jebl.evolution.alignments
Constructor and Description |
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BasicAlignment()
Constructs a basic alignment with no sequences.
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BasicAlignment(java.util.Collection<? extends Sequence> sequences)
Constructs a basic alignment from a collection of sequences.
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BasicAlignment(Sequence[] sequences)
Constructs a basic alignment from an array of sequences.
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Modifier and Type | Method and Description |
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void |
addSequence(Sequence sequence)
Adds a sequence to this alignment
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int |
getPatternCount() |
int |
getPatternLength() |
java.util.List<Pattern> |
getPatterns()
Get a list of all the patterns
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Sequence |
getSequence(Taxon taxon) |
java.util.List<Sequence> |
getSequenceList() |
java.util.Set<Sequence> |
getSequences() |
SequenceType |
getSequenceType() |
int |
getSiteCount() |
java.util.List<Taxon> |
getTaxa() |
public BasicAlignment()
public BasicAlignment(java.util.Collection<? extends Sequence> sequences)
sequences
- public BasicAlignment(Sequence[] sequences)
sequences
- public java.util.Set<Sequence> getSequences()
getSequences
in interface Sequences
public java.util.List<Sequence> getSequenceList()
getSequenceList
in interface Alignment
public SequenceType getSequenceType()
getSequenceType
in interface Patterns
public Sequence getSequence(Taxon taxon)
getSequence
in interface Sequences
public int getSiteCount()
getSiteCount
in interface Alignment
public int getPatternCount()
getPatternCount
in interface Patterns
public int getPatternLength()
getPatternLength
in interface Patterns
public java.util.List<Pattern> getPatterns()
Patterns
getPatterns
in interface Patterns
public java.util.List<Taxon> getTaxa()
public void addSequence(Sequence sequence)
sequence
- the new sequence.http://code.google.com/p/jebl2/