AlignmentPair (biojava-legacy 1.9.5 API)

Nested Class Summary
- Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList
  AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater
- Nested classes/interfaces inherited from interface org.biojava.bio.alignment.Alignment
  Alignment.SymbolListIterator

Field Summary
- Fields inherited from interface org.biojava.bio.alignment.Alignment
  CONTENT
- Fields inherited from interface org.biojava.bio.symbol.SymbolList
  EDIT, EMPTY_LIST

Constructors
Constructor	Description
`AlignmentPair(Sequence query, Sequence subject, int queryStart, int queryEnd, int subjectStart, int subjectEnd, SubstitutionMatrix subMatrix)`
`AlignmentPair(Sequence query, Sequence subject, SubstitutionMatrix subMatrix)`

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static AlignmentPair`	`align(Sequence query, Sequence subject, AlignmentAlgorithm algorithm)`
`String`	`formatOutput()`
`String`	`formatOutput(int width)`	This method provides a BLAST-like formated alignment from the given `String`s, in which the sequence coordinates and the information "Query" or "Sbjct", respectively is added to each line.
`long`	`getComputationTime()`
`int`	`getNumGapsInQuery()`
`int`	`getNumGapsInSubject()`
`int`	`getNumIdenticals()`
`int`	`getNumSimilars()`
`float`	`getPercentGapsQuery()`
`float`	`getPercentGapsTarget()`
`float`	`getPercentIdentityQuery()`
`float`	`getPercentIdentitySubject()`
`float`	`getPercentSimilarityQuery()`
`float`	`getPercentSimilaritySubject()`
`GappedSequence`	`getQuery()`	Return the query sequence as a gapped sequence.
`int`	`getQueryEnd()`
`int`	`getQueryLength()`
`int`	`getQueryStart()`
`GappedSequence`	`getSubject()`	Return the subject sequence as a gapped sequence.
`int`	`getSubjectEnd()`
`int`	`getSubjectLength()`
`int`	`getSubjectStart()`
`SubstitutionMatrix`	`getSubstitutionMatrix()`

Methods inherited from class java.lang.Object
clone, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, iterator, seqString, subList, subStr, toList