jgromacs.data
Class Sequence

java.lang.Object
  extended by jgromacs.data.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
Sequence()
          Constructs a new Sequence object
Sequence(java.lang.String name)
          Constructs a new Sequence object of given name
 
Method Summary
 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(ResidueType type, java.lang.String annotation)
          Adds a new position of given residue type and annotation to the sequence
 void addPosition(SequencePosition pos)
          Adds a new position 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, 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
 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
 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, ResidueType type, java.lang.String annotation)
          Replaces position #i with the a sequence position of given residue type and annotation
 void setPosition(int i, SequencePosition pos)
          Replaces position #i with the given sequence position
 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
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