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java.lang.Objectbelka.align.SeqAligner
public class SeqAligner
Objects of this class perform sequence alignemnts by Needleman-Wunsch and Smith-Waterman algorithms.
Constructor Summary | |
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SeqAligner()
Contructor of SeqAligner object with default values: scoring matrix: BLOSUM62 gap open penalty: -10 gap extend penalty: -1 |
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SeqAligner(String matrix,
int gap_open,
int gap_extend)
Contructor of SeqAligner object with specified scoring matrix, gap open penalty, and gap extend penalty. |
Method Summary | |
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int |
align_nw(Chain chain1,
Chain chain2)
Alignes two sets of assemblies (residues/nucleotides) with default parameters using Needleman-Wunsch method. |
int |
align_sw(Chain chain1,
Chain chain2)
Alignes two sets of assemblies (residues/nucleotides) with default parameters using Smith-Waterman method. |
void |
applyToChains()
The function introduces gaps in chains to reflect the calculated alignment. |
int |
getAliLength()
Returns lengths of alignment; |
String |
getAliSequence1()
Returns aligned part of first sequence. |
String |
getAliSequence2()
Returns aligned part of second sequence. |
int |
getGapExtend()
Returns current value of gap extension penatly. |
int |
getGapOpen()
Returns current value of gap open penatly. |
int |
getLength1()
Returns lengths of first aligned sequence. |
int |
getLength2()
Returns lengths of second aligned sequence. |
int |
getNumGaps()
Returns number of gaps in alignment. |
int |
getNumIdentical()
Returns number of identical residues in alignment. |
int |
getNumPositive()
Returns number of aligned residues with positive score. |
int |
getScore()
Returns score of the alignment. |
String |
getScoringMatrix()
Returns current scoring matrix. |
boolean |
hasAlignment()
Returns true if the object has alignment, false otherwise. |
boolean |
setGapExtend(int gap_extend)
Sets new value for gap extention penatly. |
boolean |
setGapOpen(int gap_open)
Sets new value for gap open penatly. |
boolean |
setScoringMatrix(String matrix)
Sets new scoring matrix. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SeqAligner()
public SeqAligner(String matrix, int gap_open, int gap_extend)
matrix
- name of scoring matrix.gap_open
- gap open penalty.gap_extend
- gap extend penalty.Method Detail |
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public boolean hasAlignment()
public int getLength1()
public int getLength2()
public String getAliSequence1()
public String getAliSequence2()
public int getAliLength()
public int getNumIdentical()
public int getNumPositive()
public int getNumGaps()
public int getScore()
public void applyToChains()
public boolean setScoringMatrix(String matrix)
matrix
- name of scoring matrix.
public String getScoringMatrix()
public boolean setGapOpen(int gap_open)
gap_open
- gap open penalty.
public int getGapOpen()
public boolean setGapExtend(int gap_extend)
gap_extend
- gap extend penalty.
public int getGapExtend()
public int align_sw(Chain chain1, Chain chain2)
chain1
- first chain to be aligned.chain2
- second chain to be aligned.
public int align_nw(Chain chain1, Chain chain2)
chain1
- first chain to be aligned.chain2
- second chain to be aligned.
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