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public interface AnnotationAlignment
The AnnotationAlignment interface is designed to provide annotation for an alignment. This annotation can include information on chromosomal location, site positions, names of loci, and the type of position (exon, intron, etc.) This interface also permits 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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Fields inherited from interface pal.alignment.Alignment |
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GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA |
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 a specific site, which could differ by site in complex 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 locus (handles gaps) |
void |
report(java.io.PrintWriter out)
Returns a report for the alignment |
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 |
Method Detail |
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float getChromosomePosition(int site)
int getChromosome(int site)
float getWeightedLocusPosition(int site)
int getLocusPosition(int site)
char getPositionType(int site)
java.lang.String getLocusName(int site)
DataType getDataType(int site)
void report(java.io.PrintWriter out)
report
in interface Report
out
- output stream
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