edu.mssm.crover.tools.tm
Class HmmTopLocal

java.lang.Object
  |
  +--edu.mssm.crover.tools.tm.HmmTopLocal
All Implemented Interfaces:
TmPredictor

public class HmmTopLocal
extends java.lang.Object
implements TmPredictor

Wraps around the HMMTOP (local command interface). For details, see

  • HMMTOP web site
  • G.E Tusnády and I. Simon (1998) Principles Governing Amino Acid Composition of Integral Membrane Proteins: Applications to Topology Prediction. J. Mol. Biol. 283, 489-506. (JMB) PubMed The following properties need to be defined before this predictor can be used:
  • hmmtop.executable.path must be equivalent to HMMTOP_PATH, location where the data files are stored, together with the executables for different architecture.
  • hmmtop.executable.name Name of the executable to use on this platform. Through the use of this property, the appropriate platform executable must be selected. Scripts that redirect to a given platform cannot be used.


    Field Summary
    static boolean debug
               
    static java.lang.String DEFAULT_COMMAND_NAME
               
    static java.lang.String DEFAULT_COMMAND_PATH
               
     
    Constructor Summary
    HmmTopLocal()
              default constructor.
     
    Method Summary
     java.lang.String getDescription()
              Return a string which describes the method, its availability, etc.
     java.lang.String getReferenceURL()
              Return an URL which describe the method, its availability, etc.
     boolean installed(java.lang.String cmdPath, java.lang.String execName)
              Checks if the predictor is installed on this machine.
    static void main(java.lang.String[] args)
               
     TmDomain_Annotation parse_topology(java.lang.String topology)
               
     TmDomain_Annotation[] parse(java.io.InputStream result, int numpreds)
              Parses HmmTop short output and extracts TM annotations.
     TmDomain_Annotation predict(BiologicalSequence seq)
              Predict the trans-membrane domain of a protein sequence.
     TmDomain_Annotation[] predict(BiologicalSequence[] seqs)
              Predict the trans-membrane domains of a set of protein sequences.
     boolean useWebAccess()
              Return whether this predictor uses an HTTP connection to the prediction web service.
     
    Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
     

    Field Detail

    DEFAULT_COMMAND_PATH

    public static final java.lang.String DEFAULT_COMMAND_PATH
    See Also:
    Constant Field Values

    DEFAULT_COMMAND_NAME

    public static final java.lang.String DEFAULT_COMMAND_NAME
    See Also:
    Constant Field Values

    debug

    public static boolean debug
    Constructor Detail

    HmmTopLocal

    public HmmTopLocal()
                throws CommandNotInstalled
    default constructor. Obtain command configuration from the system properties and check that the command is installed.

    Method Detail

    parse

    public TmDomain_Annotation[] parse(java.io.InputStream result,
                                       int numpreds)
                                throws WrapperFailed
    Parses HmmTop short output and extracts TM annotations.

    Parameters:
    result - InputStream that contains the HmmTop short output to be parsed.
    numpreds - The number of predictions to be read from the result stream.
    WrapperFailed

    parse_topology

    public TmDomain_Annotation parse_topology(java.lang.String topology)
                                       throws WrapperFailed
    WrapperFailed

    predict

    public TmDomain_Annotation predict(BiologicalSequence seq)
                                throws WrapperFailed
    Predict the trans-membrane domain of a protein sequence.

    Specified by:
    predict in interface TmPredictor
    WrapperFailed

    predict

    public TmDomain_Annotation[] predict(BiologicalSequence[] seqs)
                                  throws WrapperFailed
    Predict the trans-membrane domains of a set of protein sequences.

    Specified by:
    predict in interface TmPredictor
    WrapperFailed

    installed

    public boolean installed(java.lang.String cmdPath,
                             java.lang.String execName)
    Checks if the predictor is installed on this machine.

    Returns:
    True when the predictor can be used from this machine, False otherwise.

    main

    public static void main(java.lang.String[] args)

    getReferenceURL

    public java.lang.String getReferenceURL()
    Return an URL which describe the method, its availability, etc.

    Specified by:
    getReferenceURL in interface TmPredictor

    getDescription

    public java.lang.String getDescription()
    Return a string which describes the method, its availability, etc. The description can contain the literature reference, author names, short explanation of how the method works, etc.

    Specified by:
    getDescription in interface TmPredictor

    useWebAccess

    public boolean useWebAccess()
    Return whether this predictor uses an HTTP connection to the prediction web service.

    Specified by:
    useWebAccess in interface TmPredictor
    Returns:
    True if the predictor connects to a web service through the web, false otherwise (in this case the tool must be installed locally).


    Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.