Package pal.alignment
Class AlignmentReaders.UnalignedAlignment
java.lang.Object
pal.alignment.AlignmentReaders.UnalignedAlignment
- All Implemented Interfaces:
Serializable
,Alignment
,IdGroup
- Enclosing class:
AlignmentReaders
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetAlignedSequenceString
(int sequence) Returns string representation of single sequence in alignment with gap characters included.char
getData
(int seq, int site) sequence alignment at (sequence, site)Return DataType of this alignment.double[]
int
Returns the number of identifiers in this groupgetIdentifier
(int i) Returns the ith identifier.int
Return number of sequences in this alignmentint
void
setDataType
(DataType dataType) void
setFrequency
(double[] frequencies) void
setIdentifier
(int i, Identifier id) Sets the ith identifier.toString()
int
returns the index of the identifier with the given name.
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Constructor Details
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UnalignedAlignment
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Method Details
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getData
public char getData(int seq, int site) sequence alignment at (sequence, site) -
getSiteCount
public int getSiteCount()- Specified by:
getSiteCount
in interfaceAlignment
- Returns:
- number of sites for each sequence in this alignment
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getSequenceCount
public int getSequenceCount()Description copied from interface:Alignment
Return number of sequences in this alignment- Specified by:
getSequenceCount
in interfaceAlignment
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getDataType
Description copied from interface:Alignment
Return DataType of this alignment.- Specified by:
getDataType
in interfaceAlignment
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setDataType
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getAlignedSequenceString
Description copied from interface:Alignment
Returns string representation of single sequence in alignment with gap characters included.- Specified by:
getAlignedSequenceString
in interfaceAlignment
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getFrequency
public double[] getFrequency() -
setFrequency
public void setFrequency(double[] frequencies) -
getIdCount
public int getIdCount()Description copied from interface:IdGroup
Returns the number of identifiers in this group- Specified by:
getIdCount
in interfaceIdGroup
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getIdentifier
Description copied from interface:IdGroup
Returns the ith identifier.- Specified by:
getIdentifier
in interfaceIdGroup
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setIdentifier
Description copied from interface:IdGroup
Sets the ith identifier.- Specified by:
setIdentifier
in interfaceIdGroup
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whichIdNumber
Description copied from interface:IdGroup
returns the index of the identifier with the given name.- Specified by:
whichIdNumber
in interfaceIdGroup
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toString
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