNA_BASE

public static final char[] VALID_CHARS_RNA_BASE
Default valid characters of RNA base {'A', 'G', 'U', 'C'}.

Constructor Detail

Engine

public Engine()
Method Detail

getGapCount

public int getGapCount()
Return founded gap count during alignment.

Returns:
Gap count.

getMatchCount

public int getMatchCount()
Return founded matched elements count during alignment.

Returns:
Matched elements count.

getMatchLine

public java.lang.String getMatchLine()
Returns match/mismatch info line.


getMatrix

public int[][] getMatrix()
Returns working matrix.

Returns:
Working matrix.

getMismatchCount

public int getMismatchCount()
Return founded mismatched elements count during alignment.

Returns:
Mismatched elements count.

getResultSequenceA

public java.lang.String getResultSequenceA()
Returns aligned characters of input sequence A.

Returns:
Aligned characters of input sequence A.

getResultSequenceB

public java.lang.String getResultSequenceB()
Returns aligned characters of input sequence B.

Returns:
Aligned characters of input sequence B.

getScore

public int getScore()
Return final score.

Returns:
Final score.

getTraceResult

public int[][] getTraceResult()
Returns result of best path tracing.

Returns:
Coordinate of trace result.

getValidChars

public java.lang.String getValidChars()
Valid character that recognizable to (Align) Engine.

Returns:
Valid characters.

getValidInputSequenceA

public char[] getValidInputSequenceA()
Returns valid input sequence that recognizable to (Align) Engine.

Returns:
Valid input sequence.

getValidInputSequenceB

public char[] getValidInputSequenceB()
Returns valid input sequence that recognizable to (Align) Engine.

Returns:
Valid input sequence.

isCaseSentitive

public boolean isCaseSentitive()
Returns case sentitiviness.

Returns:
Ture if case sentitive, otherwise false.

process

public void process(java.lang.String seqA,
                    java.lang.String seqB,
                    int match,
                    int mismatch,
                    int gap,
                    boolean global)
Aligns two input sequences.

Parameters:
seqA - Input sequence A.
seqB - Input sequence B.
match - Point added to matched elements.
mismatch - Point added to mismatched elements.
gap - Gap penalty point added to gap.
global - Global alignment or local alignment.

setCaseSentitive

public void setCaseSentitive(boolean caseSentitive)
Sets case sentitive of not.

Parameters:
caseSentitive - Case sentitive or not.

setValidChars

public void setValidChars(java.lang.String validChars)
Sets valid character that recognizable to (Align) Engine.

Parameters:
validChars - Valid characters.