Package jgromacs.data

Class Sequence

java.lang.Object
jgromacs.data.Sequence
All Implemented Interfaces:
Cloneable

public class Sequence extends Object implements Cloneable
Objects of this class represent a single amino acid sequence
  • Constructor Details

    • Sequence

      public Sequence()
      Constructs a new Sequence object
    • Sequence

      public Sequence(String name)
      Constructs a new Sequence object of given name
  • Method Details

    • getName

      public String getName()
      Returns the name of sequence
      Returns:
      name of sequence
    • setName

      public void setName(String name)
      Sets the name of sequence
      Parameters:
      name - name of sequence
    • getAsArrayList

      public ArrayList<SequencePosition> getAsArrayList()
      Returns sequence as an ArrayList object
      Returns:
      sequence as an ArrayList
    • getSequenceLength

      public int getSequenceLength()
      Returns the length of sequence (gaps excluded)
      Returns:
      length of sequence
    • getSequenceLengthWithGaps

      public int getSequenceLengthWithGaps()
      Returns the length of sequence (gaps included)
      Returns:
      length of sequence
    • getPosition

      public SequencePosition getPosition(int i)
      Returns sequence position #i
      Returns:
      sequence position #i
    • getPositionByIndex

      public SequencePosition getPositionByIndex(int index)
      Returns sequence position of given index
      Parameters:
      index - index of position
      Returns:
      sequence position of given index
    • getIndexOfPosition

      public int getIndexOfPosition(int i)
      Returns the index of sequence position #i
      Returns:
      index of sequence position
    • getResidueTypeOfPosition

      public ResidueType getResidueTypeOfPosition(int i)
      Returns the residue type of sequence position #i
      Returns:
      residue type of sequence position
    • getAnnotationOfPosition

      public String getAnnotationOfPosition(int i)
      Returns the annotation of sequence position #i
      Returns:
      annotation of sequence position
    • getResidueTypeOfPositionOfIndex

      public ResidueType getResidueTypeOfPositionOfIndex(int index)
      Returns the residue type of sequence position of given index
      Parameters:
      index - index of position
      Returns:
      residue type of sequence position
    • getAnnotationOfPositionOfIndex

      public String getAnnotationOfPositionOfIndex(int index)
      Returns the annotation of sequence position of given index
      Parameters:
      index - index of position
      Returns:
      annotation of sequence position
    • addPosition

      public void addPosition(SequencePosition pos)
      Adds a new position to the sequence
      Parameters:
      pos - new sequence position
    • addPosition

      public void addPosition(ResidueType type, String annotation)
      Adds a new position of given residue type and annotation to the sequence
      Parameters:
      type - residue type of new position
      annotation - annotation of new position
    • addPosition

      public void addPosition(int index, ResidueType type)
      Adds a new position of given index and residue type to the sequence
      Parameters:
      index - index of new position
      type - residue type of new position
    • addPosition

      public void addPosition(int index, ResidueType type, String annotation)
      Adds a new position of given index, residue type and annotation to the sequence
      Parameters:
      index - index of new position
      type - residue type of new position
      annotation - annotation of new position
    • addPositionsFromString

      public void addPositionsFromString(String str)
      Adds a series of new positions to the sequence taken from a String object
      Parameters:
      str - String object encoding a series of sequence positions
    • addGap

      public void addGap()
      Adds a new gap to the sequence
    • insertGap

      public void insertGap(int i)
      Inserts a new gap to position #i
    • setPosition

      public void setPosition(int i, SequencePosition pos)
      Replaces position #i with the given sequence position
      Parameters:
      pos - new sequence position
    • setPosition

      public void setPosition(int i, ResidueType type, String annotation)
      Replaces position #i with the a sequence position of given residue type and annotation
      Parameters:
      type - residue type of new sequence position
      annotation - annotation of new sequence position
    • setPosition

      public void setPosition(int i, int index, ResidueType type)
      Replaces position #i with the a sequence position of given index and residue type
      Parameters:
      index - index of new sequence position
      type - residue type of new sequence position
    • setPosition

      public void setPosition(int i, int index, ResidueType type, String annotation)
      Replaces position #i with the a sequence position of given index, residue type and annotation
      Parameters:
      index - index of new sequence position
      type - residue type of new sequence position
      annotation - annotation of new sequence position
    • setPositionByIndex

      public void setPositionByIndex(int index, ResidueType type, String annotation)
      Replaces the position of given index with the a sequence position of given residue type and annotation
      Parameters:
      index - index of sequence position
      type - residue type of new sequence position
      annotation - annotation of new sequence position
    • setPositionByIndex

      public void setPositionByIndex(int index, ResidueType type)
      Replaces the position of given index with the a sequence position of given residue type
      Parameters:
      index - index of sequence position
      type - residue type of new sequence position
    • removePosition

      public void removePosition(int i)
      Removes sequence position #i
    • removePosition

      public void removePosition(SequencePosition pos)
      Removes the given sequence position
      Parameters:
      pos - sequence position to be removed
    • removePositionByIndex

      public void removePositionByIndex(int index)
      Removes the sequence position of given index
      Parameters:
      index - index of sequence position to be removed
    • removeGaps

      public void removeGaps()
      Removes all gaps from the sequence
    • reIndexPositions

      public void reIndexPositions(int startindex)
      Reindexes all positions in the sequence starting from a given index
      Parameters:
      startindex - index of position #0
    • reIndexPositions

      public void reIndexPositions()
      Reindexes all positions in the sequence starting from 1
    • insertPosition

      public void insertPosition(int i, SequencePosition pos)
      Inserts the given sequence position to position #i Note that you may have to re-index sequence positions after using this method
      Parameters:
      pos - new sequence position
    • insertPosition

      public void insertPosition(int i, ResidueType type, String annotation)
      Inserts sequence position of given residue type and annotation to position #i Note that you may have to re-index sequence positions after using this method
      Parameters:
      type - residue type of new sequence position
      annotation - annotation of new sequence position
    • insertPosition

      public void insertPosition(int i, int index, ResidueType type)
      Inserts sequence position of given index and residue type to position #i Note that you may have to re-index sequence positions after using this method
      Parameters:
      index - index of new sequence position
      type - residue type of new sequence position
    • insertPosition

      public void insertPosition(int i, int index, ResidueType type, String annotation)
      Inserts sequence position of given index, residue type and annotation to position #i Note that you may have to re-index sequence positions after using this method
      Parameters:
      index - index of new sequence position
      type - residue type of new sequence position
      annotation - annotation of new sequence position
    • isPositionAGap

      public boolean isPositionAGap(int i)
      Returns true if sequence position #i is a gap
    • getSubSequence

      public Sequence getSubSequence(int begin, int end)
      Returns subsequence beginning at sequence position #begin and ending at sequence position #end
      Parameters:
      begin - start position of subsequence
      end - end position of subsequence
      Returns:
      subsequence
    • getSubSequenceFrom

      public Sequence getSubSequenceFrom(int begin)
      Returns subsequence beginning at sequence position #begin
      Parameters:
      begin - start position of subsequence
      Returns:
      subsequence
    • getSubSequenceTo

      public Sequence getSubSequenceTo(int end)
      Returns subsequence ending at sequence position #end
      Parameters:
      end - end position of subsequence
      Returns:
      subsequence
    • getReverse

      public Sequence getReverse()
      Returns the reverse sequence
      Returns:
      reverse sequence
    • concat

      public Sequence concat(Sequence other)
      Returns the given sequence concatenated to this sequence
      Parameters:
      other - second sequence
      Returns:
      concatenated sequence
    • containsSubSequence

      public boolean containsSubSequence(Sequence subsequence)
      Returns true if the given subsequence is contained in this sequence
      Parameters:
      subsequence - subsequence to search for
    • toString

      public String toString()
      Returns the String representation of sequence
      Overrides:
      toString in class Object
      Returns:
      String representation
    • toString1Letter

      public String toString1Letter()
      Returns a String representation in which each residue is represented by its 1 letter code
      Returns:
      String representation
    • toString3Letter

      public String toString3Letter()
      Returns a String representation in which each residue is represented by its 3 letter code
      Returns:
      String representation
    • toString1Letter

      public String toString1Letter(int lengthOfLine)
      Returns a String representation in which each residue is represented by its 1 letter code and the string is split to lines of the given length
      Parameters:
      lengthOfLine - max length of a line in the string
      Returns:
      String representation
    • toString3Letter

      public String toString3Letter(int lengthOfLine)
      Returns a String representation in which each residue is represented by its 3 letter code and the string is split to lines of the given length
      Parameters:
      lengthOfLine - max length of a line (number of residues) in the string
      Returns:
      String representation
    • toStringInfo

      public String toStringInfo()
      Returns summary information about the sequence
      Returns:
      summary information
    • clone

      public Object clone()
      Returns an identical Sequence object
      Overrides:
      clone in class Object
      Returns:
      clone of the sequence
    • equals

      public boolean equals(Object other)
      Returns true if the two sequences are identical
      Overrides:
      equals in class Object
      Parameters:
      other - the other sequence
    • hashCode

      public int hashCode()
      Returns hash code
      Overrides:
      hashCode in class Object