Protein

java.lang.Object
- org.mathIT.genes.Protein

All Implemented Interfaces:

Serializable
```
public class Protein
extends Object
implements Serializable
```
This class represents a protein as a sequence of amino acids. An amino acid sequence consisting of some 20 million letters requires a heap memory of about 256 MB, which can be allocated by invoking the application via
java -ms256m -mx256m org.mathIT.genes.Protein

Version:

1.0

Author:

Andreas de Vries

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description
`Protein(String name, ArrayList<Character> sequence)` Constructor of a protein with the specified name and the specified sequence of amino acids, i.e., the letters A, C, G, T (or U for an RNA protein).
`Protein(String name, char[] sequence)` Constructor of a protein with the specified name and the specified sequence of amino acids, i.e., the letters A, C, G, T (or U for an RNA protein).
`Protein(String name, CharSequence sequence)` Constructor of a protein with the specified name and the specified sequence of amino acids, i.e., the letters A, C, G, T (or U for an RNA protein).

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`asHTMLString()` Returns a string representing this protein, with line breaks encoded by "<br>" instead of '\n'.
`double`	`entropy()` Returns the entropy of the frequency distribution of the amino acids of this protein.
`protected static String`	`getAsCSVTable(Map<String,Integer> map)` Returns the specified map as a CSV data table string.
`TreeMap<String,Integer>`	`getExtremalTripletFrequencies(int highest, int lowest)` Returns the absolute frequency distribution of the amino acids triplets with the highest n_high frequencies and the lowest n_low frequencies, specified by the to parameters `highest` and `lowest`.
`TreeMap<Character,Integer>`	`getFrequencies()` Returns the absolute frequency distribution of the amino acids.
`protected String`	`getFrequenciesAsCSVTable()` Returns the frequency distribution of this protein as a CSV data table string.
`String`	`getFrequenciesAsHTMLGraph()` Returns the frequency distribution of the amino acids as HTML graph.
`static String`	`getFrequenciesAsHTMLGraph(TreeMap<String,Integer> frequencies)` Returns the frequency distribution of amino acid triplets as HTML graph.
`String`	`getFrequenciesAsHTMLGraph2()` Returns the frequency distribution of the amino acids as HTML graph in landscape format.
`String`	`getFrequenciesAsHTMLTable()` Returns the frequency distribution of the amino acids as HTML table.
`String`	`getName()` Returns the name of this protein.
`TreeMap<String,Integer>`	`getPairFrequencies()` Returns the absolute frequency distribution of the amino acid pairs.
`String`	`getPairFrequenciesAsHTMLGraph()` Returns the frequency distribution of amino acid pairs as HTML graph.
`StringBuilder`	`getSequence()` Returns the amino acid sequence of this protein.
`ArrayList<Character>`	`getSequenceAsArrayList()` Returns the amino acid sequence of this protein.
`TreeMap<String,Integer>`	`getTripletFrequencies()` Returns the absolute frequency distribution of the amino acids.
`static Protein`	`loadFASTA()` Returns a protein after opening a file in FASTA format, determined by a file chooser dialog.
`static Protein`	`loadProtein()` Returns a protein after opening a file in GNOM format, found by a file chooser dialog.
`double`	`p(char b)` Returns the probability to obtain the specified amino acid of this protein sequence.
`void`	`save()` Saves this protein in PROT format.
`void`	`saveAsCSV()` Saves this protein as CSV file.
`String`	`toString()` Returns a string representing this protein.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Protein
```
public Protein(String name,
               ArrayList<Character> sequence)
```
    Constructor of a protein with the specified name and the specified sequence of amino acids, i.e., the letters A, C, G, T (or U for an RNA protein). Also accepted are letters specified by the FASTA format, but all letters ≠ 'N' are stored as '?'
    
    Parameters:
    
    name - the name of the protein
    
    sequence - the sequence of amino acids
  - Protein
```
public Protein(String name,
               char[] sequence)
```
    Constructor of a protein with the specified name and the specified sequence of amino acids, i.e., the letters A, C, G, T (or U for an RNA protein).
    
    Parameters:
    
    name - the name of the protein
    
    sequence - the sequence of amino acids
  - Protein
```
public Protein(String name,
               CharSequence sequence)
```
    Constructor of a protein with the specified name and the specified sequence of amino acids, i.e., the letters A, C, G, T (or U for an RNA protein).
    
    Parameters:
    
    name - the name of the protein
    
    sequence - sequence of amino acids
- Method Detail
  - getName
```
public String getName()
```
    Returns the name of this protein.
    
    Returns:
    
    the name of this protein
  - getSequence
```
public StringBuilder getSequence()
```
    Returns the amino acid sequence of this protein.
    
    Returns:
    
    the amino acid sequence of this protein
  - getSequenceAsArrayList
```
public ArrayList<Character> getSequenceAsArrayList()
```
    Returns the amino acid sequence of this protein.
    
    Returns:
    
    the amino acid sequence of this protein
  - getFrequencies
```
public TreeMap<Character,Integer> getFrequencies()
```
    Returns the absolute frequency distribution of the amino acids.
    
    Returns:
    
    the frequency distribution of the amino acids
  - getPairFrequencies
```
public TreeMap<String,Integer> getPairFrequencies()
```
    Returns the absolute frequency distribution of the amino acid pairs.
    
    Returns:
    
    the frequency distribution of the amino acid pairs
  - getTripletFrequencies
```
public TreeMap<String,Integer> getTripletFrequencies()
```
    Returns the absolute frequency distribution of the amino acids.
    
    Returns:
    
    the frequency distribution of the amino acid triplets
  - getExtremalTripletFrequencies
```
public TreeMap<String,Integer> getExtremalTripletFrequencies(int highest,
                                                             int lowest)
```
    Returns the absolute frequency distribution of the amino acids triplets with the highest n_high frequencies and the lowest n_low frequencies, specified by the to parameters highest and lowest.
    
    Parameters:
    
    highest - the limit of most frequent triplets to be returned
    
    lowest - the limit of least frequent triplets to be returned
    
    Returns:
    
    the frequency distribution of the extremal amino acid triplets
  - getFrequenciesAsHTMLTable
```
public String getFrequenciesAsHTMLTable()
```
    Returns the frequency distribution of the amino acids as HTML table.
    
    Returns:
    
    an HTML string representing the frequency distribution of the amino acids
  - getFrequenciesAsCSVTable
```
protected String getFrequenciesAsCSVTable()
```
    Returns the frequency distribution of this protein as a CSV data table string. The data separator is the tabulator sign '\t'.
    
    Returns:
    
    CSV data table string
  - getAsCSVTable
```
protected static String getAsCSVTable(Map<String,Integer> map)
```
    Returns the specified map as a CSV data table string. The data separator is the tabulator sign '\t'.
    
    Parameters:
    
    map - data map
    
    Returns:
    
    CSV data table string
  - getFrequenciesAsHTMLGraph
```
public String getFrequenciesAsHTMLGraph()
```
    Returns the frequency distribution of the amino acids as HTML graph.
    
    Returns:
    
    a graphical HTML string representing the frequency distribution of the amino acids
  - getFrequenciesAsHTMLGraph2
```
public String getFrequenciesAsHTMLGraph2()
```
    Returns the frequency distribution of the amino acids as HTML graph in landscape format.
    
    Returns:
    
    a graphical HTML string in landscape format representing the frequency distribution of the amino acids
  - getPairFrequenciesAsHTMLGraph
```
public String getPairFrequenciesAsHTMLGraph()
```
    Returns the frequency distribution of amino acid pairs as HTML graph.
    
    Returns:
    
    a graphical HTML string representing the frequency distribution of amino acid pairs
  - getFrequenciesAsHTMLGraph
```
public static String getFrequenciesAsHTMLGraph(TreeMap<String,Integer> frequencies)
```
    Returns the frequency distribution of amino acid triplets as HTML graph.
    
    Parameters:
    
    frequencies - frequency distribution
    
    Returns:
    
    a graphical HTML string representing the frequency distribution of the amino acid triplets
  - p
```
public double p(char b)
```
    Returns the probability to obtain the specified amino acid of this protein sequence.
    
    Parameters:
    
    b - the specified amino acid
    
    Returns:
    
    the probability of the amino acid of this protein
  - entropy
```
public double entropy()
```
    Returns the entropy of the frequency distribution of the amino acids of this protein. The entropy is computed to the basis 2, i.e., H = - ∑ p_i log₂p_i.
    
    Returns:
    
    the entropy of the frequency distribution of this protein
  - asHTMLString
```
public String asHTMLString()
```
    Returns a string representing this protein, with line breaks encoded by "<br>" instead of '\n'.
    
    Returns:
    
    an HTML string representing this protein
  - toString
```
public String toString()
```
    Returns a string representing this protein.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    a string representing this protein
  - loadFASTA
```
public static Protein loadFASTA()
```
    Returns a protein after opening a file in FASTA format, determined by a file chooser dialog.
    
    Returns:
    
    a protein determined by the FASTA file, or null if no file is selected
  - save
```
public void save()
```
    Saves this protein in PROT format.
  - saveAsCSV
```
public void saveAsCSV()
```
    Saves this protein as CSV file.
  - loadProtein
```
public static Protein loadProtein()
```
    Returns a protein after opening a file in GNOM format, found by a file chooser dialog.
    
    Returns:
    
    a protein determined by the GNOM file, or null if no file is selected

Class Protein

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Protein

Protein

Protein

Method Detail

getName

getSequence

getSequenceAsArrayList

getFrequencies

getPairFrequencies

getTripletFrequencies

getExtremalTripletFrequencies

getFrequenciesAsHTMLTable

getFrequenciesAsCSVTable

getAsCSVTable

getFrequenciesAsHTMLGraph

getFrequenciesAsHTMLGraph2

getPairFrequenciesAsHTMLGraph

getFrequenciesAsHTMLGraph

p

entropy

asHTMLString

toString

loadFASTA

save

saveAsCSV

loadProtein