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 Details

  • Constructor Details

    • 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 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

      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

      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

      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

      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

      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