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java.lang.Objectpal.alignment.AbstractAlignment
pal.alignment.SimpleAlignment
pal.alignment.MultiLocusAnnotatedAlignment
public class MultiLocusAnnotatedAlignment
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci. Separate annotation information is stored from each sites. This would be good SNP SSR type of data, but it would be inefficient for single gene data.
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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int[] |
chromosome
used to designate chromosome |
float[] |
chromosomePosition
used to designate position along chromosome |
java.lang.String[] |
locusName
used to designate locus name |
int[] |
locusPosition
used to designate position; do not account for gaps |
char[] |
positionType
used to designate position Type |
DataType[] |
siteDataType
provides datatype for each locus separately |
float[] |
weightedPosition
used to designate weighted position; accounts for gaps |
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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MultiLocusAnnotatedAlignment()
null constructor. |
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MultiLocusAnnotatedAlignment(Alignment a)
Basic constructor. |
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MultiLocusAnnotatedAlignment(AnnotationAlignment a)
Clone constructor for Annotated alignment |
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MultiLocusAnnotatedAlignment(AnnotationAlignment a,
IdGroup newGroup)
This constructor will subset the alignment based on the taxa in IdGroup |
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MultiLocusAnnotatedAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
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MultiLocusAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
DataType dt)
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MultiLocusAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
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Method Summary | |
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int |
getChromosome(int site)
Returns chromosome |
float |
getChromosomePosition(int site)
Return the position along chromosome |
DataType |
getDataType(int site)
Returns the datatype |
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) |
protected void |
init(IdGroup group,
java.lang.String[] sequences)
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protected void |
initMatrices()
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void |
setChromosome(int chromosome,
int site)
Sets chromosome |
void |
setChromosomePosition(float position,
int site)
Set the position along chromosome |
void |
setLocusName(java.lang.String locusName,
int site)
Sets the name of the locus |
void |
setLocusPosition(int position,
int site)
Set the position within the locus |
void |
setPositionType(int site,
char posType)
Set thes position type (eg. |
void |
setWeightedLocusPosition(int site,
float weightedPos)
Sets the weighted position along the gene (handles gaps) |
Methods inherited from class pal.alignment.SimpleAlignment |
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getAlignedSequenceString, getData |
Methods inherited from class pal.alignment.AbstractAlignment |
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getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, 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.AnnotationAlignment |
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report |
Methods inherited from interface pal.alignment.Alignment |
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getAlignedSequenceString, getData, getDataType, getSequenceCount, getSiteCount |
Methods inherited from interface pal.misc.IdGroup |
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getIdCount, getIdentifier, setIdentifier, whichIdNumber |
Field Detail |
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public float[] chromosomePosition
public int[] chromosome
public float[] weightedPosition
public int[] locusPosition
public char[] positionType
public java.lang.String[] locusName
public DataType[] siteDataType
Constructor Detail |
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public MultiLocusAnnotatedAlignment(Alignment a)
public MultiLocusAnnotatedAlignment()
public MultiLocusAnnotatedAlignment(AnnotationAlignment a)
public MultiLocusAnnotatedAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
public MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, DataType dt)
public MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
public MultiLocusAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
Method Detail |
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protected void initMatrices()
protected void init(IdGroup group, java.lang.String[] sequences)
public float getChromosomePosition(int site)
getChromosomePosition
in interface AnnotationAlignment
public void setChromosomePosition(float position, int site)
public int getChromosome(int site)
getChromosome
in interface AnnotationAlignment
public void setChromosome(int chromosome, int site)
public float getWeightedLocusPosition(int site)
getWeightedLocusPosition
in interface AnnotationAlignment
public void setWeightedLocusPosition(int site, float weightedPos)
public int getLocusPosition(int site)
getLocusPosition
in interface AnnotationAlignment
public void setLocusPosition(int position, int site)
public char getPositionType(int site)
getPositionType
in interface AnnotationAlignment
public void setPositionType(int site, char posType)
public java.lang.String getLocusName(int site)
getLocusName
in interface AnnotationAlignment
public void setLocusName(java.lang.String locusName, int site)
public DataType getDataType(int site)
getDataType
in interface AnnotationAlignment
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