charite.christo.interfaces
Class AbstractPredictionFromAminoacidSequence

java.lang.Object
  charite.christo.interfaces.AbstractPredictionFromAminoacidSequence

All Implemented Interfaces:

CacheResult.Cacheable, 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 Object
implements PredictionFromAminoacidSequence, CacheResult.Cacheable, Disposable

Field Summary

Container	controlPanel
boolean	disposed
char[][]	prediction
int	resultNumber
String[]	sequences

Constructor Summary

AbstractPredictionFromAminoacidSequence()

Method Summary

void	compute() Computation is started and may take long time.
abstract char[]	compute(String sequ)
int	countResults()
void	dispose()
String	findUrlInText(String txt)
Class	getCacheClass() The class name determins the directory on HD
String	getCacheKey() Several values are stored in one and the same file on HD to avoid making too many files.
String	getCacheSection() The class determines a parent directory to save the files.
Container	getControlPanel()
ByteArray	getIndirectResult(String SERVER, Object[][] postData)
char[][]	getPrediction() Returns a character for each sequence position.
ByteArray	getResult(String SERVER, Object[][] postData)
int	getResultNumber()
String	getUrlOfResult()
void	log(Object... oo)
String	serverRoot()
void	setGappedSequences(String[] ss) set the sequences.
void	setResultNumber(int resNr)

Methods inherited from class java.lang.Object

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

Field Detail

resultNumber

public int resultNumber

sequences

public String[] sequences

prediction

public char[][] prediction

controlPanel

public Container controlPanel

disposed

public boolean disposed

Constructor Detail

AbstractPredictionFromAminoacidSequence

public AbstractPredictionFromAminoacidSequence()

Method Detail

setResultNumber

public void setResultNumber(int resNr)

getResultNumber

public int getResultNumber()

countResults

public int countResults()

getControlPanel

public Container getControlPanel()

setGappedSequences

public void setGappedSequences(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

log

public void log(Object... oo)

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

getCacheSection

public String getCacheSection()

Description copied from interface: CacheResult.Cacheable

The class determines a parent directory to save the files.

Specified by:

getCacheSection in interface CacheResult.Cacheable

getCacheKey

public String getCacheKey()

Description copied from interface: CacheResult.Cacheable

Several values are stored in one and the same file on HD to avoid making too many files. The file name is made from this String.

Specified by:

getCacheKey in interface CacheResult.Cacheable

getCacheClass

public Class getCacheClass()

Description copied from interface: CacheResult.Cacheable

The class name determins the directory on HD

Specified by:

getCacheClass in interface CacheResult.Cacheable

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(String sequ)

getResult

public ByteArray getResult(String SERVER,
                           Object[][] postData)

findUrlInText

public String findUrlInText(String txt)

serverRoot

public String serverRoot()

getIndirectResult

public ByteArray getIndirectResult(String SERVER,
                                   Object[][] postData)

getUrlOfResult

public String getUrlOfResult()