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java.lang.Object | +--seq.engine.Engine
Alignment engine.
| 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()
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| 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 |
public static final char[] VALID_CHARS_AMINO_ACID
public static final char[] VALID_CHARS_DNA_BASE
public static final char[] VALID_CHARS_RNA_BASE
| Constructor Detail |
public Engine()
| Method Detail |
public int getGapCount()
public int getMatchCount()
public java.lang.String getMatchLine()
public int[][] getMatrix()
public int getMismatchCount()
public java.lang.String getResultSequenceA()
public java.lang.String getResultSequenceB()
public int getScore()
public int[][] getTraceResult()
public java.lang.String getValidChars()
public char[] getValidInputSequenceA()
public char[] getValidInputSequenceB()
public boolean isCaseSentitive()
public void process(java.lang.String seqA,
java.lang.String seqB,
int match,
int mismatch,
int gap,
boolean global)
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.public void setCaseSentitive(boolean caseSentitive)
caseSentitive - Case sentitive or not.public void setValidChars(java.lang.String validChars)
validChars - Valid characters.
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