charite.christo.strap.extensions
Class SecondaryStructure_Jnet

java.lang.Object
  charite.christo.BasicExecutable
      charite.christo.strap.extensions.SecondaryStructure_Jnet

All Implemented Interfaces:

CanBeStopped, ChRunnable, Disposable, HasControlPanel, PredictionFromAminoacidSequence, SecondaryStructure_Predictor

public class SecondaryStructure_Jnet
extends BasicExecutable
implements SecondaryStructure_Predictor

Web: HOME_PAGE:SecondaryStructure_Jnet
Author: James Cuff and Geoff Barton
Publication: PUBMED:10861942
Download: http://www.compbio.dundee.ac.uk/~www-jpred/jnet/download.html
The following modification was necessary for Windows:

• jnet.h "#define MAXSEQNUM 600" changed to "#define MAXSEQNUM 60";

Field Summary

java.lang.String[]

sequences

Fields inherited from class charite.christo.BasicExecutable

DEFAULT_BINARY, PFX_ADD_INCLUDE_LIMITS, PFX_DPKG, PFX_FIX_INCLUDE, REPLACEME_INLCUDE_STRING, RPLC_WIN_DOT_EXE

Fields inherited from interface charite.christo.CanBeStopped

vALIGNMENTS

Fields inherited from interface charite.christo.Disposable

NONE

Fields inherited from interface charite.christo.ChRunnable

APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT

Constructor Summary

SecondaryStructure_Jnet()

Method Summary

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

Methods inherited from class charite.christo.BasicExecutable

checkForUpdates, defineParameters, dirBinaries, dirTemp, dispose, exec, exec, failedToLaunch, fileExecutable, fileIn, fileOut, getControlPanel, getName, getPrgParas, getSharedInstance, init, initExecutable, installBioPerl, installPackage, isBioPerlInstalled, isPerlInstalled, isStopped, msgInstallCompilers, perlCommand, run, setBinaryPackageURLs, setFileExecutable, setName, setSharedInstance, setSourceInstallationScript, setSourcePackageURLs, stop, toString

Methods inherited from class java.lang.Object

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

Field Detail

sequences

public java.lang.String[] sequences

Constructor Detail

SecondaryStructure_Jnet

public SecondaryStructure_Jnet()

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

compute

public void compute()

Description copied from interface: PredictionFromAminoacidSequence

Computation is started and may take long time.

Specified by:

compute in interface PredictionFromAminoacidSequence