Package chemaxon.sss.search

Class JChemSearchOptions

java.lang.Object

chemaxon.sss.search.SearchOptions

chemaxon.sss.search.JChemSearchOptions

All Implemented Interfaces:

SearchConstants, Serializable, Cloneable

@PublicAPI
public class JChemSearchOptions
extends SearchOptions
implements Serializable, SearchConstants, Cloneable

Class to encapsulate search parameters used by JChemSearch.

Since:

5.0

See Also:

• Serialized Form

Field Summary

Fields inherited from class chemaxon.sss.search.SearchOptions

DEFAULT_TIMEOUT_LIMIT, dirty, timeoutLimitMilliseconds, verbose

Fields inherited from interface chemaxon.sss.SearchConstants

ABS_STEREO_ALWAYS_ON, ABS_STEREO_CHIRAL_FLAG, ABS_STEREO_TABLE_OPTION, ATTACHED_DATA_MATCH_EXACT, ATTACHED_DATA_MATCH_GENERAL, ATTACHED_DATA_MATCH_IGNORE, ATTACHMENT_ATOM, ATTACHMENT_LABEL, ATTACHMENT_MAP, ATTACHMENT_NONE, ATTACHMENT_POINT, ATTACHMENT_RLABEL, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SEARCHTYPE, DISSIMILARITY_PROPERTY_NAME, DUPLICATE, FULL, FULL_FRAGMENT, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, HIT_EXCLUDEDQ, HIT_LP, HIT_MULTICENTER, HIT_NON_R, HIT_ORDERING_NONE, HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST, HIT_R, HIT_R_EMPTY_MATCH, HIT_UNMAPABLE, IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, IMPLICIT_H_MATCHING_ENABLED, IMPLICIT_H_MATCHING_IGNORE, ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, MARKUSH_HIT_INNER, MARKUSH_HIT_ORIGINAL, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, NO_ABAS, NO_SCREEN, POSITION_ON_0TH_HEAVY_ATOM, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, SEARCH_MODE_NAMES, SEARCH_TYPE_NAMES, SIMILARITY, STEREO_DIASTEREOMER, STEREO_ENANTIOMER, STEREO_EXACT, STEREO_IGNORE, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, STEREO_SPECIFIC, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_DEFAULT, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO, UNDEF_R_MATCHING_ALL, UNDEF_R_MATCHING_GROUP, UNDEF_R_MATCHING_GROUP_H, UNDEF_R_MATCHING_GROUP_H_EMPTY, UNDEF_R_MATCHING_UNDEF_R, VAGUE_BOND_DEFAULT, VAGUE_BOND_LEVEL_HALF, VAGUE_BOND_LEVEL1, VAGUE_BOND_LEVEL2, VAGUE_BOND_LEVEL3, VAGUE_BOND_LEVEL4, VAGUE_BOND_OFF

Constructor Summary

Constructors

Constructor	Description
JChemSearchOptions(int searchType)	Creates a JChemSearchOptions object while setting different search options according to a predefined search type.

Method Summary

Modifier and Type	Method	Description
Object	clone()	Makes an identical copy of this SearchObject.
void	clonecopy(SearchOptions other)	Copies parameters to other.
void	clonecopyOptions(SearchOptions other)	Copies all search options except search type to other.
int	getAbsoluteStereo()	Get the absolute stereo matching mode.
String	getDescriptorConfig()	Get the screening configuration string used for descriptor dissimilarity search.
String	getDescriptorName()	Get the name of descriptor used for descriptor similarity search
String	getDissimilarityMetric()	Get the property dissimilarity metric property.
String	getDissimilarityMetricParameters()	Get the parameters of the dissimilarity metric.
float	getDissimilarityThreshold()	Get the dissimilarity threshold.
String	getFilterQuery()	Get the filter query property.
String	getFormulaSearchQuery()	Get the query set for formula search.
int	getFormulaSearchType()	Gets the type set for formula search.
HaltOnErrorOption	getHaltOnError()	Get the current error handling behaviour option.
boolean	getMarkushScreeningType(chemaxon.sss.search.options.MarkushScreeningType type)	Internal use only! Gets whether a given Markush screening is enabled or disabled
MatchCountOptions	getMatchCountOptions()	Get the match count options.
int	getMaxResultCount()	Get the maximum result count.
int	getTimeoutLimitMilliseconds()	The search on a single target timeouts reaching this amount of time.
final int	getTotalSearchTimeoutLimitMilliseconds()	The total search on a database table timeouts reaching this amount of time.
boolean	isCacheRegistrationNeeded()	Only for internal use!
boolean	isDissimilarityThresholdExcluded()	Get the dissimilarity threshold exclusion option.
boolean	isMarkushScreeningEnabled()	Gets whether screening methods are used for Markush search before ABAS step.
boolean	isOptimizeQueries()	Get whether query should be optimized.
boolean	isReturnsNonHits()	Indicates if an inverse hit list is to be returned.
void	setAbsoluteStereo(int absoluteStereo)	Sets the absolute stereo matching mode.
void	setCacheRegistrationNeeded(boolean value)	Only for internal use!
void	setDescriptorConfig(String descriptorConfig)	Sets the screening configuration string used for descriptor dissimilarity search.
void	setDescriptorName(String descriptorName)	Sets the name of descriptor used for descriptor similarity search
void	setDissimilarityMetric(String dissimilarityMetric)	Sets the metric to be used during similarity search.
void	setDissimilarityMetricParameters(String dissimilarityMetricParam)	Sets the parameters of dissimilarity metric to be used during similarity search.
void	setDissimilarityThreshold(float dissimilarityThreshold)	Setter for property dissimilarityThreshold.
void	setDissimilarityThresholdExcluded(boolean thresholdExcluded)	Setter for property dissimilarityThresholdExcluded.
void	setFilterQuery(String filterQuery)	Setter for property filterQuery.
void	setFormulaSearchQuery(String formulaSearchQuery)	Sets the query for the formula search.
void	setFormulaSearchType(int formulaSearchType)	Sets the type for the formula search.
void	setHaltOnError(HaltOnErrorOption value)	Set whether search should stop at first error or log the error and continue search if possible.
void	setMarkushScreeningEnabled(boolean value)	Set whether to use screening for Markush search before ABAS step.
void	setMarkushScreeningType(chemaxon.sss.search.options.MarkushScreeningType type, boolean enabled)	Internal use only! Sets the use of a given Markush screening options.
void	setMarkushScreeningTypes(String types)	Internal use only! Enables all Markush screening options represented by the given option string.
void	setMatchCountOptions(MatchCountOptions matchCountOptions)	Setter for MatchCountOptions
void	setMaxResultCount(int maxResultCount)	Sets the maximum number of molecules returned by the search.
void	setOptimizeQueries(boolean value)	Sets whether the query molecule should be optimized.
void	setReturnsNonHits(boolean returnsNonHits)	Determines if the inverse of the hit set should be returned.
void	setTotalSearchTimeoutLimitMilliseconds(int value)	The total search on a database timeouts reaching this amount of time.
ArrayList<String>	toList()

Methods inherited from class chemaxon.sss.search.SearchOptions

addUserComparator, areMonomersTransformed, clearChangesInUserComparators, deleteAllUserComparators, deleteUserComparator, getAllOptionsAsString, getAllOptionsAsString, getAttachedDataMatch, getAttachedDataPrefixes, getBoolean, getChargeMatching, getCheckSpHyb, getChemTermsFilter, getChemTermsFilterConfig, getChemTermsFilterOption, getCompleteHG, getDoubleBondStereoMatchingMode, getExactSpecialAtomMatching, getExhaustiveModeLimit, getHCountMatching, getHitOrdering, getHomologyBroadTranslation, getHomologyNarrowTranslation, getImplicitHMatching, getIsotopeMatching, getMarkushAromHandling, getOption, getOptionNames, getRadicalMatching, getRLigandEqualityCheck, getSearchType, getSearchType, getSSRType, getStereoModel, getStereoSearchType, getTargetHomologyMatchingMode, getTautomerSearch, getUndefinedRAtom, getUserComparators, getVagueBondLevel, hasChangesInUserComparators, hasUserComparators, isBridgingRAllowed, isCopolymerMatching, isDirty, isEndgroupMatching, isExactBondMatching, isExactQueryAtomMatching, isIgnoreAxialStereo, isIgnoreCumuleneOrRingCisTransStereo, isIgnoreDoubleBondStereo, isIgnoreSynAntiStereo, isIgnoreTetrahedralStereo, isKeepQueryOrder, isMixSgroupMatching, isOrderSensitiveSearch, isPhaseShiftedMatching, isPolymerMatching, isReactionUnpairedMapMatching, isThrowExceptionOnTimeout, isUndefinedRAtomMatchingGroup, isValenceMatching, isVerbose, nonPositiveToInfinite, returnOptionString, setAttachedDataMatch, setAttachedDataPrefixes, setBridgingRAllowed, setChargeMatching, setCheckSpHyb, setChemTermsFilter, setChemTermsFilterConfig, setChemTermsFilterConfig, setChemTermsFilterOption, setCompleteHG, setCopolymerMatching, setDirty, setDoubleBondStereoMatchingMode, setEndgroupMatching, setExactBondMatching, setExactQueryAtomMatching, setExactSpecialAtomMatching, setExhaustiveModeLimit, setHCountMatching, setHitOrdering, setHomologyBroadTranslation, setHomologyNarrowTranslation, setIgnoreAxialStereo, setIgnoreCumuleneOrRingCisTransStereo, setIgnoreDoubleBondStereo, setIgnoreSynAntiStereo, setIgnoreTetrahedralStereo, setImplicitHMatching, setIsotopeMatching, setKeepQueryOrder, setMarkushAromHandling, setMixSgroupMatching, setMonomerTransform, setOption, setOptions, setOrderSensitiveSearch, setPhaseShiftedMatching, setPolymerMatching, setRadicalMatching, setReactionUnpairedMapMatching, setRLigandEqualityCheck, setSSRType, setStereoModel, setStereoSearchType, setTargetHomologyMatchingMode, setTautomerSearch, setThrowExceptionOnTimeout, setTimeoutLimitMilliseconds, setUndefinedRAtom, setUndefinedRAtomUserDefined, setVagueBondLevel, setValenceMatching, setVerbose, toString, toString

Methods inherited from class java.lang.Object

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

Constructor Details

JChemSearchOptions

public JChemSearchOptions(int searchType)

Creates a JChemSearchOptions object while setting different search options according to a predefined search type. For full explanation see JChem Query Guide. Acceptable values: SearchConstants.NO_SCREEN, SearchConstants.NO_ABAS, SearchConstants.SUBSTRUCTURE (default), SearchConstants.SUPERSTRUCTURE (no query features allowed), SearchConstants.SIMILARITY, SearchConstants.FULL, SearchConstants.DUPLICATE and SearchConstants.FULL_FRAGMENT.

Parameters:

searchType - the predefined search type

Method Details

setAbsoluteStereo

public void setAbsoluteStereo(int absoluteStereo)

Sets the absolute stereo matching mode.

Parameters:

absoluteStereo - absolute stereo matching mode
Default value is SearchConstants.ABS_STEREO_TABLE_OPTION.

See Also:

• SearchConstants.ABS_STEREO_TABLE_OPTION
• SearchConstants.ABS_STEREO_CHIRAL_FLAG
• SearchConstants.ABS_STEREO_ALWAYS_ON

getAbsoluteStereo

public int getAbsoluteStereo()

Get the absolute stereo matching mode.

Returns:

selected absolute stereo matching mode.
Default value is SearchConstants.ABS_STEREO_TABLE_OPTION.

See Also:

• SearchConstants.ABS_STEREO_TABLE_OPTION
• SearchConstants.ABS_STEREO_CHIRAL_FLAG
• SearchConstants.ABS_STEREO_ALWAYS_ON
• setAbsoluteStereo(int)

setFormulaSearchType

public void setFormulaSearchType(int formulaSearchType)

Sets the type for the formula search.

Parameters:

formulaSearchType - Formula search type.
Default value is FormulaSearch.NONE.

See Also:

• getFormulaSearchType()
• FormulaSearch.NONE
• FormulaSearch.EXACT
• FormulaSearch.EXACT_SUBFORMULA
• FormulaSearch.SUBFORMULA

getFormulaSearchType

public int getFormulaSearchType()

Gets the type set for formula search.

Returns:

formula search type.
Default value is FormulaSearch.NONE.

See Also:

• setFormulaSearchType(int)
• FormulaSearch.NONE
• FormulaSearch.EXACT
• FormulaSearch.EXACT_SUBFORMULA
• FormulaSearch.SUBFORMULA

setFormulaSearchQuery

public void setFormulaSearchQuery(String formulaSearchQuery)

Sets the query for the formula search.

Parameters:

formulaSearchQuery - Formula search query. E.g. "C6-8 H-20 N1"
Default value is null.

See Also:

• getFormulaSearchQuery()
• setFormulaSearchType(int)
• FormulaSearch

getFormulaSearchQuery

public String getFormulaSearchQuery()

Get the query set for formula search.

Returns:

the chemical formula set for the query.
Default value is null.

See Also:

• setFormulaSearchQuery(String)
• setFormulaSearchType(int)
• FormulaSearch

getFilterQuery

public String getFilterQuery()

Get the filter query property.

Returns:

Value of property filterQuery.
Default value is null.

See Also:

• setFilterQuery(String)

setFilterQuery

public void setFilterQuery(String filterQuery)

Setter for property filterQuery. SQL query for filtering. The result should contain the cd_id values. Example:

    searchOptions.setFilterQuery("select cd_id from mystructures where cd_id > 1000");
 

If the SELECT contains an "ORDER BY" clause, the results will be ordered accordingly, the setting for JChemSearch.setOrder(int) will be ignored, except when an inverse hit list is requested.

NOTE: The filtered cd_id values are cached. Invoke setFilterQuery again before the next search, if the filter needs to be refreshed.

Parameters:

filterQuery - New value of property filterQuery.
Default value is null.

Since:

JChem 2.3

See Also:

• getFilterQuery()

setDissimilarityThreshold

public void setDissimilarityThreshold(float dissimilarityThreshold)

Setter for property dissimilarityThreshold. Sets the threshold for similarity searches. A lower threshold results less hits that are more similar to the query structure.

Parameters:

dissimilarityThreshold - value of the dissimilarity threshold.
Default value is 0.3.

See Also:

• getDissimilarityThreshold()

getDissimilarityThreshold

public float getDissimilarityThreshold()

Get the dissimilarity threshold.

Returns:

Value of property dissimilarityThreshold.
Default value is 0.3.

See Also:

• setDissimilarityThreshold(float)

setDissimilarityThresholdExcluded

public void setDissimilarityThresholdExcluded(boolean thresholdExcluded)

Setter for property dissimilarityThresholdExcluded. Determines whether dissimilarity values equaling the threshold value are considered hits or not.

Parameters:

thresholdExcluded - If true, only dissimilarity values less than the threshold value are considered hits. If false, dissimilarity values equaling the threshold value are also considered hits. (Defaults to false.)
Default value is false.

See Also:

• isDissimilarityThresholdExcluded()

isDissimilarityThresholdExcluded

public boolean isDissimilarityThresholdExcluded()

Get the dissimilarity threshold exclusion option.

Returns:

the value of the dissimilarity threshold exclusion.
Default value is false.

See Also:

• setDissimilarityThresholdExcluded(boolean)

getMaxResultCount

public int getMaxResultCount()

Get the maximum result count.

Returns:

number of maximum results.
Default value is 0.

See Also:

• setMaxResultCount(int)

setMaxResultCount

public void setMaxResultCount(int maxResultCount)
                       throws IllegalArgumentException

Sets the maximum number of molecules returned by the search. If the given parameter is 0, then there is no limit.

NOTE:

• In case of non-similarity search, the search process will be stopped when the maximum result count is reached. This can save time when there would be too many results.
• In case of similarity searches, the full search is performed and the maxResultCount most similar results will be given back. In this case this option does not mean speedup.

Parameters:

maxResultCount - New value of property maxResultCount. Default value is 0, i.e. there is no limit.

Throws:

IllegalArgumentException - if maxResultCount was negative number.

See Also:

• getMaxResultCount()

setReturnsNonHits

public void setReturnsNonHits(boolean returnsNonHits)

Determines if the inverse of the hit set should be returned.

Parameters:

returnsNonHits - set to true to get non-hit structures. Default is false.
Default value is false.

See Also:

• isReturnsNonHits()

isReturnsNonHits

public boolean isReturnsNonHits()

Indicates if an inverse hit list is to be returned.

Returns:

true if inverse hit list it to be returned.
Default value is false.

See Also:

• setReturnsNonHits(boolean)

setDissimilarityMetric

public void setDissimilarityMetric(String dissimilarityMetric)

Sets the metric to be used during similarity search.

Parameters:

dissimilarityMetric - the name of the metric to be used. Specify null for the default metric. For reaction tables see ReactionFingerprint. For molecule and any tables the default metrics can be replaced by the metrics described in SimilarityCalculatorFactory.create(String).
Default value is null.

See Also:

• JChemSearch.getDissimilarityMetrics(chemaxon.util.ConnectionHandler, String)
• getDissimilarityMetric()
• setDissimilarityThreshold(float)
• getDissimilarityThreshold()
• SimilarityCalculatorFactory.create(String)
• ReactionFingerprint

getDissimilarityMetric

public String getDissimilarityMetric()

Get the property dissimilarity metric property.

Returns:

value of dissimilarityMetric
Default value is null.

See Also:

• setDissimilarityMetric(String)
• setDissimilarityThreshold(float)
• getDissimilarityThreshold()

setDissimilarityMetricParameters

public void setDissimilarityMetricParameters(String dissimilarityMetricParam)

Sets the parameters of dissimilarity metric to be used during similarity search.

Parameters:

dissimilarityMetricParam - parameters of the dissimilarity metric e.g. for Tversky: "0.3,0.7" or equivalenly: "queryWeight=0.3,targetWeight=0.7" Specify empty string for no parameters or default parameter.

For molecule and any tables the available metrics are the ones described in SimilarityCalculatorFactory.create(String).
Default value is null.

See Also:

• getDissimilarityMetricParameters()
• JChemSearch.getDissimilarityMetrics(chemaxon.util.ConnectionHandler, String)
• getDissimilarityMetric()
• setDissimilarityThreshold(float)
• getDissimilarityThreshold()
• SimilarityCalculatorFactory.create(String)
• ReactionFingerprint

getDissimilarityMetricParameters

public String getDissimilarityMetricParameters()

Get the parameters of the dissimilarity metric.

Returns:

dissimilarity metric parameters
Default value is null.

See Also:

• setDissimilarityMetricParameters(String)
• setDissimilarityMetric(String)
• setDissimilarityThreshold(float)
• getDissimilarityThreshold()

setDescriptorConfig

public void setDescriptorConfig(String descriptorConfig)

Sets the screening configuration string used for descriptor dissimilarity search.

Parameters:

descriptorConfig - the configuration string used for dissimilarity search calculation. Default value: null (means default configuration)
Default value is null.

See Also:

• getDescriptorConfig()
• MDTableHandler.getMDConfig(String, String)
• setDescriptorName(String)
• getDescriptorName()

getDescriptorConfig

public String getDescriptorConfig()

Get the screening configuration string used for descriptor dissimilarity search.

Returns:

the screening configuration string
Default value is null.

See Also:

• setDescriptorConfig(String)
• setDescriptorName(String)
• getDescriptorName()

setDescriptorName

public void setDescriptorName(String descriptorName)

Sets the name of descriptor used for descriptor similarity search

Parameters:

descriptorName - the descriptor identifier used for similarity search. If not specified or null, structural fingerprint similarity search performed by default.
Default value is null.

Since:

JChem 2.0

See Also:

• getDescriptorName()
• setDescriptorConfig(String)
• getDescriptorConfig()

getDescriptorName

public String getDescriptorName()

Get the name of descriptor used for descriptor similarity search

Returns:

the name of the descriptor
Default value is null.

See Also:

• setDescriptorName(String)
• setDescriptorConfig(String)
• getDescriptorConfig()

setMatchCountOptions

public void setMatchCountOptions(MatchCountOptions matchCountOptions)

Setter for MatchCountOptions

Parameters:

matchCountOptions - a predefined MatchCountOptions object

See Also:

• getMatchCountOptions()

getMatchCountOptions

public MatchCountOptions getMatchCountOptions()

Get the match count options.

Returns:

the matchCountOptions

See Also:

• MatchCountOptions
• setMatchCountOptions(MatchCountOptions)

isOptimizeQueries

public boolean isOptimizeQueries()

Get whether query should be optimized. (Certain atomlists and bondlists are enumerated.)

Returns:

true if the query molecule should be optimized
Default value is true.

See Also:

• setOptimizeQueries(boolean)

setOptimizeQueries

public void setOptimizeQueries(boolean value)

Sets whether the query molecule should be optimized. (certain atomlists and bondlists are enumerated)

Parameters:

value - true if the query molecule should be optimized.
Default value is true.

See Also:

• isOptimizeQueries()

setCacheRegistrationNeeded

public void setCacheRegistrationNeeded(boolean value)

Only for internal use!

Parameters:

value - new value for cacheRegistration

isCacheRegistrationNeeded

public boolean isCacheRegistrationNeeded()

Only for internal use!

Returns:

current value

setMarkushScreeningEnabled

public void setMarkushScreeningEnabled(boolean value)

Set whether to use screening for Markush search before ABAS step. If set to true all known screening methods are enabled, if set to false all known screening methods are disabled.
By default all known Markush screening methods are enabled.

Parameters:

value - markush screening should be used or not.
Default value is true.

See Also:

• isMarkushScreeningEnabled()
• setMarkushScreeningType(MarkushScreeningType, boolean)
• MarkushScreeningType

isMarkushScreeningEnabled

public boolean isMarkushScreeningEnabled()

Gets whether screening methods are used for Markush search before ABAS step.

Returns:

true if screening is used, false otherwise.

See Also:

• setMarkushScreeningEnabled(boolean)
• setMarkushScreeningType(MarkushScreeningType, boolean)
• getMarkushScreeningType(MarkushScreeningType)

setMarkushScreeningType

public void setMarkushScreeningType(chemaxon.sss.search.options.MarkushScreeningType type,
 boolean enabled)

Internal use only!
Sets the use of a given Markush screening options. Enables or disables its usage while performing Markush table searches

Parameters:

type - Markush screening option enabled or disabled

enabled - true to enable screening option, false to disable screening option

See Also:

• setMarkushScreeningEnabled(boolean)
• getMarkushScreeningType(MarkushScreeningType)
• MarkushScreeningType

setMarkushScreeningTypes

public void setMarkushScreeningTypes(String types)

Internal use only!
Enables all Markush screening options represented by the given option string.

Parameters:

types - Markush screening options to enable separated by a comma. If null (default), all screening options are enabled. If empty string, no methods are enabled.

getMarkushScreeningType

public boolean getMarkushScreeningType(chemaxon.sss.search.options.MarkushScreeningType type)

Internal use only!
Gets whether a given Markush screening is enabled or disabled

Parameters:

type - Markush screening option to check

Returns:

true if screening is enabled, false if screening method is disabled

See Also:

• getMarkushScreeningType(MarkushScreeningType)
• MarkushScreeningType

setHaltOnError

public void setHaltOnError(HaltOnErrorOption value)

Set whether search should stop at first error or log the error and continue search if possible.

Parameters:

value - stop at first error or not.
Default value is HaltOnErrorOption.DEFAULT

See Also:

• HaltOnErrorOption
• getHaltOnError()

getHaltOnError

public HaltOnErrorOption getHaltOnError()

Get the current error handling behaviour option.

Returns:

the option set for error handling behaviour

See Also:

• HaltOnErrorOption
• setHaltOnError(HaltOnErrorOption)

clone

public Object clone()
             throws CloneNotSupportedException

Makes an identical copy of this SearchObject.

Overrides:

clone in class SearchOptions

Throws:

CloneNotSupportedException

clonecopy

public void clonecopy(SearchOptions other)

Copies parameters to other. It copies
- all parameters if other is a JchemSearchOptions object
- only the parameters defined in SearchOptions if it is a SearchOptions or MolSearchOptions object

Overrides:

clonecopy in class SearchOptions

Parameters:

other - search option to overwrite.

clonecopyOptions

public void clonecopyOptions(SearchOptions other)

Description copied from class: SearchOptions

Copies all search options except search type to other.

Overrides:

clonecopyOptions in class SearchOptions

Parameters:

other - search option object to overwrite

getTimeoutLimitMilliseconds

public int getTimeoutLimitMilliseconds()

The search on a single target timeouts reaching this amount of time. If the total timeout limit is less than the single search timeout limit, this function returns with the total timeout limit.

Overrides:

getTimeoutLimitMilliseconds in class SearchOptions

Returns:

The timeout limit in milliseconds.
Default value is 120000

See Also:

• SearchOptions.getTimeoutLimitMilliseconds()
• SearchOptions.setTimeoutLimitMilliseconds(int)
• setTotalSearchTimeoutLimitMilliseconds(int)

getTotalSearchTimeoutLimitMilliseconds

public final int getTotalSearchTimeoutLimitMilliseconds()

The total search on a database table timeouts reaching this amount of time.

Returns:

The timeout limit in milliseconds.

See Also:

• setTotalSearchTimeoutLimitMilliseconds(int)
• getTimeoutLimitMilliseconds()

setTotalSearchTimeoutLimitMilliseconds

public void setTotalSearchTimeoutLimitMilliseconds(int value)

The total search on a database timeouts reaching this amount of time. Set it to a negative value if you do not want to the search time out. Note: if SearchOptions.setTimeoutLimitMilliseconds(int) is set the search still can time out.
If the search is running in asynchronous mode, JChemSearch.isRunning() must be constantly called within the specified time interval, otherwise the search stops. Useful if the user no longer monitors the search process, e.g. closes the browser window. It also means that in asynchronous mode if JChemSearch.isRunning() is called constantly, then the search will not be stopped even if setTotalSearchTimeoutLimitMilliseconds(int) is set. The time limit is calcualated from the last call of JChemSearch.isRunning().

Parameters:

value - The time limit to set in milliseconds. Negative values are treated as Integer.MAX_VALUE.

See Also:

• getTotalSearchTimeoutLimitMilliseconds()
• SearchOptions.setTimeoutLimitMilliseconds(int)

toList

public ArrayList<String> toList()

Overrides:

toList in class SearchOptions

Returns:

An arraylist that contains strings of format "optionname:optionvalue". Doesn't contain options that have their default value.

See Also:

• SearchOptions.setOptions(String)
• SearchOptions.toString()