pal.alignment
Class StrippedAnnotatedAlignment
java.lang.Object
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+--pal.alignment.AbstractAlignment
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+--pal.alignment.StrippedAlignment
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+--pal.alignment.StrippedAnnotatedAlignment
- All Implemented Interfaces:
- Alignment, AnnotationAlignment, IdGroup, Report, java.io.Serializable
- public class StrippedAnnotatedAlignment
- extends StrippedAlignment
- implements AnnotationAlignment
This is the stripped implementation of the Annotation interface, which is designed to
provide stripped and annotated alignments. This annotation can
include information on chromosomal location, site positions, locus name, and the
type of position (exon, intron, etc.)
This class also add some methods for stripping sites based on frequency, count, and a
range of positions.
- See Also:
- Serialized Form
Methods inherited from class pal.alignment.AbstractAlignment |
getAlignedSequenceString, getDataType, getFrequency, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getStates, guessDataType, isGap, setDataType, setFrequency, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
minimumProportion
protected double minimumProportion
minimumCount
protected int minimumCount
firstSite
protected int firstSite
lastSite
protected int lastSite
StrippedAnnotatedAlignment
public StrippedAnnotatedAlignment(AnnotationAlignment a)
- Simple constructor
getChromosomePosition
public float getChromosomePosition(int site)
- Return the position along chromosome
- Specified by:
getChromosomePosition
in interface AnnotationAlignment
getChromosome
public int getChromosome(int site)
- Returns chromosome
- Specified by:
getChromosome
in interface AnnotationAlignment
getWeightedLocusPosition
public float getWeightedLocusPosition(int site)
- Return the weighted position along the gene (handles gaps)
- Specified by:
getWeightedLocusPosition
in interface AnnotationAlignment
getLocusPosition
public int getLocusPosition(int site)
- Return the position along the locus (ignores gaps)
- Specified by:
getLocusPosition
in interface AnnotationAlignment
getPositionType
public char getPositionType(int site)
- Returns position type (eg. I=intron, E-exon, P=promoter, 1=first, 2=second, 3=third, etc.
- Specified by:
getPositionType
in interface AnnotationAlignment
getLocusName
public java.lang.String getLocusName(int site)
- Returns the name of the locus
- Specified by:
getLocusName
in interface AnnotationAlignment
getDataType
public DataType getDataType(int site)
- Returns the datatype
- Specified by:
getDataType
in interface AnnotationAlignment
removeSitesOutsideRange
public void removeSitesOutsideRange(int firstSite,
int lastSite)
- Remove sites based on site position (excluded sites are lastSite)
This not effect any prior exclusions.
- Parameters:
firstSite
- first site to keep in the rangelastSite
- last site to keep in the range
removeConstantSitesIgnoreGapsMissing
public void removeConstantSitesIgnoreGapsMissing()
- remove constant sites but ignore gaps and missing data (- and ?)
removeSitesBasedOnFreqIgnoreGapsMissing
public void removeSitesBasedOnFreqIgnoreGapsMissing(double minimumProportion,
int minimumCount)
- remove sites based on minimum frequency (the count of good bases)
and based on the proportion of good sites different from consensus
- Parameters:
minimumProportion
- minimum proportion of sites different from the consensusminimumCount
- minimum number of sequences with a good bases (not - or ?)
report
public void report(java.io.PrintWriter out)
- Description copied from interface:
AnnotationAlignment
- Returns a report for the alignment
- Specified by:
report
in interface AnnotationAlignment
- Overrides:
report
in class AbstractAlignment
- Following copied from interface:
pal.misc.Report
- Parameters:
out
- output stream