public class AAindex extends SimpleSymbolPropertyTable
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)
Modifier and Type | Field and Description |
---|---|
static Alphabet |
PROTEIN_ALPHABET
The alphabet of the symbol property table, that is
protein.
|
AVG_MASS, HYDROPATHICITY, MONO_MASS, PK, PK_Cterm, PK_Nterm
Constructor and Description |
---|
AAindex(java.lang.String accessionNumber)
Initializes the AAindex symbol property table.
|
Modifier and Type | Method and Description |
---|---|
java.lang.String |
accessionNumber()
Gets the accession number of the AAindex entry.
|
java.lang.String |
getArticleAuthors()
Gets the names of the authors which first published an article about the
AAindex entry.
|
java.lang.String |
getArticleTitle()
Gets the title of the article which describes the AAindex entry.
|
java.lang.String |
getComment()
Gets the user comment for the AAindex entry.
|
java.lang.String |
getDescription()
Gets the description for the AAindex entry.
|
java.lang.String |
getJournalReference()
Gets a reference to the journal which published the article about the
AAindex entry.
|
java.lang.String[] |
getLITDBEntryNumbers()
Gets the list of literature database identifiers for the AAindex entry.
|
void |
setArticleAuthors(java.lang.String articleAuthors)
Sets the names of the authors which first published an article about the
AAindex entry.
|
void |
setArticleTitle(java.lang.String articleTitle)
Sets the title of the article which describes the AAindex entry.
|
void |
setComment(java.lang.String comment)
Sets the user comment for the AAindex entry.
|
void |
setDescription(java.lang.String description)
Sets the description for the AAindex entry.
|
void |
setJournalReference(java.lang.String journalReference)
Sets a reference to the journal which published the article about the
AAindex entry.
|
void |
setLITDBEntryNumbers(java.lang.String[] litdbEntryNumbers)
Sets the list of literature database identifiers for the AAindex entry.
|
java.util.Map |
similarEntries()
Returns a map with the names of similar AAindex entries and its
correlation coefficients.
|
getAlphabet, getDoubleValue, getName, setDoubleProperty
public AAindex(java.lang.String accessionNumber) throws java.lang.NullPointerException
accessionNumber
- the AAindex accession number (same as the table
name)java.lang.NullPointerException
- if accessionNumber
is
null
.public java.lang.String accessionNumber()
SymbolPropertyTable.getName()
public java.lang.String getArticleAuthors()
null
.public void setArticleAuthors(java.lang.String articleAuthors)
articleAuthors
- May be null
.public java.lang.String getComment()
null
.public void setComment(java.lang.String comment)
comment
- free text. May be null
.public java.lang.String getArticleTitle()
null
.public void setArticleTitle(java.lang.String articleTitle)
articleTitle
- the article title. May be null
.public java.lang.String getDescription()
null
.public void setDescription(java.lang.String description)
description
- a human readable description.
May be null
.public java.lang.String getJournalReference()
null
.public void setJournalReference(java.lang.String journalReference)
journalReference
- the journal reference. May be null
.public java.lang.String[] getLITDBEntryNumbers()
null
.public void setLITDBEntryNumbers(java.lang.String[] litdbEntryNumbers)
litdbEntryNumbers
- a list of identifierspublic java.util.Map similarEntries()