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).