|
'STRAP:multiple sequence alignments ' | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object charite.christo.blast.AbstractBlaster
public abstract class AbstractBlaster
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 |
---|
public static final int BUT_XML
public static final int BUT_XMLb
public static final int BUT_TXT
public static final int BUT_TXTe
public static final int BUT_IN_BROWSER
public final ChButton[] button
public static final java.util.Map<java.lang.Class,java.lang.String[][]> _mapDB
Constructor Detail |
---|
public AbstractBlaster()
Method Detail |
---|
public void setSensitivity(int n)
setSensitivity
in interface SequenceBlaster
public void setAAQuerySequence(java.lang.String s)
SequenceBlaster
setAAQuerySequence
in interface SequenceBlaster
public void setNTQuerySequence(java.lang.String s)
SequenceBlaster
setNTQuerySequence
in interface SequenceBlaster
public java.lang.String getQuerySequence()
public int getSensitivity()
public int getNumberOfAlignments()
public void setNumberOfAlignments(int n)
SequenceBlaster
setNumberOfAlignments
in interface SequenceBlaster
public boolean isAAQuery()
public java.lang.String getBlastProgram()
public java.lang.String getQuery()
public BA getResultXml()
getResultXml
in interface SequenceBlaster
public void setUrlResultHtml(java.lang.String url)
public void setMatrix(java.lang.String mx) throws java.lang.IllegalArgumentException
setMatrix
in interface SequenceBlaster
mx
- matrix is the name of a similarity matrix such as blosum62
which contains a value for each pair of amino acids
java.lang.IllegalArgumentException
public java.lang.String[] getAvailableMatrices()
getAvailableMatrices
in interface SequenceBlaster
public java.lang.String getMatrix()
getMatrix
in interface SequenceBlaster
public void setDatabase(java.lang.String s)
setDatabase
in interface SequenceBlaster
s
- db is the name of a database such as "uniprot", "pdb" or "uniref50"public java.lang.String getDatabase()
getDatabase
in interface SequenceBlaster
public final BA log()
public javax.swing.JComponent getControlPanel(boolean real)
getControlPanel
in interface HasControlPanel
public ChButton button(int type)
public final PrgParas getPrgParas()
public final void setSharedInstance(java.lang.Object shared)
public final java.lang.Object getSharedInstance()
public void defineParameters(long opt, java.lang.String s)
public java.lang.String cacheSK(char type)
public void cachedResultsNotOlderThanSec(int time)
SequenceBlaster
cachedResultsNotOlderThanSec
in interface SequenceBlaster
public void dispose()
dispose
in interface Disposable
public boolean isDisposed()
public abstract BA computeIt()
public final void compute()
SequenceBlaster
compute
in interface SequenceBlaster
public void enableDisable()
public void actionPerformed(java.awt.event.ActionEvent ev)
actionPerformed
in interface java.awt.event.ActionListener
public void skipDatabases(java.lang.String[] skip, java.lang.String[] notSkip)
public abstract java.lang.String[] getAvailableDBs(int opt)
public java.lang.String[] getAvailableDatabases(int options)
getAvailableDatabases
in interface SequenceBlaster
|
'STRAP:multiple sequence alignments ' | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |