org.biojava.bio.proteomics.aaindex

Class AAindex

java.lang.Object

org.biojava.bio.symbol.SimpleSymbolPropertyTable

org.biojava.bio.proteomics.aaindex.AAindex

All Implemented Interfaces:

SymbolPropertyTable

public class AAindex
extends SimpleSymbolPropertyTable

Symbol property table based on the Amino Acid Index Database. Each AAindex object represents a single entry of an AAindex1 file. Each entry contains twenty numeric values for the twenty amino acids, e.g. describing the hydrophobicity of an amino acid. To get this value for a certain amino acid call the SymbolPropertyTable.getDoubleValue(org.biojava.bio.symbol.Symbol) method with the appropriate symbol, e.g. aaindex.getDoubleValue(ProteinTools.gln()). The remaining data fields, i.e. object properties, are fully described in the AAindex manual .

References:

AAindex web site.

Kawashima, S. and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 28, 374 (2000).

Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996).

Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2, 93-100 (1988)

Version:

$Revision$

Author:

Martin Szugat

Field Summary

Fields

Modifier and Type	Field and Description
static Alphabet	PROTEIN_ALPHABET The alphabet of the symbol property table, that is protein.

Fields inherited from interface org.biojava.bio.symbol.SymbolPropertyTable

AVG_MASS, HYDROPATHICITY, MONO_MASS, PK, PK_Cterm, PK_Nterm

Constructor Summary

Constructors

Constructor and Description
AAindex(String accessionNumber) Initializes the AAindex symbol property table.

Method Summary

Methods

Modifier and Type	Method and Description
String	accessionNumber() Gets the accession number of the AAindex entry.
String	getArticleAuthors() Gets the names of the authors which first published an article about the AAindex entry.
String	getArticleTitle() Gets the title of the article which describes the AAindex entry.
String	getComment() Gets the user comment for the AAindex entry.
String	getDescription() Gets the description for the AAindex entry.
String	getJournalReference() Gets a reference to the journal which published the article about the AAindex entry.
String[]	getLITDBEntryNumbers() Gets the list of literature database identifiers for the AAindex entry.
void	setArticleAuthors(String articleAuthors) Sets the names of the authors which first published an article about the AAindex entry.
void	setArticleTitle(String articleTitle) Sets the title of the article which describes the AAindex entry.
void	setComment(String comment) Sets the user comment for the AAindex entry.
void	setDescription(String description) Sets the description for the AAindex entry.
void	setJournalReference(String journalReference) Sets a reference to the journal which published the article about the AAindex entry.
void	setLITDBEntryNumbers(String[] litdbEntryNumbers) Sets the list of literature database identifiers for the AAindex entry.
Map	similarEntries() Returns a map with the names of similar AAindex entries and its correlation coefficients.

Methods inherited from class org.biojava.bio.symbol.SimpleSymbolPropertyTable

getAlphabet, getDoubleValue, getName, setDoubleProperty

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PROTEIN_ALPHABET

public static final Alphabet PROTEIN_ALPHABET

The alphabet of the symbol property table, that is protein.

Constructor Detail

AAindex

public AAindex(String accessionNumber)
        throws NullPointerException

Initializes the AAindex symbol property table.

Parameters:

accessionNumber - the AAindex accession number (same as the table name)

Throws:

NullPointerException - if accessionNumber is null.

Method Detail

accessionNumber

public String accessionNumber()

Gets the accession number of the AAindex entry.

Returns:

the accession number (same as SymbolPropertyTable.getName()

getArticleAuthors

public String getArticleAuthors()

Gets the names of the authors which first published an article about the AAindex entry.

Returns:

a list of names. May be null.

setArticleAuthors

public void setArticleAuthors(String articleAuthors)

Sets the names of the authors which first published an article about the AAindex entry.

Parameters:

articleAuthors - May be null.

getComment

public String getComment()

Gets the user comment for the AAindex entry.

Returns:

free text. May be null.

setComment

public void setComment(String comment)

Sets the user comment for the AAindex entry.

Parameters:

comment - free text. May be null.

getArticleTitle

public String getArticleTitle()

Gets the title of the article which describes the AAindex entry.

Returns:

the article title. May be null.

setArticleTitle

public void setArticleTitle(String articleTitle)

Sets the title of the article which describes the AAindex entry.

Parameters:

articleTitle - the article title. May be null.

getDescription

public String getDescription()

Gets the description for the AAindex entry.

Returns:

a human readable description. May be null.

setDescription

public void setDescription(String description)

Sets the description for the AAindex entry.

Parameters:

description - a human readable description. May be null.

getJournalReference

public String getJournalReference()

Gets a reference to the journal which published the article about the AAindex entry.

Returns:

the journal reference. May be null.

setJournalReference

public void setJournalReference(String journalReference)

Sets a reference to the journal which published the article about the AAindex entry.

Parameters:

journalReference - the journal reference. May be null.

getLITDBEntryNumbers

public String[] getLITDBEntryNumbers()

Gets the list of literature database identifiers for the AAindex entry.

Returns:

a list of identifiers. May be null.

setLITDBEntryNumbers

public void setLITDBEntryNumbers(String[] litdbEntryNumbers)

Sets the list of literature database identifiers for the AAindex entry.

Parameters:

litdbEntryNumbers - a list of identifiers

similarEntries

public Map similarEntries()

Returns a map with the names of similar AAindex entries and its correlation coefficients.

Returns:

a map which keys are the names of the similar AAindex entries and which values are the corresponding correlation coefficients