Serialized Form

Package org.biojava.bio.alignment

Class org.biojava.bio.alignment.AlignmentPair

class AlignmentPair extends SimpleAlignment implements Serializable

serialVersionUID:

-8834131912021612261L

Serialized Fields

identicals

int identicals

Number of identical elements in both sequences

nGapsQ

int nGapsQ

Number of gaps in query

nGapsS

int nGapsS

Number of gaps in subject

query

Sequence query

Length of the query sequence

queryEnd

int queryEnd

End position in the query

queryStart

int queryStart

Start position in the query

similars

int similars

Number of similar symbols

subject

Sequence subject

The subject sequence.

subjectEnd

int subjectEnd

End position in the subject

subjectStart

int subjectStart

Start position in the subject

subMatrix

SubstitutionMatrix subMatrix

Reference to the underlying substitution matrix of this alignment.

time

long time

Time consumption to create this alignment.

Exception Class org.biojava.bio.alignment.IllegalAlignmentEditException

class IllegalAlignmentEditException extends BioRuntimeException implements Serializable

serialVersionUID:

4662428071284597336L

Class org.biojava.bio.alignment.SimpleAlignment

class SimpleAlignment extends AbstractSymbolList implements Serializable

serialVersionUID:

-1760075176220928440L

Serialized Fields

alphabet

Alphabet alphabet

labels

List<String> labels

labelToSymbolList

LinkedHashMap<String,SymbolList> labelToSymbolList

length

int length

score

int score

Class org.biojava.bio.alignment.SubstitutionMatrix

class SubstitutionMatrix extends Object implements Serializable

Serialized Fields

alphabet

FiniteAlphabet alphabet

The alphabet used by this matrix.

colSymbols

Map<Symbol,Integer> colSymbols

description

String description

Name and description of this matrix.

matrix

short[][] matrix

max

short max

Minimal and maximal entry in this matrix

min

short min

Minimal and maximal entry in this matrix

name

String name

Name and description of this matrix.

rowSymbols

Map<Symbol,Integer> rowSymbols