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java.lang.Objectpal.alignment.AbstractAlignment
pal.alignment.ConcatenatedAnnotatedAlignment
public class ConcatenatedAnnotatedAlignment
This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences. It will merge by either union or intersection. Missing taxa will return missing values on getData.
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.IdGroup |
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IdGroup.Utils |
Field Summary |
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Fields inherited from class pal.alignment.AbstractAlignment |
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idGroup, numSeqs, numSites |
Fields inherited from interface pal.alignment.Alignment |
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GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA |
Constructor Summary | |
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ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list,
boolean mergeByID,
boolean union)
concatenate alignments |
Method Summary | |
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int |
getChromosome(int site)
Returns chromosome |
float |
getChromosomePosition(int site)
Return the position along chromosome |
char |
getData(int seq,
int site)
sequence alignment at (sequence, site) |
DataType |
getDataType(int site)
Return the datatype for a given site, which can differ between source alignments |
java.lang.String |
getLocusName(int site)
Returns the name of the locus |
int |
getLocusPosition(int site)
Return the position along the locus (ignores gaps) |
char |
getPositionType(int site)
Returns position type (eg. |
float |
getWeightedLocusPosition(int site)
Return the weighted position along the gene (handles gaps) |
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
void |
sortSites()
sort the sites by chromosome, then by chromosomal location, and final locusPosition |
Methods inherited from class pal.alignment.AbstractAlignment |
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getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, setDataType, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface pal.alignment.Alignment |
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getAlignedSequenceString, getDataType, getSequenceCount, getSiteCount |
Methods inherited from interface pal.misc.IdGroup |
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getIdCount, getIdentifier, setIdentifier, whichIdNumber |
Constructor Detail |
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public ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list, boolean mergeByID, boolean union) throws java.lang.IllegalArgumentException
list
- array with alignments to concatenatemergeByID
- if true it will be by ID nameunion
- if true it will create the union of the list, if false the intersection will be produced
java.lang.IllegalArgumentException
Method Detail |
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public char getData(int seq, int site)
getData
in interface Alignment
getData
in class AbstractAlignment
public DataType getDataType(int site)
getDataType
in interface AnnotationAlignment
public float getChromosomePosition(int site)
getChromosomePosition
in interface AnnotationAlignment
public int getChromosome(int site)
getChromosome
in interface AnnotationAlignment
public float getWeightedLocusPosition(int site)
getWeightedLocusPosition
in interface AnnotationAlignment
public int getLocusPosition(int site)
getLocusPosition
in interface AnnotationAlignment
public char getPositionType(int site)
getPositionType
in interface AnnotationAlignment
public java.lang.String getLocusName(int site)
getLocusName
in interface AnnotationAlignment
public void sortSites()
public void report(java.io.PrintWriter out)
Report
report
in interface AnnotationAlignment
report
in interface Report
report
in class AbstractAlignment
out
- output stream
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