Package org.biojava.nbio.core.sequence

Class ChromosomeSequence

java.lang.Object
org.biojava.nbio.core.sequence.template.AbstractSequence<NucleotideCompound>
org.biojava.nbio.core.sequence.DNASequence
org.biojava.nbio.core.sequence.ChromosomeSequence
All Implemented Interfaces:
Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>
public class ChromosomeSequence extends DNASequence
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
Author:
Scooter Willis

  • Constructor Details

    • ChromosomeSequence

      public ChromosomeSequence()
      Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction. Not recommended

    • ChromosomeSequence

      public ChromosomeSequence(String seqString) throws CompoundNotFoundException
      String is king and assume DNA
      Parameters:
      seqString -
      Throws:
      CompoundNotFoundException

    • ChromosomeSequence

      public ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader)
      Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory. Could also be a NCBI proxy to load sequence data as needed from remote web server.
      Parameters:
      proxyLoader -

    • ChromosomeSequence

      public ChromosomeSequence(String seqString, CompoundSet<NucleotideCompound> compoundSet) throws CompoundNotFoundException
      Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
      Parameters:
      seqString -
      compoundSet -
      Throws:
      CompoundNotFoundException

    • ChromosomeSequence

      public ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)
      Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
      Parameters:
      proxyLoader -
      compoundSet -

  • Method Details

    • getChromosomeNumber

      public int getChromosomeNumber()
      Returns:
      the chromosomeNumber

    • setChromosomeNumber

      public void setChromosomeNumber(int chromosomeNumber)
      Parameters:
      chromosomeNumber - the chromosomeNumber to set

    • getGeneSequences

      public LinkedHashMap<String,GeneSequence> getGeneSequences()
      Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key. The list retains the order the genes are added
      Returns:

    • removeGeneSequence

      public GeneSequence removeGeneSequence(String accession)
      Parameters:
      accession -
      Returns:

    • addGene

      public GeneSequence addGene(AccessionID accession, int bioBegin, int bioEnd, Strand strand)
      Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0. The GeneSequence that is returned will have a reference to parent chromosome sequence which actually contains the sequence data. Strand is important for positive and negative direction where negative strand means we need reverse complement. If negative strand then bioBegin will be greater than bioEnd
      Parameters:
      accession -
      begin -
      end -
      strand -
      Returns:

    • getGene

      public GeneSequence getGene(String accession)
      Get the gene based on accession. Will return null if not found
      Parameters:
      accession -
      Returns: