org.sigpath.task
Class TSearchMolecules

java.lang.Object
  org.sigpath.task.DBTask
      org.sigpath.task.TSearchMolecules

All Implemented Interfaces:

ITSearchTask, Task

public class TSearchMolecules
extends DBTask
implements ITSearchTask

Performs a molecule search based on search criteria, including: keyword, category, and organism.

Author:

Ethan Cerami

Field Summary

static String	AC_TARGET
static String	ALL_TARGET
static String	SPID_TARGET

Fields inherited from class org.sigpath.task.DBTask

dbManager, embeddedTask, entityManager, errors, ftsm, progressListener, sigpathFactory, unitManager, userManager, xdebug

Constructor Summary

TSearchMolecules(String keyword, String category, String organism, int startIndex)
Constructor

Method Summary

protected void	_execute() Perform Molecule Search
List	getCurrentList() Get List of Results
FTSManagerMeasurements	getFTSManagerMeasurements() Get Measurements of he last execution.
Collection	getRelatedKeywords() Get Related Keywords
int	getTotalNumResults() Get Total Number of Results
void	setRecordNumber(int recnum) Sets the maximum number of elements retrieved in one bunch.
void	setResults(ArrayList list) set List of Results
void	setStartIndex(int index) sets the start index.

Methods inherited from class org.sigpath.task.DBTask

close, delete, execute, getDbManager, getErrors, isEmbeddedTask, isTaskThrewException, reindex, resolve, setDbManager, setEmbeddedTask, setEmbeddedTask, setObtainTransactionsFrom, setProgressListener, setTaskThrewException

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.sigpath.task.Task

execute

Field Detail

SPID_TARGET

public static final String SPID_TARGET

See Also:

Constant Field Values

AC_TARGET

public static final String AC_TARGET

See Also:

Constant Field Values

ALL_TARGET

public static final String ALL_TARGET

See Also:

Constant Field Values

Constructor Detail

TSearchMolecules

public TSearchMolecules(String keyword,
                        String category,
                        String organism,
                        int startIndex)

Constructor

Parameters:

keyword - Search Keyword

category - Molecule Category, e.g. "small_molecules", "proteins", "complexes"

organism - Organism String, e.g. "Human", "all"

startIndex - startIndex for retrieved list of results

Method Detail

getFTSManagerMeasurements

public FTSManagerMeasurements getFTSManagerMeasurements()

Get Measurements of he last execution.

Returns:

filled FTSManagerMeasurements object

getCurrentList

public List getCurrentList()

Get List of Results

Specified by:

getCurrentList in interface ITSearchTask

Returns:

List of SigPathEntityBeans

setResults

public void setResults(ArrayList list)

set List of Results

Specified by:

setResults in interface ITSearchTask

getTotalNumResults

public int getTotalNumResults()

Get Total Number of Results

Specified by:

getTotalNumResults in interface ITSearchTask

getRelatedKeywords

public Collection getRelatedKeywords()

Get Related Keywords

setRecordNumber

public void setRecordNumber(int recnum)

Sets the maximum number of elements retrieved in one bunch. The default is the value stored in PagedCollection.RESULTS_PER_PAGE; Call this methode before execute().

Parameters:

recnum - the number of elements you want to retrieve

_execute

protected void _execute()
                 throws SigPathDatabaseException

Perform Molecule Search

Specified by:

_execute in class DBTask

Throws:

SigPathDatabaseException - error connecting to database

setStartIndex

public void setStartIndex(int index)

sets the start index.

Specified by:

setStartIndex in interface ITSearchTask

Parameters:

index - index less than getTotalNumResults and greater or equal to 0.