Uses of Class

Packages that use Sequence
jaligner Core classes for the implementation of Smith-Waterman-Gotoh algorithm 
jaligner.formats Group of formats for output alignments. 
jaligner.util Utility classes for helping core and GUI classes. 

Uses of Sequence in jaligner

Methods in jaligner that return Sequence
 Sequence Alignment.getOriginalSequence1()
          Returns original Sequence #1
 Sequence Alignment.getOriginalSequence2()
          Returns original Sequence #2

Methods in jaligner with parameters of type Sequence
static Alignment SmithWatermanGotoh.align(Sequence s1, Sequence s2, Matrix matrix, float o, float e)
          Aligns two sequences by Smith-Waterman (local)
static Alignment NeedlemanWunschGotoh.align(Sequence s1, Sequence s2, Matrix matrix, float o, float e)
          Aligns two sequences by Needleman-Wunsch (global)
static Alignment NeedlemanWunsch.align(Sequence s1, Sequence s2, Matrix matrix, float gap)
          Aligns two sequences by Needleman-Wunsch (global)
 void Alignment.setOriginalSequence1(Sequence originalSequence1)
 void Alignment.setOriginalSequence2(Sequence originalSequence2)

Uses of Sequence in jaligner.formats

Methods in jaligner.formats with parameters of type Sequence
 java.lang.String FASTA.format(Sequence sequence)
          Returns the name, description and sequence combined in one string.

Uses of Sequence in jaligner.util

Methods in jaligner.util that return Sequence
static Sequence SequenceParser.parse(java.lang.String sequence)
          Returns a parsed Sequence from a string.
static Sequence SequenceParser.parse(java.io.File file)
          Returns a Sequence parsed and loaded from a file


Ahmed Moustafa (ahmed@users.sf.net)SourceForge.net
The source code of JAligner is licensed under The GNU General Public License (GPL)