charite.christo.blast
Class AbstractBlaster

java.lang.Object
  charite.christo.blast.AbstractBlaster

All Implemented Interfaces:

SequenceBlaster, Disposable, HasControlPanel, java.awt.event.ActionListener, java.util.EventListener

Direct Known Subclasses:

Blaster_local_Wu, Blaster_SOAP_ebi

public abstract class AbstractBlaster
extends java.lang.Object
implements SequenceBlaster, HasControlPanel, Disposable, java.awt.event.ActionListener

Field Summary

static java.util.Map<java.lang.Class,java.lang.String[][]>	_mapDB
static int	BUT_IN_BROWSER
static int	BUT_TXT
static int	BUT_TXTe
static int	BUT_XML
static int	BUT_XMLb
ChButton[]	button

Fields inherited from interface charite.christo.blast.SequenceBlaster

DATABASES_FULL_LIST, DATABASES_NUCLEOTIDES

Fields inherited from interface charite.christo.Disposable

NONE

Constructor Summary

AbstractBlaster()

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
ChButton	button(int type)
void	cachedResultsNotOlderThanSec(int time) Use cached results only when new
java.lang.String	cacheSK(char type)
void	compute() Computation is typically very time consuming
abstract BA	computeIt()
void	defineParameters(long opt, java.lang.String s)
void	dispose()
void	enableDisable()
java.lang.String[]	getAvailableDatabases(int options)
abstract java.lang.String[]	getAvailableDBs(int opt)
java.lang.String[]	getAvailableMatrices() FIXME
java.lang.String	getBlastProgram()
javax.swing.JComponent	getControlPanel(boolean real)
java.lang.String	getDatabase()
java.lang.String	getMatrix()
int	getNumberOfAlignments()
PrgParas	getPrgParas()
java.lang.String	getQuery()
java.lang.String	getQuerySequence()
BA	getResultXml()
int	getSensitivity()
java.lang.Object	getSharedInstance()
boolean	isAAQuery()
boolean	isDisposed()
BA	log()
void	setAAQuerySequence(java.lang.String s) set the amino acid sequence query
void	setDatabase(java.lang.String s)
void	setMatrix(java.lang.String mx)
void	setNTQuerySequence(java.lang.String s) the nucleotide sequence query sequence
void	setNumberOfAlignments(int n) Upper Limit of the number of alignments to be shown
void	setSensitivity(int n)
void	setSharedInstance(java.lang.Object shared)
void	setUrlResultHtml(java.lang.String url)
void	skipDatabases(java.lang.String[] skip, java.lang.String[] notSkip)

Methods inherited from class java.lang.Object

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

Field Detail

BUT_XML

public static final int BUT_XML

See Also:

Constant Field Values

BUT_XMLb

public static final int BUT_XMLb

See Also:

Constant Field Values

BUT_TXT

public static final int BUT_TXT

See Also:

Constant Field Values

BUT_TXTe

public static final int BUT_TXTe

See Also:

Constant Field Values

BUT_IN_BROWSER

public static final int BUT_IN_BROWSER

See Also:

Constant Field Values

button

public final ChButton[] button

_mapDB

public static final java.util.Map<java.lang.Class,java.lang.String[][]> _mapDB

Constructor Detail

AbstractBlaster

public AbstractBlaster()

Method Detail

setSensitivity

public void setSensitivity(int n)

Specified by:

setSensitivity in interface SequenceBlaster

setAAQuerySequence

public void setAAQuerySequence(java.lang.String s)

Description copied from interface: SequenceBlaster

set the amino acid sequence query

Specified by:

setAAQuerySequence in interface SequenceBlaster

setNTQuerySequence

public void setNTQuerySequence(java.lang.String s)

Description copied from interface: SequenceBlaster

the nucleotide sequence query sequence

Specified by:

setNTQuerySequence in interface SequenceBlaster

getQuerySequence

public java.lang.String getQuerySequence()

getSensitivity

public int getSensitivity()

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 java.lang.String getBlastProgram()

getQuery

public java.lang.String getQuery()

getResultXml

public BA getResultXml()

Specified by:

getResultXml in interface SequenceBlaster

setUrlResultHtml

public void setUrlResultHtml(java.lang.String url)

setMatrix

public void setMatrix(java.lang.String mx)
               throws java.lang.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:

java.lang.IllegalArgumentException

getAvailableMatrices

public java.lang.String[] getAvailableMatrices()

FIXME

Specified by:

getAvailableMatrices in interface SequenceBlaster

getMatrix

public java.lang.String getMatrix()

Specified by:

getMatrix in interface SequenceBlaster

setDatabase

public void setDatabase(java.lang.String s)

Specified by:

setDatabase in interface SequenceBlaster

Parameters:

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

getDatabase

public java.lang.String getDatabase()

Specified by:

getDatabase in interface SequenceBlaster

log

public final BA log()

getControlPanel

public javax.swing.JComponent getControlPanel(boolean real)

Specified by:

getControlPanel in interface HasControlPanel

button

public ChButton button(int type)

getPrgParas

public final PrgParas getPrgParas()

setSharedInstance

public final void setSharedInstance(java.lang.Object shared)

getSharedInstance

public final java.lang.Object getSharedInstance()

defineParameters

public void defineParameters(long opt,
                             java.lang.String s)

cacheSK

public java.lang.String cacheSK(char type)

cachedResultsNotOlderThanSec

public void cachedResultsNotOlderThanSec(int time)

Description copied from interface: SequenceBlaster

Use cached results only when new

Specified by:

cachedResultsNotOlderThanSec in interface SequenceBlaster

dispose

public void dispose()

Specified by:

dispose in interface Disposable

isDisposed

public boolean isDisposed()

computeIt

public abstract BA computeIt()

compute

public final void compute()

Description copied from interface: SequenceBlaster

Computation is typically very time consuming

Specified by:

compute in interface SequenceBlaster

enableDisable

public void enableDisable()

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ev)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

skipDatabases

public void skipDatabases(java.lang.String[] skip,
                          java.lang.String[] notSkip)

getAvailableDBs

public abstract java.lang.String[] getAvailableDBs(int opt)

getAvailableDatabases

public java.lang.String[] getAvailableDatabases(int options)

Specified by:

getAvailableDatabases in interface SequenceBlaster