Sequence

java.lang.Object
- 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

Constructors
Constructor and Description

Sequence()
Constructs a new Sequence object

Sequence(java.lang.String name)
Constructs a new Sequence object of given name

Constructors
Constructor and 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 and 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(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
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

Class Sequence

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Sequence

Sequence

Method Detail

getName

setName

getAsArrayList

getSequenceLength

getSequenceLengthWithGaps

getPosition

getPositionByIndex

getIndexOfPosition

getResidueTypeOfPosition

getAnnotationOfPosition

getResidueTypeOfPositionOfIndex

getAnnotationOfPositionOfIndex

addPosition

addPosition

addPosition

addPosition

addPositionsFromString

addGap

insertGap

setPosition

setPosition

setPosition

setPosition

setPositionByIndex

setPositionByIndex

removePosition

removePosition

removePositionByIndex

removeGaps

reIndexPositions

reIndexPositions

insertPosition

insertPosition

insertPosition

insertPosition

isPositionAGap

getSubSequence

getSubSequenceFrom

getSubSequenceTo

getReverse

concat

containsSubSequence

toString

toString1Letter

toString3Letter

toString1Letter

toString3Letter

toStringInfo

clone

equals

hashCode