Package jgromacs.data

Class Sequence

  • All Implemented Interfaces:
    java.lang.Cloneable

    public class Sequence
    extends java.lang.Object
    implements java.lang.Cloneable
    Objects of this class represent a single amino acid sequence
    • Constructor Summary

      Constructors 
      Constructor Description
      Sequence()
      Constructs a new Sequence object
      Sequence​(java.lang.String name)
      Constructs a new Sequence object of given name
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addGap()
      Adds a new gap to the sequence
      void addPosition​(int index, ResidueType type)
      Adds a new position of given index and residue type to the sequence
      void addPosition​(int index, ResidueType type, java.lang.String annotation)
      Adds a new position of given index, residue type and annotation to the sequence
      void addPosition​(SequencePosition pos)
      Adds a new position to the sequence
      void addPosition​(ResidueType type, java.lang.String annotation)
      Adds a new position of given residue type and annotation to the sequence
      void addPositionsFromString​(java.lang.String str)
      Adds a series of new positions to the sequence taken from a String object
      java.lang.Object clone()
      Returns an identical Sequence object
      Sequence concat​(Sequence other)
      Returns the given sequence concatenated to this sequence
      boolean containsSubSequence​(Sequence subsequence)
      Returns true if the given subsequence is contained in this sequence
      boolean equals​(java.lang.Object other)
      Returns true if the two sequences are identical
      java.lang.String getAnnotationOfPosition​(int i)
      Returns the annotation of sequence position #i
      java.lang.String getAnnotationOfPositionOfIndex​(int index)
      Returns the annotation of sequence position of given index
      java.util.ArrayList<SequencePosition> getAsArrayList()
      Returns sequence as an ArrayList object
      int getIndexOfPosition​(int i)
      Returns the index of sequence position #i
      java.lang.String getName()
      Returns the name of sequence
      SequencePosition getPosition​(int i)
      Returns sequence position #i
      SequencePosition getPositionByIndex​(int index)
      Returns sequence position of given index
      ResidueType getResidueTypeOfPosition​(int i)
      Returns the residue type of sequence position #i
      ResidueType getResidueTypeOfPositionOfIndex​(int index)
      Returns the residue type of sequence position of given index
      Sequence getReverse()
      Returns the reverse sequence
      int getSequenceLength()
      Returns the length of sequence (gaps excluded)
      int getSequenceLengthWithGaps()
      Returns the length of sequence (gaps included)
      Sequence getSubSequence​(int begin, int end)
      Returns subsequence beginning at sequence position #begin and ending at sequence position #end
      Sequence getSubSequenceFrom​(int begin)
      Returns subsequence beginning at sequence position #begin
      Sequence getSubSequenceTo​(int end)
      Returns subsequence ending at sequence position #end
      int hashCode()
      Returns hash code
      void insertGap​(int i)
      Inserts a new gap to position #i
      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
      void insertPosition​(int i, int index, ResidueType type, java.lang.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
      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
      void insertPosition​(int i, ResidueType type, java.lang.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
      boolean isPositionAGap​(int i)
      Returns true if sequence position #i is a gap
      void reIndexPositions()
      Reindexes all positions in the sequence starting from 1
      void reIndexPositions​(int startindex)
      Reindexes all positions in the sequence starting from a given index
      void removeGaps()
      Removes all gaps from the sequence
      void removePosition​(int i)
      Removes sequence position #i
      void removePosition​(SequencePosition pos)
      Removes the given sequence position
      void removePositionByIndex​(int index)
      Removes the sequence position of given index
      void setName​(java.lang.String name)
      Sets the name of sequence
      void setPosition​(int i, int index, ResidueType type)
      Replaces position #i with the a sequence position of given index and residue type
      void setPosition​(int i, int index, ResidueType type, java.lang.String annotation)
      Replaces position #i with the a sequence position of given index, residue type and annotation
      void setPosition​(int i, SequencePosition pos)
      Replaces position #i with the given sequence position
      void setPosition​(int i, ResidueType type, java.lang.String annotation)
      Replaces position #i with the a sequence position of given residue type and annotation
      void setPositionByIndex​(int index, ResidueType type)
      Replaces the position of given index with the a sequence position of given residue type
      void setPositionByIndex​(int index, ResidueType type, java.lang.String annotation)
      Replaces the position of given index with the a sequence position of given residue type and annotation
      java.lang.String toString()
      Returns the String representation of sequence
      java.lang.String toString1Letter()
      Returns a String representation in which each residue is represented by its 1 letter code
      java.lang.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
      java.lang.String toString3Letter()
      Returns a String representation in which each residue is represented by its 3 letter code
      java.lang.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
      java.lang.String toStringInfo()
      Returns summary information about the sequence
      • Methods inherited from class java.lang.Object

        finalize, getClass, notify, notifyAll, wait, wait, wait
    • Constructor Detail

      • Sequence

        public Sequence()
        Constructs a new Sequence object
      • Sequence

        public Sequence​(java.lang.String name)
        Constructs a new Sequence object of given name
    • Method Detail

      • getName

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

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

        public java.util.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 java.lang.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 java.lang.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,
                                java.lang.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,
                                java.lang.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​(java.lang.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,
                                java.lang.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,
                                java.lang.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,
                                       java.lang.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,
                                   java.lang.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,
                                   java.lang.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 java.lang.String toString()
        Returns the String representation of sequence
        Overrides:
        toString in class java.lang.Object
        Returns:
        String representation
      • toString1Letter

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

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

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

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

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

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