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java.lang.Objectpal.alignment.AbstractAlignment
pal.alignment.SimpleAlignment
pal.alignment.SimpleAnnotatedAlignment
public class SimpleAnnotatedAlignment
This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment. This annotation can include information on chromosomal location, site positions, locus name, and the type of position (exon, intron, etc.) This class is designed for alignments with a single locus but multiple sites within the locus. This class does not permit multiple datatypes per alignment.
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 |
char[] |
positionType
used to designate position Type |
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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SimpleAnnotatedAlignment(Alignment a)
Clone constructor from an unannotated alignment. |
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SimpleAnnotatedAlignment(AnnotationAlignment a)
Clone constructor. |
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SimpleAnnotatedAlignment(AnnotationAlignment a,
IdGroup newGroup)
This constructor will subset the alignment based on the taxa in IdGroup |
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SimpleAnnotatedAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
This constructor creates a basic SimpleAnnotatedAlignment. |
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SimpleAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
DataType dt)
This constructor creates a basic SimpleAnnotatedAlignment. |
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SimpleAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
This constructor creates a basic SimpleAnnotatedAlignment. |
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 (for SimpleAnnotatedAlignment there is only one 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) |
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
void |
setChromosome(int chromosome)
Sets chromosome |
void |
setChromosomePosition(float position)
Set the position along chromosome |
void |
setLocusName(java.lang.String locusName)
Sets the name of 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, 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, 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 char[] positionType
public java.lang.String locusName
Constructor Detail |
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public SimpleAnnotatedAlignment(Alignment a)
public SimpleAnnotatedAlignment(AnnotationAlignment a)
public SimpleAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
public SimpleAnnotatedAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
public SimpleAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, DataType dt)
public SimpleAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
Method Detail |
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public float getChromosomePosition(int site)
getChromosomePosition
in interface AnnotationAlignment
public void setChromosomePosition(float position)
public int getChromosome(int site)
getChromosome
in interface AnnotationAlignment
public void setChromosome(int chromosome)
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 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)
public DataType getDataType(int site)
getDataType
in interface AnnotationAlignment
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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