Package org.biojava.nbio.core.sequence.loader

Class StringProxySequenceReader<C extends Compound>

java.lang.Object
org.biojava.nbio.core.sequence.loader.StringProxySequenceReader<C>
Type Parameters:
C -
All Implemented Interfaces:
Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>
Direct Known Subclasses:
GenbankProxySequenceReader
public class StringProxySequenceReader<C extends Compound> extends Object implements ProxySequenceReader<C>
An example of a ProxySequenceReader that is created from a String. Used for testing
Author:
Scooter Willis

  • Constructor Details

  • Method Details

    • setCompoundSet

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

    • setContents

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

    • setContents

      public void setContents(String sequence, ArrayList features) throws CompoundNotFoundException
      Throws:
      CompoundNotFoundException

    • getLength

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

    • 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 - Biological index (1 to n)
      Returns:
      Compound at the specified position

    • 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 - Compounds to look for
      Returns:
      Index of the first position of the compound in the sequence (1 to n)

    • 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 - Compounds to look for
      Returns:
      Index of the last position of the compound in the sequence (1 to n)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • 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>

    • 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>

    • getSequenceAsString

      public String getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand)

    • 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 - Biological index start; must be greater than 0
      bioEnd - Biological end; must be less than length + 1
      Returns:
      A SequenceView of the offset

    • iterator

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

    • 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>

    • getAccession

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

    • 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 - Vargs of the compounds to count
      Returns:
      Number of times a compound was found

    • 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>