charite.christo.strap.extensions
Class TransmembraneHelix_TOPPRED

java.lang.Object
  charite.christo.strap.extensions.TransmembraneHelix_TOPPRED

All Implemented Interfaces:

Disposable, HasNativeExec, PredictionFromAminoacidSequence, TransmembraneHelix_Predictor

public class TransmembraneHelix_TOPPRED
extends java.lang.Object
implements TransmembraneHelix_Predictor, HasNativeExec, Disposable

HELP Web site: HOME_PAGE:Toppred",
Publication: PUBMED:7704669
Authors: von Heijne, Claros, Deveaud and Schuerer
SEE_CLASS:ResidueHydrophobicity_TOPPRED

Field Summary

java.lang.String[]	sequences
Toppred	toppred

Fields inherited from interface charite.christo.Disposable

NONE

Constructor Summary

TransmembraneHelix_TOPPRED()

Method Summary

void	compute() Computation is started and may take long time.
void	dispose()
BasicExecutable	getNativeExec(boolean createNew)
char[][]	getPrediction() Returns a character for each sequence position.
void	setGappedSequences(java.lang.String[] ss) set the sequences.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

sequences

public java.lang.String[] sequences

toppred

public final Toppred toppred

Constructor Detail

TransmembraneHelix_TOPPRED

public TransmembraneHelix_TOPPRED()

Method Detail

setGappedSequences

public void setGappedSequences(java.lang.String[] ss)

Description copied from interface: PredictionFromAminoacidSequence

set the sequences. Since some prediction methods take an alignment as input we pass several sequences that might be aligned. For example a secondary structure predictore might compute refine the prediction using multiple sequences

Specified by:

setGappedSequences in interface PredictionFromAminoacidSequence

getPrediction

public char[][] getPrediction()

Description copied from interface: PredictionFromAminoacidSequence

Returns a character for each sequence position. For example 'H' for Helix..

Specified by:

getPrediction in interface PredictionFromAminoacidSequence

getNativeExec

public BasicExecutable getNativeExec(boolean createNew)

Specified by:

getNativeExec in interface HasNativeExec

dispose

public void dispose()

Specified by:

dispose in interface Disposable

compute

public void compute()

Description copied from interface: PredictionFromAminoacidSequence

Computation is started and may take long time.

Specified by:

compute in interface PredictionFromAminoacidSequence