Class MarkerFileIterator<M extends Marker>

    • Field Detail

      • createChromos

        protected boolean createChromos
      • genome

        protected Genome genome
      • ignoreChromosomeErrors

        protected boolean ignoreChromosomeErrors
      • inOffset

        protected int inOffset
    • Constructor Detail

      • MarkerFileIterator

        public MarkerFileIterator​(java.io.BufferedReader reader,
                                  int inOffset)
      • MarkerFileIterator

        public MarkerFileIterator​(java.lang.String fileName,
                                  Genome genome,
                                  int inOffset)
      • MarkerFileIterator

        public MarkerFileIterator​(java.lang.String fileName,
                                  int inOffset)
    • Method Detail

      • getChromosome

        public Chromosome getChromosome​(java.lang.String chromoName)
        Find chromosome 'chromoName'. If it does not exists and 'createChromos' is true, the chromosome is created
      • getGenome

        public Genome getGenome()
      • init

        protected void init​(java.lang.String fileName,
                            int inOffset)
        Initialize
        Overrides:
        init in class FileIterator<M extends Marker>
        Parameters:
        fileName - : Can be null (no file is opened)
      • isIgnoreChromosomeErrors

        public boolean isIgnoreChromosomeErrors()
      • loadMarkers

        public Markers loadMarkers()
      • parsePosition

        public int parsePosition​(java.lang.String posStr)
        Parse a string as a 'position'. Note: It subtracts 'inOffset' so that all coordinates are zero-based
      • sanityCheckChromo

        public void sanityCheckChromo​(java.lang.String chromoName,
                                      Chromosome chromo)
        Sanity check
      • setCreateChromos

        public void setCreateChromos​(boolean createChromos)
      • setIgnoreChromosomeErrors

        public void setIgnoreChromosomeErrors​(boolean ignoreChromosomeErrors)
      • setInOffset

        public void setInOffset​(int inOffset)