charite.christo.protein
Class AbstractPredictionFromAminoacidSequence

java.lang.Object
  charite.christo.protein.AbstractPredictionFromAminoacidSequence

All Implemented Interfaces:

Disposable, PredictionFromAminoacidSequence

Direct Known Subclasses:

SecondaryStructure_NNPREDICT, SecondaryStructure_Sopma, TransmembraneHelix_DAS, TransmembraneHelix_HMMTOP, TransmembraneHelix_MEMSAT, TransmembraneHelix_ORIENTM, TransmembraneHelix_Phobius, TransmembraneHelix_PRED_TMR, TransmembraneHelix_SOSUI, TransmembraneHelix_SPLIT3, TransmembraneHelix_SPLIT4, TransmembraneHelix_THUMBUP, TransmembraneHelix_TMAP, TransmembraneHelix_TMHMM2, TransmembraneHelix_TMPRED, TransmembraneHelix_WaveTM

public abstract class AbstractPredictionFromAminoacidSequence
extends java.lang.Object
implements PredictionFromAminoacidSequence, Disposable

Field Summary

Fields inherited from interface charite.christo.Disposable

NONE

Constructor Summary

AbstractPredictionFromAminoacidSequence()

Method Summary

void	compute() Computation is started and may take long time.
abstract char[]	compute(java.lang.String sequ)
int	countResults()
void	dispose()
java.lang.String	findUrlInText(java.lang.String txt)
javax.swing.JComponent	getControlPanel(boolean real)
char[][]	getPrediction() Returns a character for each sequence position.
BA	getResultText(java.lang.String sequence, java.lang.String SERVER, java.lang.Object[][] postData, boolean indirect)
java.lang.Object	getSharedInstance()
java.lang.String	getUrlOfResult()
java.lang.String	serverRoot()
void	setGappedSequences(java.lang.String[] ss) set the sequences.
void	setSharedInstance(java.lang.Object shared)

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractPredictionFromAminoacidSequence

public AbstractPredictionFromAminoacidSequence()

Method Detail

countResults

public int countResults()

getControlPanel

public javax.swing.JComponent getControlPanel(boolean real)

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

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

compute

public abstract char[] compute(java.lang.String sequ)

findUrlInText

public java.lang.String findUrlInText(java.lang.String txt)

serverRoot

public java.lang.String serverRoot()

getResultText

public BA getResultText(java.lang.String sequence,
                        java.lang.String SERVER,
                        java.lang.Object[][] postData,
                        boolean indirect)

getUrlOfResult

public java.lang.String getUrlOfResult()

setSharedInstance

public void setSharedInstance(java.lang.Object shared)

getSharedInstance

public java.lang.Object getSharedInstance()