Package org.biojava.bio.proteomics.aaindex

Class 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

    • 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

      • 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