Package pal.alignment

Class SimpleAnnotatedAlignment

java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.SimpleAlignment
pal.alignment.SimpleAnnotatedAlignment
All Implemented Interfaces:
Serializable, Alignment, AnnotationAlignment, IdGroup, Report
public class SimpleAnnotatedAlignment extends SimpleAlignment implements AnnotationAlignment
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.
Version:
$Id: SimpleAnnotatedAlignment.java,v 1
Author:
Ed Buckler
See Also:

  • Field Details

    • chromosomePosition

      public float chromosomePosition
      used to designate position along chromosome

    • chromosome

      public int chromosome
      used to designate chromosome

    • weightedPosition

      public float[] weightedPosition
      used to designate weighted position; accounts for gaps

    • positionType

      public char[] positionType
      used to designate position Type

    • locusName

      public String locusName
      used to designate locus name

  • Constructor Details

    • SimpleAnnotatedAlignment

      public SimpleAnnotatedAlignment(Alignment a)
      Clone constructor from an unannotated alignment. All annotation is set to defaults

    • SimpleAnnotatedAlignment

      public SimpleAnnotatedAlignment(AnnotationAlignment a)
      Clone constructor.

    • SimpleAnnotatedAlignment

      public SimpleAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
      This constructor will subset the alignment based on the taxa in IdGroup

    • SimpleAnnotatedAlignment

      public SimpleAnnotatedAlignment(Identifier[] ids, String[] sequences, String gaps, DataType dt)
      This constructor creates a basic SimpleAnnotatedAlignment. The annotation should be added with the set commands.

    • SimpleAnnotatedAlignment

      public SimpleAnnotatedAlignment(IdGroup group, String[] sequences, DataType dt)
      This constructor creates a basic SimpleAnnotatedAlignment. The annotation should be added with the set commands.

    • SimpleAnnotatedAlignment

      public SimpleAnnotatedAlignment(IdGroup group, String[] sequences, String gaps, DataType dt)
      This constructor creates a basic SimpleAnnotatedAlignment. The annotation should be added with the set commands.

  • Method Details

    • getChromosomePosition

      public float getChromosomePosition(int site)
      Return the position along chromosome
      Specified by:
      getChromosomePosition in interface AnnotationAlignment

    • setChromosomePosition

      public void setChromosomePosition(float position)
      Set the position along chromosome

    • getChromosome

      public int getChromosome(int site)
      Returns chromosome
      Specified by:
      getChromosome in interface AnnotationAlignment

    • setChromosome

      public void setChromosome(int chromosome)
      Sets chromosome

    • getWeightedLocusPosition

      public float getWeightedLocusPosition(int site)
      Return the weighted position along the gene (handles gaps)
      Specified by:
      getWeightedLocusPosition in interface AnnotationAlignment

    • setWeightedLocusPosition

      public void setWeightedLocusPosition(int site, float weightedPos)
      Sets the weighted position along the gene (handles gaps)

    • 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

    • setPositionType

      public void setPositionType(int site, char posType)
      Set thes position type (eg. I=intron, E-exon, P=promoter, 1=first, 2=second, 3=third, etc.

    • getLocusName

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

    • setLocusName

      public void setLocusName(String locusName)
      Sets the name of the locus

    • getDataType

      public DataType getDataType(int site)
      Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)
      Specified by:
      getDataType in interface AnnotationAlignment

    • 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