Package pal.alignment

Class ConcatenatedAnnotatedAlignment

java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.ConcatenatedAnnotatedAlignment
All Implemented Interfaces:
Serializable, Alignment, AnnotationAlignment, IdGroup, Report
public class ConcatenatedAnnotatedAlignment extends AbstractAlignment implements AnnotationAlignment
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.
Version:
$Id:
Author:
Ed Buckler
See Also:

  • Constructor Details

    • ConcatenatedAnnotatedAlignment

      public ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list, boolean mergeByID, boolean union) throws IllegalArgumentException
      concatenate alignments
      Parameters:
      list - array with alignments to concatenate
      mergeByID - if true it will be by ID name
      union - if true it will create the union of the list, if false the intersection will be produced
      Throws:
      IllegalArgumentException

  • Method Details

    • getData

      public char getData(int seq, int site)
      sequence alignment at (sequence, site)
      Specified by:
      getData in interface Alignment
      Specified by:
      getData in class AbstractAlignment

    • getDataType

      public DataType getDataType(int site)
      Return the datatype for a given site, which can differ between source alignments
      Specified by:
      getDataType in interface AnnotationAlignment

    • 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 String getLocusName(int site)
      Returns the name of the locus
      Specified by:
      getLocusName in interface AnnotationAlignment

    • sortSites

      public void sortSites()
      sort the sites by chromosome, then by chromosomal location, and final locusPosition

    • report

      public void report(PrintWriter out)
      Description copied from interface: Report
      print human readable report (e.g., on parameters and associated model)
      Specified by:
      report in interface AnnotationAlignment
      Specified by:
      report in interface Report
      Overrides:
      report in class AbstractAlignment
      Parameters:
      out - output stream