Class AAindex
java.lang.Object
org.biojava.bio.symbol.SimpleSymbolPropertyTable
org.biojava.bio.proteomics.aaindex.AAindex
- All Implemented Interfaces:
SymbolPropertyTable
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:
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
FieldsModifier and TypeFieldDescriptionstatic final 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 -
Method Summary
Modifier and TypeMethodDescriptionGets the accession number of the AAindex entry.Gets the names of the authors which first published an article about the AAindex entry.Gets the title of the article which describes the AAindex entry.Gets the user comment for the AAindex entry.Gets the description for the AAindex entry.Gets a reference to the journal which published the article about the AAindex entry.String[]
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.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
-
Field Details
-
PROTEIN_ALPHABET
The alphabet of the symbol property table, that is protein.
-
-
Constructor Details
-
AAindex
Initializes the AAindex symbol property table.- Parameters:
accessionNumber
- the AAindex accession number (same as the table name)- Throws:
NullPointerException
- ifaccessionNumber
isnull
.
-
-
Method Details
-
accessionNumber
Gets the accession number of the AAindex entry.- Returns:
- the accession number (same as
SymbolPropertyTable.getName()
-
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
Sets the names of the authors which first published an article about the AAindex entry.- Parameters:
articleAuthors
- May benull
.
-
getComment
Gets the user comment for the AAindex entry.- Returns:
- free text. May be
null
.
-
setComment
Sets the user comment for the AAindex entry.- Parameters:
comment
- free text. May benull
.
-
getArticleTitle
Gets the title of the article which describes the AAindex entry.- Returns:
- the article title. May be
null
.
-
setArticleTitle
Sets the title of the article which describes the AAindex entry.- Parameters:
articleTitle
- the article title. May benull
.
-
getDescription
Gets the description for the AAindex entry.- Returns:
- a human readable description. May be
null
.
-
setDescription
Sets the description for the AAindex entry.- Parameters:
description
- a human readable description. May benull
.
-
getJournalReference
Gets a reference to the journal which published the article about the AAindex entry.- Returns:
- the journal reference. May be
null
.
-
setJournalReference
Sets a reference to the journal which published the article about the AAindex entry.- Parameters:
journalReference
- the journal reference. May benull
.
-
getLITDBEntryNumbers
Gets the list of literature database identifiers for the AAindex entry.- Returns:
- a list of identifiers. May be
null
.
-
setLITDBEntryNumbers
Sets the list of literature database identifiers for the AAindex entry.- Parameters:
litdbEntryNumbers
- a list of identifiers
-
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
-