A C E G I M O S T U

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.

A C E G I M O S T U