Package jebl.evolution.alignments
Class BasicAlignment
- java.lang.Object
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- jebl.evolution.alignments.BasicAlignment
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Constructor Summary
Constructors Constructor Description BasicAlignment()
Constructs a basic alignment with no sequences.BasicAlignment(java.util.Collection<? extends Sequence> sequences)
Constructs a basic alignment from a collection of sequences.BasicAlignment(Sequence[] sequences)
Constructs a basic alignment from an array of sequences.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addSequence(Sequence sequence)
Adds a sequence to this alignmentint
getPatternCount()
int
getPatternLength()
java.util.List<Pattern>
getPatterns()
Get a list of all the patternsSequence
getSequence(Taxon taxon)
java.util.List<Sequence>
getSequenceList()
java.util.Set<Sequence>
getSequences()
SequenceType
getSequenceType()
int
getSiteCount()
java.util.List<Taxon>
getTaxa()
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Constructor Detail
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BasicAlignment
public BasicAlignment()
Constructs a basic alignment with no sequences.
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BasicAlignment
public BasicAlignment(java.util.Collection<? extends Sequence> sequences)
Constructs a basic alignment from a collection of sequences. The sequence objects are not copied.- Parameters:
sequences
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BasicAlignment
public BasicAlignment(Sequence[] sequences)
Constructs a basic alignment from an array of sequences. The sequence objects are not copied.- Parameters:
sequences
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Method Detail
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getSequences
public java.util.Set<Sequence> getSequences()
- Specified by:
getSequences
in interfaceSequences
- Returns:
- a set containing all the sequences in this alignment.
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getSequenceList
public java.util.List<Sequence> getSequenceList()
- Specified by:
getSequenceList
in interfaceAlignment
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getSequenceType
public SequenceType getSequenceType()
- Specified by:
getSequenceType
in interfacePatterns
- Returns:
- the data type of the states in these site patterns.
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getSequence
public Sequence getSequence(Taxon taxon)
- Specified by:
getSequence
in interfaceSequences
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getSiteCount
public int getSiteCount()
- Specified by:
getSiteCount
in interfaceAlignment
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getPatternCount
public int getPatternCount()
- Specified by:
getPatternCount
in interfacePatterns
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getPatternLength
public int getPatternLength()
- Specified by:
getPatternLength
in interfacePatterns
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getPatterns
public java.util.List<Pattern> getPatterns()
Description copied from interface:Patterns
Get a list of all the patterns- Specified by:
getPatterns
in interfacePatterns
- Returns:
- the list
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getTaxa
public java.util.List<Taxon> getTaxa()
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addSequence
public void addSequence(Sequence sequence)
Adds a sequence to this alignment- Parameters:
sequence
- the new sequence.
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