Package pal.alignment

Class StrippedAlignment

    • Field Detail

      • rawAlignment

        protected Alignment rawAlignment
      • rawNumSites

        protected int rawNumSites
      • alias

        protected int[] alias
      • notDropped

        protected boolean[] notDropped
    • Constructor Detail

      • StrippedAlignment

        public StrippedAlignment​(Alignment raw)
        Constructor
        Parameters:
        raw - original alignment
    • Method Detail

      • 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