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 Summary

      Constructors 
      Constructor Description
      AAindex​(java.lang.String accessionNumber)
      Initializes the AAindex symbol property table.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method 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.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • AAindex

        public AAindex​(java.lang.String accessionNumber)
                throws java.lang.NullPointerException
        Initializes the AAindex symbol property table.
        Parameters:
        accessionNumber - the AAindex accession number (same as the table name)
        Throws:
        java.lang.NullPointerException - if accessionNumber is null.
    • Method Detail

      • getArticleAuthors

        public java.lang.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​(java.lang.String articleAuthors)
        Sets the names of the authors which first published an article about the AAindex entry.
        Parameters:
        articleAuthors - May be null.
      • getComment

        public java.lang.String getComment()
        Gets the user comment for the AAindex entry.
        Returns:
        free text. May be null.
      • setComment

        public void setComment​(java.lang.String comment)
        Sets the user comment for the AAindex entry.
        Parameters:
        comment - free text. May be null.
      • getArticleTitle

        public java.lang.String getArticleTitle()
        Gets the title of the article which describes the AAindex entry.
        Returns:
        the article title. May be null.
      • setArticleTitle

        public void setArticleTitle​(java.lang.String articleTitle)
        Sets the title of the article which describes the AAindex entry.
        Parameters:
        articleTitle - the article title. May be null.
      • getDescription

        public java.lang.String getDescription()
        Gets the description for the AAindex entry.
        Returns:
        a human readable description. May be null.
      • setDescription

        public void setDescription​(java.lang.String description)
        Sets the description for the AAindex entry.
        Parameters:
        description - a human readable description. May be null.
      • getJournalReference

        public java.lang.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​(java.lang.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 java.lang.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​(java.lang.String[] litdbEntryNumbers)
        Sets the list of literature database identifiers for the AAindex entry.
        Parameters:
        litdbEntryNumbers - a list of identifiers
      • similarEntries

        public java.util.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