compbio.data.sequence
Class Alignment
java.lang.Object
compbio.data.sequence.Alignment
@Immutable
public final class Alignment
- extends java.lang.Object
Multiple sequence alignment.
Does not give any guarantees on the content of individual FastaSequece
records. That is it does not guarantee that the neither the names of
sequences or the sequences themselves are unique.
- Author:
- pvtroshin
Date September 2009
- See Also:
FastaSequence
,
AlignmentMetadata
Methods inherited from class java.lang.Object |
getClass, hashCode, notify, notifyAll, wait, wait, wait |
Alignment
public Alignment(java.util.List<FastaSequence> sequences,
Program program,
char gapchar)
- Parameters:
sequences
- program
- gapchar
-
Alignment
public Alignment(java.util.List<FastaSequence> sequences,
AlignmentMetadata metadata)
- Parameters:
sequences
- metadata
-
getSequences
public java.util.List<FastaSequence> getSequences()
- Returns:
- list of FastaSequence records
getSize
public int getSize()
- Returns:
- a number of sequence in the alignment
getMetadata
public AlignmentMetadata getMetadata()
- Returns:
- AlignmentMetadata object
toString
public java.lang.String toString()
- Overrides:
toString
in class java.lang.Object
equals
public boolean equals(java.lang.Object obj)
- Please note that this implementation does not take the order of sequences
into account!
- Overrides:
equals
in class java.lang.Object