Package pal.alignment

Class StrippedAlignment

java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.StrippedAlignment
All Implemented Interfaces:
Serializable, Alignment, IdGroup, Report
Direct Known Subclasses:
StrippedAnnotatedAlignment
public class StrippedAlignment extends AbstractAlignment
takes an alignment and repeatedly removes sites
Version:
$Id: StrippedAlignment.java,v 1.6 2002/02/27 22:25:59 matt Exp $
Author:
Korbinian Strimmer
See Also:

  • Field Details

    • rawAlignment

      protected Alignment rawAlignment

    • rawNumSites

      protected int rawNumSites

    • alias

      protected int[] alias

    • notDropped

      protected boolean[] notDropped

  • Constructor Details

    • StrippedAlignment

      public StrippedAlignment(Alignment raw)
      Constructor
      Parameters:
      raw - original alignment

  • 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

    • dropSite

      public void dropSite(int s)
      drop a site
      Parameters:
      s - site of original alignment

    • removeSites

      public void removeSites(char c)
      remove site that contain a specified character
      Parameters:
      c - character that will cause the removal of a site

    • removeGaps

      public void removeGaps()
      remove sites with gaps

    • removeUnknowns

      public void removeUnknowns()
      remove sites with unknowns

    • removeConstantSites

      public void removeConstantSites()
      remove constant sites

    • removeNoninformativeSites

      public void removeNoninformativeSites()
      remove noninformative sites