charite.christo.strap.extensions
Class AbstractBlaster

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

All Implemented Interfaces:

CacheResult.Cacheable, ChRunnable, Disposable, HasControlPanel, SequenceBlaster, ActionListener, EventListener

Direct Known Subclasses:

AbstractBlasterHTTP, Blaster_local_Wu

public abstract class AbstractBlaster
extends Object
implements SequenceBlaster, HasControlPanel, Disposable, ActionListener, ChRunnable

Nested Class Summary

static class

AbstractBlaster.Result

Field Summary

boolean	isAAQuery
String	matrix
String	urlResultHtml

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE

Constructor Summary

AbstractBlaster()

Method Summary

void	actionPerformed(ActionEvent ev)
ChButton	butViewTxt()
ChButton	butViewXml()
void	compute() Computation is typically very time consuming
abstract AbstractBlaster.Result	computeIt()
void	dispose()
String[]	getAvailableMatrices() FIXME
String	getBlastProgram()
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.
abstract Container	getControlPanel()
String	getDatabase()
String	getMatrix()
int	getNumberOfAlignments()
String	getQuery()
String	getQuerySequence()
ByteArray	getResultXml()
boolean	isAAQuery()
boolean	isDisposed()
ChTextArea	log(Object... oo)
Object	run(String id, Object arg)
void	setAAQuerySequence(String s) This can be overridden
void	setDatabase(String s)
void	setMatrix(String mx)
void	setNTQuerySequence(String s) the nucleotide sequence query sequence
void	setNumberOfAlignments(int n) Upper Limit of the number of alignments to be shown
String	urlResultHtml()

Methods inherited from class java.lang.Object

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

Methods inherited from interface charite.christo.interfaces.SequenceBlaster

getAvailableDatabases

Field Detail

isAAQuery

public boolean isAAQuery

urlResultHtml

public String urlResultHtml

matrix

public String matrix

Constructor Detail

AbstractBlaster

public AbstractBlaster()

Method Detail

setAAQuerySequence

public void setAAQuerySequence(String s)

This can be overridden

Specified by:

setAAQuerySequence in interface SequenceBlaster

setNTQuerySequence

public void setNTQuerySequence(String s)

Description copied from interface: SequenceBlaster

the nucleotide sequence query sequence

Specified by:

setNTQuerySequence in interface SequenceBlaster

getQuerySequence

public String getQuerySequence()

Specified by:

getQuerySequence in interface SequenceBlaster

getNumberOfAlignments

public int getNumberOfAlignments()

setNumberOfAlignments

public void setNumberOfAlignments(int n)

Description copied from interface: SequenceBlaster

Upper Limit of the number of alignments to be shown

Specified by:

setNumberOfAlignments in interface SequenceBlaster

isAAQuery

public boolean isAAQuery()

getBlastProgram

public String getBlastProgram()

getQuery

public String getQuery()

getResultXml

public ByteArray getResultXml()

Specified by:

getResultXml in interface SequenceBlaster

urlResultHtml

public String urlResultHtml()

setMatrix

public void setMatrix(String mx)
               throws IllegalArgumentException

Specified by:

setMatrix in interface SequenceBlaster

Parameters:

mx - matrix is the name of a similarity matrix such as blosum62 which contains a value for each pair of amino acids

Throws:

IllegalArgumentException

getAvailableMatrices

public String[] getAvailableMatrices()

FIXME

Specified by:

getAvailableMatrices in interface SequenceBlaster

getMatrix

public String getMatrix()

Specified by:

getMatrix in interface SequenceBlaster

setDatabase

public void setDatabase(String s)
                 throws IllegalArgumentException

Specified by:

setDatabase in interface SequenceBlaster

Parameters:

s - db is the name of a database such as "uniprot", "pdb" or "uniref50"

Throws:

IllegalArgumentException

getDatabase

public String getDatabase()

Specified by:

getDatabase in interface SequenceBlaster

log

public ChTextArea log(Object... oo)

getControlPanel

public abstract Container getControlPanel()

Specified by:

getControlPanel in interface HasControlPanel

butViewXml

public ChButton butViewXml()

butViewTxt

public ChButton butViewTxt()

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

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

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

dispose

public void dispose()

Specified by:

dispose in interface Disposable

isDisposed

public boolean isDisposed()

computeIt

public abstract AbstractBlaster.Result computeIt()

compute

public final void compute()

Description copied from interface: SequenceBlaster

Computation is typically very time consuming

Specified by:

compute in interface SequenceBlaster

run

public Object run(String id,
                  Object arg)

Specified by:

run in interface ChRunnable

actionPerformed

public void actionPerformed(ActionEvent ev)

Specified by:

actionPerformed in interface ActionListener