Package org.biojava.nbio.core.sequence.storage

Class ArrayListSequenceReader<C extends Compound>

java.lang.Object
org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader<C>
Type Parameters:
C -
All Implemented Interfaces:
Iterable<C>, Accessioned, Sequence<C>, SequenceReader<C>
Direct Known Subclasses:
ArrayListProxySequenceReader
public class ArrayListSequenceReader<C extends Compound> extends Object implements SequenceReader<C>
Stores a Sequence as a collection of compounds in an ArrayList

  • Constructor Details

  • Method Details

    • getSequenceAsString

      public String getSequenceAsString()
      Description copied from interface: Sequence
      Returns the String representation of the Sequence
      Specified by:
      getSequenceAsString in interface Sequence<C extends Compound>
      Returns:

    • getSequenceAsString

      public String getSequenceAsString(Integer begin, Integer end, Strand strand)
      Parameters:
      begin -
      end -
      strand -
      Returns:

    • getAsList

      public List<C> getAsList()
      Description copied from interface: Sequence
      Returns the Sequence as a List of compounds
      Specified by:
      getAsList in interface Sequence<C extends Compound>
      Returns:

    • getCompoundAt

      public C getCompoundAt(int position)
      Description copied from interface: Sequence
      Returns the Compound at the given biological index
      Specified by:
      getCompoundAt in interface Sequence<C extends Compound>
      Parameters:
      position -
      Returns:

    • getIndexOf

      public int getIndexOf(C compound)
      Description copied from interface: Sequence
      Scans through the Sequence looking for the first occurrence of the given compound
      Specified by:
      getIndexOf in interface Sequence<C extends Compound>
      Parameters:
      compound -
      Returns:

    • getLastIndexOf

      public int getLastIndexOf(C compound)
      Description copied from interface: Sequence
      Scans through the Sequence looking for the last occurrence of the given compound
      Specified by:
      getLastIndexOf in interface Sequence<C extends Compound>
      Parameters:
      compound -
      Returns:

    • getLength

      public int getLength()
      Description copied from interface: Sequence
      Returns the length of the Sequence
      Specified by:
      getLength in interface Sequence<C extends Compound>
      Returns:

    • iterator

      public Iterator<C> iterator()
      Specified by:
      iterator in interface Iterable<C extends Compound>
      Returns:

    • setCompoundSet

      public void setCompoundSet(CompoundSet<C> compoundSet)
      Specified by:
      setCompoundSet in interface SequenceReader<C extends Compound>
      Parameters:
      compoundSet -

    • getCompoundSet

      public CompoundSet<C> getCompoundSet()
      Description copied from interface: Sequence
      Gets the compound set used to back this Sequence
      Specified by:
      getCompoundSet in interface Sequence<C extends Compound>
      Returns:

    • setContents

      public void setContents(String sequence) throws CompoundNotFoundException
      Specified by:
      setContents in interface SequenceReader<C extends Compound>
      Parameters:
      sequence -
      Throws:
      CompoundNotFoundException

    • setContents

      public void setContents(List<C> list)
      Parameters:
      list -

    • getSubSequence

      public SequenceView<C> getSubSequence(Integer bioBegin, Integer bioEnd)
      Description copied from interface: Sequence
      Returns a portion of the sequence from the different positions. This is indexed from 1
      Specified by:
      getSubSequence in interface Sequence<C extends Compound>
      Parameters:
      bioBegin -
      bioEnd -
      Returns:

    • getAccession

      public AccessionID getAccession()
      Description copied from interface: Accessioned
      Returns the AccessionID this location is currently bound with
      Specified by:
      getAccession in interface Accessioned
      Returns:

    • countCompounds

      public int countCompounds(C... compounds)
      Description copied from interface: Sequence
      Returns the number of times we found a compound in the Sequence
      Specified by:
      countCompounds in interface Sequence<C extends Compound>
      Parameters:
      compounds -
      Returns:

    • getInverse

      public SequenceView<C> getInverse()
      Description copied from interface: Sequence
      Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.
      Specified by:
      getInverse in interface Sequence<C extends Compound>
      Returns:

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object