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java.lang.Object | +--neobio.alignment.PairwiseAlignment
This class is the product of a pairwise alignment, generated by one subclasses of
 PairwiseAlignmentAlgorithm. It contains the two sequences strings with
 gaps, a score tag line, and a score value. It is typically displayed in three rows as
 in the following example of an alignment between parts of two protein sequences:
 
 MDEIHQLEDMFTVDSETLRKVVKHFILPHD-----MRTTKHQEELWSFIAELDSLKDFMVEQE    // sequence 1
 M +I   E +FTV +ETL+ V KHFILP D     MRTT++ +ELW FIA  DSLK F+ EQ     // score tag line
 MQQIENFEKIFTVPTETLQAVTKHFILP-DATETLMRTTQNPDELWEFIA--DSLKAFIDEQF    // sequence 2
 
Each column has one character of each sequence and a score tag. The same character is displayed in all three rows when a column has an exact match (character of sequences 1 and 2 are equal). When a mismatch occurs (substitution of different characters), the score tag is left blank. A '+' in the score line signals a partial match (a substitution of similar characters). The difference between a partial match and a mismatch is that the score of a partial match is positive whereas the score of a mismatch is zero or negative (each case is determined by the scoring scheme).
Gaps are usually represented by dashes ('-') and have a blank score tag. Insertions have dashes in sequence 1 and the inserted character in sequence 2. Deletions, by contrast, have the deleted character in sequence 1 and dashes in sequence 2.
Each column carries a score value for the corresponding operation (as defined by the scoring scheme). The overall score of a pairwise alignment is the sum of all columns scores values.
When the scoring schemes does not support partial matches, a match is usually signaled by a '|' character.
Note that these special characters are defined by the
 PairwiseAlignmentAlgorithm class. Consult that class specification for the
 actual configuration. For instance, an alignment between two DNA fragmens may look like
 this:
 A--C--TAAAAAGCA--TT-AATAATAAA-A
 |  |  ||||  |||  || ||||| ||| |
 AAGCCCTAAACCGCAAGTTTAATAA-AAATA
 
This class is serializable, so it can be saved to a file (or any other output). It
 overrides the default equals method of the Object class to
 allow a proper comparsion of alignments produced by different algorithms or even
 different runs of the same algorithm. However, it does not override the
 hashCode method as it is generally the case to maintain the contract for
 the hashCode method (which states that equal objects must have equal hash
 codes). Hence, as it is, its use in a hash table is not supported.
PairwiseAlignmentAlgorithm, 
PairwiseAlignmentAlgorithm.MATCH_TAG, 
PairwiseAlignmentAlgorithm.APPROXIMATE_MATCH_TAG, 
PairwiseAlignmentAlgorithm.MISMATCH_TAG, 
PairwiseAlignmentAlgorithm.GAP_TAG, 
PairwiseAlignmentAlgorithm.GAP_CHARACTER, 
ScoringScheme, 
ScoringScheme.isPartialMatchSupported(), 
Serialized Form| Field Summary | |
| protected  java.lang.String | gapped_seq1First gapped sequence. | 
| protected  java.lang.String | gapped_seq2Second gapped sequence. | 
| protected  int | scoreThe overall score value for this alignment. | 
| protected  java.lang.String | score_tag_lineThe score tag line. | 
| Constructor Summary | |
| PairwiseAlignment(java.lang.String gapped_seq1,
                                   java.lang.String score_tag_line,
                                   java.lang.String gapped_seq2,
                                   int score)Creates a PairwiseAlignmentinstance with the specified gapped
 sequences, score tag line and score value. | |
| Method Summary | |
|  boolean | equals(java.lang.Object obj)Compares this object to the specified object. | 
|  java.lang.String | getGappedSequence1()Returns the first gapped sequence. | 
|  java.lang.String | getGappedSequence2()Returns the second gapped sequence. | 
|  int | getScore()Returns the score for this alignment. | 
|  java.lang.String | getScoreTagLine()Returns the score tag line. | 
|  java.lang.String | toString()Returns a four-line String representation of this alignment in the following order: first gapped sequence, score tag line, second gapped sequence and the score value. | 
| Methods inherited from class java.lang.Object | 
| clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait | 
| Field Detail | 
protected java.lang.String gapped_seq1
protected java.lang.String score_tag_line
protected java.lang.String gapped_seq2
protected int score
| Constructor Detail | 
public PairwiseAlignment(java.lang.String gapped_seq1,
                         java.lang.String score_tag_line,
                         java.lang.String gapped_seq2,
                         int score)
PairwiseAlignment instance with the specified gapped
 sequences, score tag line and score value.
gapped_seq1 - the first gapped sequencescore_tag_line - the score tag linegapped_seq2 - the second gapped sequencescore - the overall score value for this alignment| Method Detail | 
public java.lang.String getGappedSequence1()
public java.lang.String getScoreTagLine()
public java.lang.String getGappedSequence2()
public int getScore()
public java.lang.String toString()
toString in class java.lang.Objectpublic boolean equals(java.lang.Object obj)
true if
 and only if the argument is not null and is an
 PairwiseAlignment object that contains the same values as this object,
 i.e. the same gapped sequences, the same score tag line and the same score.
equals in class java.lang.Objectobj - the object to compare with
true if objects are the same, false otherwise| 
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