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A
Aligner
- interface org.sStu.
Aligner
.
Implements abstract aligner.
AlignerFactory
- class org.sStu.
AlignerFactory
.
AlignerFactory creates and returns various aligners with the given parameters
AlignerFactory()
- Constructor for class org.sStu.
AlignerFactory
Constructs the AlignerFactory.
Alignment
- interface org.sStu.
Alignment
.
Represents the alignment.
AlignmentRangeAligner
- interface org.sStu.
AlignmentRangeAligner
.
Defines a most comprehensive (but slowest) alingner able to return the range of suboptimal alignments when required.
align()
- Method in interface org.sStu.
Aligner
Compute the alignment now.
C
CharComparator
- class org.sStu.
CharComparator
.
Class for comparing two characters in the sequence.
CharComparator()
- Constructor for class org.sStu.
CharComparator
comparator
- Variable in class org.sStu.
AlignerFactory
Set the class responsible for the character comparison.
compare(char, char)
- Method in class org.sStu.
CharComparator
Return the score of comparison of the two characters.
compare(char[], int, char[], int)
- Method in class org.sStu.
CharComparator
Compares characters at A[i] and B[j].
createAlignmentRangeAligner()
- Method in class org.sStu.
AlignerFactory
Create the most comperhensive version of aligner, able to return range of suboptimal alignments.
createScoreOnlyAligner()
- Method in class org.sStu.
AlignerFactory
Create the fastest version of aligner, able to return the best score only.
createSingleAlingmentAligner()
- Method in class org.sStu.
AlignerFactory
Create the intermediate version of aligner, able to return the single best alignment.
E
End_gap_penalty
- Variable in class org.sStu.
AlignerFactory
Normally the unaligned start and end of the global alignment do not contribute to the score.
G
Gap_weight
- Variable in class org.sStu.
AlignerFactory
The gap weigth (used only in gapped aligners).
Gapped
- Variable in class org.sStu.
AlignerFactory
Request aligner that aligns both sequences over the whole length.
Global
- Variable in class org.sStu.
AlignerFactory
Request the global aligner.
getAlignmentScore()
- Method in interface org.sStu.
Alignment
Return the score of the alignment.
getAlignmentScore()
- Method in interface org.sStu.
ScoreOnlyAligner
Get the score of this alignment
getAlignments()
- Method in interface org.sStu.
AlignmentRangeAligner
Get the alignments.
getBestAlignment()
- Method in interface org.sStu.
SingleAlingmentAligner
Get the best alignment.
getComparator()
- Method in class org.sStu.
AlignerFactory
Return the comparator.
getGap_weight()
- Method in class org.sStu.
AlignerFactory
Return the gap weight.
getMatch_weight()
- Method in class org.sStu.
AlignerFactory
Return the match weight.
getMaxDifferences()
- Method in class org.sStu.
AlignerFactory
Return the maximal expected number of differences.
getMiddleString()
- Method in interface org.sStu.
Alignment
Get the "middle line" of the alignment, explaining the comparison process.
getMismatch_weigth()
- Method in class org.sStu.
AlignerFactory
Return the Mismatch_weigth.
getSequence(int)
- Method in interface org.sStu.
Alignment
Get the given sequence, previously set with setSequence(..).
I
isEnd_gap_penalty()
- Method in class org.sStu.
AlignerFactory
Normally the unaligned start and end of the global alignment do not contribute to the score.
isGapped()
- Method in class org.sStu.
AlignerFactory
Check if the requested aligner supports the gap conception.
isGlobal()
- Method in class org.sStu.
AlignerFactory
Get type of requested alingment (global or local).
isShow_Ends()
- Method in class org.sStu.
AlignerFactory
Normally the unaligned ends of sequences are not included in report.
M
Match_weight
- Variable in class org.sStu.
AlignerFactory
Match weight.
MaxDifferences
- Variable in class org.sStu.
AlignerFactory
Maximal number of differences.
Mismatch_weigth
- Variable in class org.sStu.
AlignerFactory
Weigth of mismatch.
O
org.sStu
- package org.sStu
Sequence studio main package provides classes and interfaces, needed to perform various kinds of sequence alignment.
S
ScoreOnlyAligner
- interface org.sStu.
ScoreOnlyAligner
.
Defines an aligner that returns the score of the best alignment only.
Score_matrix
- Variable in class org.sStu.
AlignerFactory
Set the score matrix.
Show_Ends
- Variable in class org.sStu.
AlignerFactory
Normally the unaligned start and end of the global alignment are not included into report.
SingleAlingmentAligner
- interface org.sStu.
SingleAlingmentAligner
.
Defines an aligner that returns one (best) alignment and its score.
setComparator(CharComparator)
- Method in class org.sStu.
AlignerFactory
Replace the default char comparator, implementig user-defined strategy of the character comparison.
setEnd_gap_penalty(boolean)
- Method in class org.sStu.
AlignerFactory
Normally the unaligned start and end of the global alignment do not contribute to the score.
setGap_weight(int)
- Method in class org.sStu.
AlignerFactory
Set gap weight for the gapped aligner.
setGapped(boolean)
- Method in class org.sStu.
AlignerFactory
Request the gapped aligner, counting gaps and not just spaces.
setGlobal(boolean)
- Method in class org.sStu.
AlignerFactory
Set the type of the requested alignment.
setMatch_weight(int)
- Method in class org.sStu.
AlignerFactory
Set match weight to the new value.
setMaxDifferences(int)
- Method in class org.sStu.
AlignerFactory
Set mismatch weigth to the new value.
setMismatch_weigth(int)
- Method in class org.sStu.
AlignerFactory
Set mismatch weigth to the new value.
setParameters(generalSimilarityBasedAligner)
- Method in class org.sStu.
AlignerFactory
Create the aligner expecting the known limited number of differences between two sequences.
setScore_matrix(char[][])
- Method in class org.sStu.
AlignerFactory
Set score matrix, defining comparison values for any expected pair of characters.
setSequence(CharSequence, int)
- Method in interface org.sStu.
Aligner
Set the sequence with the given number to the given value.
setShow_Ends(boolean)
- Method in class org.sStu.
AlignerFactory
Normally the unaligned start and end of the global alignment are not included into report.
T
toString()
- Method in interface org.sStu.
Alignment
Returns a string representation of the alignment.
U
UNSET
- Static variable in class org.sStu.
AlignerFactory
Special value indicating that the value has not been set.
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