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java.lang.Objectorg.sStu.AlignerFactory
AlignerFactory creates and returns various aligners with the given parameters.>
http://www.gnu.org/licenses/gpl.txt
Field Summary | |
protected CharComparator |
comparator
Set the class responsible for the character comparison. |
protected boolean |
End_gap_penalty
Normally the unaligned start and end of the global alignment do not contribute to the score. |
protected int |
Gap_weight
The gap weigth (used only in gapped aligners). |
protected boolean |
Gapped
Request aligner that aligns both sequences over the whole length. |
protected boolean |
Global
Request the global aligner. |
protected int |
Match_weight
Match weight. |
protected int |
MaxDifferences
Maximal number of differences. |
protected int |
Mismatch_weigth
Weigth of mismatch. |
protected int[][] |
Score_matrix
Set the score matrix. |
protected boolean |
Show_Ends
Normally the unaligned start and end of the global alignment are not included into report. |
static int |
UNSET
Special value indicating that the value has not been set. |
Constructor Summary | |
AlignerFactory()
Constructs the AlignerFactory. |
Method Summary | |
AlignmentRangeAligner |
createAlignmentRangeAligner()
Create the most comperhensive version of aligner, able to return range of suboptimal alignments. |
ScoreOnlyAligner |
createScoreOnlyAligner()
Create the fastest version of aligner, able to return the best score only. |
SingleAlingmentAligner |
createSingleAlingmentAligner()
Create the intermediate version of aligner, able to return the single best alignment. |
CharComparator |
getComparator()
Return the comparator. |
int |
getGap_weight()
Return the gap weight. |
int |
getMatch_weight()
Return the match weight. |
int |
getMaxDifferences()
Return the maximal expected number of differences. |
int |
getMismatch_weigth()
Return the Mismatch_weigth. |
boolean |
isEnd_gap_penalty()
Normally the unaligned start and end of the global alignment do not contribute to the score. |
boolean |
isGapped()
Check if the requested aligner supports the gap conception. |
boolean |
isGlobal()
Get type of requested alingment (global or local). |
boolean |
isShow_Ends()
Normally the unaligned ends of sequences are not included in report. |
void |
setComparator(CharComparator comparator)
Replace the default char comparator, implementig user-defined strategy of the character comparison. |
void |
setEnd_gap_penalty(boolean penalty)
Normally the unaligned start and end of the global alignment do not contribute to the score. |
void |
setGap_weight(int Gap_weight)
Set gap weight for the gapped aligner. |
void |
setGapped(boolean MindGaps)
Request the gapped aligner, counting gaps and not just spaces. |
void |
setGlobal(boolean Global)
Set the type of the requested alignment. |
void |
setMatch_weight(int Match_weight)
Set match weight to the new value. |
void |
setMaxDifferences(int MaxDifferences)
Set mismatch weigth to the new value. |
void |
setMismatch_weigth(int Mismatch_weigth)
Set mismatch weigth to the new value. |
protected void |
setParameters(org.sStu.Neringute.Similarity.generalSimilarityBasedAligner a)
Create the aligner expecting the known limited number of differences between two sequences. |
void |
setScore_matrix(char[][] matrix)
Set score matrix, defining comparison values for any expected pair of characters. |
void |
setShow_Ends(boolean show)
Normally the unaligned start and end of the global alignment are not included into report. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
protected boolean Global
protected boolean Gapped
protected int Gap_weight
protected int Mismatch_weigth
protected int[][] Score_matrix
protected int Match_weight
protected CharComparator comparator
protected boolean Show_Ends
protected boolean End_gap_penalty
protected int MaxDifferences
public static int UNSET
Constructor Detail |
public AlignerFactory()
Method Detail |
public boolean isGlobal()
public void setGlobal(boolean Global)
Global
- the type of the requested alignment (true for global, false for local.public boolean isGapped()
setGap_weight
public void setGapped(boolean MindGaps)
MindGaps
- true for gapper aligner, false (default) for the simple aligner.public boolean isShow_Ends()
setEnd_gap_penalty
public void setShow_Ends(boolean show)
show
- true if ends must be includedpublic boolean isEnd_gap_penalty()
public void setEnd_gap_penalty(boolean penalty)
penalty
- true if the unaligned start and end of the global alignment contribute to the score.public int getGap_weight()
public void setGap_weight(int Gap_weight)
Gap_weight
- gap weightpublic int getMismatch_weigth()
public void setMismatch_weigth(int Mismatch_weigth)
Mismatch_weigth
- Mismatch weigthpublic int getMaxDifferences()
public void setMaxDifferences(int MaxDifferences)
MaxDifferences
- Maximal expected number of differences in alignment. This is not supported in
the current version.public void setScore_matrix(char[][] matrix)
matrix
- Two dimensional of weights, default match and mismatch values.;public int getMatch_weight()
public void setMatch_weight(int Match_weight)
Match_weight
- Match weigthpublic CharComparator getComparator()
public void setComparator(CharComparator comparator)
comparator
- New comparator that must implement CharComparator interface.public ScoreOnlyAligner createScoreOnlyAligner()
public SingleAlingmentAligner createSingleAlingmentAligner()
public AlignmentRangeAligner createAlignmentRangeAligner()
protected void setParameters(org.sStu.Neringute.Similarity.generalSimilarityBasedAligner a)
a
- Implementation specific aligner class for that the parameters must be set.
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