pal.alignment
Class SitePattern
java.lang.Object
|
+--pal.alignment.AbstractAlignment
|
+--pal.alignment.SitePattern
- All Implemented Interfaces:
- Alignment, IdGroup, Report, java.io.Serializable
- public class SitePattern
- extends AbstractAlignment
takes an Alignment and determines its site patterns
- See Also:
- Serialized Form
Field Summary |
int[] |
alias
site -> site pattern |
int |
numPatterns
number of site patterns |
byte[][] |
pattern
site patterns [sequence][site pattern] |
int[] |
weight
weights of each site pattern |
Constructor Summary |
SitePattern(Alignment a)
infer site patterns for a given alignment |
SitePattern(DataType dataType,
int numSites,
int numSeqs,
IdGroup idGroup,
int numPatterns,
int[] alias,
int[] weight,
byte[][] pattern)
construct SitePattern from scratch |
Methods inherited from class pal.alignment.AbstractAlignment |
getAlignedSequenceString, getDataType, getFrequency, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getStates, guessDataType, isGap, report, setDataType, setFrequency, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
numPatterns
public int numPatterns
- number of site patterns
alias
public int[] alias
- site -> site pattern
weight
public int[] weight
- weights of each site pattern
pattern
public byte[][] pattern
- site patterns [sequence][site pattern]
SitePattern
public SitePattern(Alignment a)
- infer site patterns for a given alignment
- Parameters:
a
- alignment
SitePattern
public SitePattern(DataType dataType,
int numSites,
int numSeqs,
IdGroup idGroup,
int numPatterns,
int[] alias,
int[] weight,
byte[][] pattern)
- construct SitePattern from scratch
- Parameters:
dataType
- data typenumSites
- number of sitesnumSeqs
- number of sequencesidGroup
- sequence identifiersnumPatterns
- number of site patternsalias
- link site -> site patternweight
- frequency of a site patternpattern
- site patterns
getData
public char getData(int seq,
int site)
- sequence alignment at (sequence, site)
- Overrides:
getData
in class AbstractAlignment
getSitePattern
public static final SitePattern getSitePattern(Alignment a)
- Parameters:
a
- An alignment- Returns:
- alignment as a site pattern if it isn't already one (other wise just returns alighnment)