Package chemaxon.jchem.db

Class JChemSearch

java.lang.Object
chemaxon.util.ErrorHandler
chemaxon.jchem.db.JChemSearch
All Implemented Interfaces:
TableTypeConstants, chemaxon.license.Licensable, SearchConstants
@PublicAPI public class JChemSearch extends ErrorHandler implements SearchConstants, TableTypeConstants, chemaxon.license.Licensable
JavaBean for structure searching in structure tables of relational databases. For more information, see the corresponding section of the user's guide.

Example for using the class: 

 searcher = new JChemSearch();
 searcher.setQueryStructure("c1cnccc1Cl");
 searcher.setConnectionHandler(conHandler);
 searcher.setStructureTable("cduser.structures");

 searchOptions = new JChemSearchOptions(JChemSearch.SIMILARITY);
 searchOptions.setDissimilarityThreshold(0.8F);
 searchOptions.setMaxResultCount(100);
 searcher.setSearchOptions(searchOptions);

 searcher.setRunMode(JChemSearch.RUN_MODE_SYNCH_COMPLETE);
 searcher.run();

  • Field Details

    • NO_RESULT_TABLE

      public static final int NO_RESULT_TABLE
      Constant for the generation of result tables. Meaning: Don't store the results in a table. (Value=0)
      See Also:

    • CREATE_OR_REPLACE_RESULT_TABLE

      public static final int CREATE_OR_REPLACE_RESULT_TABLE
      Constant for the generation of result tables. Meaning: Create a result table. If a table with same name exists, replace it with the new one. (Value=2)
      See Also:

    • APPEND_TO_RESULT_TABLE

      public static final int APPEND_TO_RESULT_TABLE
      Constant for the generation of result tables. Meaning: Append to an existing result table. Create a new one if it doesn't exist (Value=3)
      See Also:

    • NO_ORDERING

      public static final int NO_ORDERING
      Constant for ordering the result. Meaning: Don't order the result (Value=0)
      See Also:

    • ORDERING_BY_ID

      public static final int ORDERING_BY_ID
      Constant for ordering the result. Meaning: Order the result according to the cd_id values (Value=1)
      See Also:

    • ORDERING_BY_ID_OR_SIMILARITY

      public static final int ORDERING_BY_ID_OR_SIMILARITY
      Constant for ordering the result. Meaning: Order the result according to the calculated dissimilarity in the case of dissimilarity searching, use the cd_id values otherwise (Value=2)
      See Also:

    • ORDERING_BY_FILTER_ID_LIST

      public static final int ORDERING_BY_FILTER_ID_LIST
      Constant for ordering the result. Meaning: Order the result according to the filterIDList
      See Also:

    • RUN_MODE_SYNCH_COMPLETE

      public static final int RUN_MODE_SYNCH_COMPLETE
      The "runner" methods (run() or setRunning(boolean) return only after all hits has been found.
      Since:
      JChem 5.0
      See Also:

    • RUN_MODE_ASYNCH_COMPLETE

      public static final int RUN_MODE_ASYNCH_COMPLETE
      Runs the search in a new thread; run() or setRunning(boolean) return immediately. Exceptions are not thrown by the run() method they should be checked by the checkException() or ErrorHandler.checkError() methods.
      Since:
      JChem 5.0
      See Also:

    • RUN_MODE_ASYNCH_PROGRESSIVE

      public static final int RUN_MODE_ASYNCH_PROGRESSIVE
      Runs the search in a new thread; run() or setRunning(boolean) return immediately. The methods hasMoreHits(), getNextHit() and getAvailableNewHits(int) can be used retrieve hits as soon as they become available. Exceptions are not thrown by the run() method they should be checked by the checkException() or ErrorHandler.checkError() methods.
      This mode doesn't support
      Since:
      JChem 5.0
      See Also:

    • searchOptions

      protected final JChemSearchOptions searchOptions
      Object to store all search parameters. This is used during the search and stores the settings of the previous search.

    • MAXIMAL_ACCEPTEDSEARCHTIME_MINUTES

      @Deprecated public static final int MAXIMAL_ACCEPTEDSEARCHTIME_MINUTES
      Deprecated.
      See Also:

  • Constructor Details

    • JChemSearch

      public JChemSearch()
      Creates new JChemSearch class

    • JChemSearch

      public JChemSearch(String indexedTable, String indexedColumn)
      For internal use only.
      Parameters:
      indexedTable - the name of the table
      indexedColumn - the name of the column

    • JChemSearch

      public JChemSearch(chemaxon.jchem.db.distributed.DistributedNodes distributedNodes, String indexedTable, String indexedColumn)
      For internal use only.
      Parameters:
      distributedNodes - the distributed nodes
      indexedTable - the name of the table
      indexedColumn - the name of the column

    • JChemSearch

      public JChemSearch(chemaxon.jchem.db.distributed.DistributedNodes distributedNodes)
      Creates a new JChemSearch class for distributed search.

      For internal use only.

      Parameters:
      distributedNodes - the distributed nodes

  • Method Details

    • checkException

      public void checkException() throws Exception
      Description copied from class: ErrorHandler
      Throws the exception stored in the object. Needed because Tomcat errorpages don't handle errors of type Throwable that are not inheritors of Exception.
      Overrides:
      checkException in class ErrorHandler
      Throws:
      Exception - the exception stored, boxed as Exception

    • getConnectionHandler

      public ConnectionHandler getConnectionHandler()
      Getter for property connectionHandler.
      Returns:
      Value of property connectionHandler.

    • setConnectionHandler

      public void setConnectionHandler(ConnectionHandler connectionHandler)
      Sets the database connection.
      Parameters:
      connectionHandler - a ConnectionHandler object containing a live connection to the database

    • getConnection

      public Connection getConnection()
      Getter for property connection.
      Returns:
      Value of property connection.

    • getDissimilarityMetrics

      public static JChemSearch.DissimilarityMetrics getDissimilarityMetrics(ConnectionHandler ch, String tableName) throws SQLException
      Returns the available dissimilarity metrics for the given table.
      Parameters:
      ch - ConnectionHandler with live connection
      tableName - the name of the JChem structure table
      Returns:
      the information about the available metrics, or null if no metrics are available
      Throws:
      SQLException - in case it encounters an sql problem.
      Since:
      JChem 3.2
      See Also:

    • getDissimilarityMetrics

      public static JChemSearch.DissimilarityMetrics getDissimilarityMetrics(ConnectionHandler ch, String tableName, String indexedTable, String indexedColumn) throws SQLException
      Throws:
      SQLException

    • getCacheError

      public String getCacheError()
      For checking for cache errors. Should be called after the search is finished.
      Returns:
      the error text, or null in case of normal execution.
      Since:
      JChem 3.0

    • getQueryStructure

      public String getQueryStructure()
      Getter for property queryStructure.
      Returns:
      Value of property queryStructure.

    • setQueryStructure

      public void setQueryStructure(String queryStructure)
      Setter for property queryStructure. The query structure may be in MDL Molfile, Smiles or other format recognized by JChem. If the specified value is null or empty string, then it is interpreted as an empty query structure. (For more information, see the user's guide.)

      NOTE for Daylight formats: If search type is SearchConstants.DUPLICATE, SearchConstants.SUPERSTRUCTURE or SearchConstants.SIMILARITY, treats SMILES/SMARTS input strings as SMILES, otherwise as SMARTS.

      Parameters:
      queryStructure - New value of property queryStructure.

    • setQueryStructure

      public void setQueryStructure(Molecule queryMol)
      Sets the query structure. If the specified value is null, then it is interpreted as an empty query structure. (For more information, see the user's guide.)
      Parameters:
      queryMol - the query structure.

    • setQueryFingerprint

      public void setQueryFingerprint(int[] queryFp)
      Currently internal use only.
      Parameters:
      queryFp - the query fingerprint.

    • getStructureTable

      public String getStructureTable()
      Getter for property structureTable.
      Returns:
      Value of property structureTable.

    • setStructureTable

      public void setStructureTable(String structureTable)
      Setter for property structureTable. It specifies the name of the table to be searched for structures containing the query.
      Parameters:
      structureTable - New value of property structureTable.

    • setFilterIDList

      public void setFilterIDList(int[] ids)
      Specifies a list of cd_id values that are allowed to be included in the result set. Useful for narrowing the result set of the search (e.g., based on the {#getResults() results} of a previous search).

      If the given array is empty, no hits will be returned. Resetting the list is possible by calling the method with null parameter.

      Parameters:
      ids - the cd_id values in an array
      Since:
      JChem 3.1

    • setFilterIDNotList

      public void setFilterIDNotList(int[] ids)
      Specifies a list of cd_id values that should not be included in the result set.
      Parameters:
      ids - the cd_id values in an array
      Since:
      JChem 3.1.2

    • isInfoToStdError

      public boolean isInfoToStdError()
      Getter for property infoToStdError.
      Returns:
      Value of property infoToStdError.

    • setInfoToStdError

      public void setInfoToStdError(boolean infoToStdError)
      Setter for property infoToStdError. If set to true, information useful for testing will be written in the servlet server's error log file. (Default: false)
      Parameters:
      infoToStdError - New value of property infoToStdError.

    • getRunMode

      public int getRunMode()
      Retruns the current run mode.
      Returns:
      the current run mode.
      Since:
      JChem 5.0
      See Also:

    • setRunMode

      public void setRunMode(int runMode)
      Specifies whether the search is performed synchronously or asychronously and if performed asynchronously, whether the hits can be obtained as soon as they are found or only after the search has completed.

      The default run mode is RUN_MODE_SYNCH_COMPLETE

      Parameters:
      runMode - Accepted values:
      Since:
      JChem 5.0

    • setSearchOptions

      public void setSearchOptions(JChemSearchOptions options)
      Sets search parameters.
      Parameters:
      options - search options. Will be copied, modification of the original object does not affect future searches unless this method is called again. The timeout limit of the new options will be applied to further searches.
      Since:
      JChem 5.0
      See Also:

    • getSearchOptions

      public JChemSearchOptions getSearchOptions()
      Returns the SearchOptions object associated with this Search object. The object returned is linked with this Search object, so modifications in the returned SearchOptions object (e.g timeout limit) will change directly the behaviour of this Search object.
      Returns:
      the current serarch options.
      Since:
      JChem 5.0
      See Also:

    • getOrder

      public int getOrder()
      Getter for property order.
      Returns:
      Value of property order.

    • setOrder

      public void setOrder(int order)
      Setter for property order. Determines the order of the result.
      Parameters:
      order - New value of property order. Acceptable values: NO_ORDERING, ORDERING_BY_ID, ORDERING_BY_ID_OR_SIMILARITY (default), and ORDERING_BY_FILTER_ID_LIST .

      If an "ORDER BY" clause is used in filter query, and no inverse hit list is requested, this setting is ignored, and the "ORDER BY" clause takes precedence.

    • setResultTable

      public void setResultTable(String resultTable)
      Setter for property resultTable. Sets the result table that will contain the cd_id of hits. In the case of searching similar structures, the similarity value is also stored in column similarity.
      Parameters:
      resultTable - New value of property resultTable.
      See Also:

    • getResultTableMode

      public int getResultTableMode()
      Getter for property resultTableMode.
      Returns:
      Value of property resultTableMode.

    • setResultTableMode

      public void setResultTableMode(int resultTableMode)
      Setter for property resultTableMode. It instructs the searcher about the way of handling the result table. Modes: (Default: NO_RESULT_TABLE)
      Parameters:
      resultTableMode - New value of property resultTableMode.
      See Also:

    • getResultTable

      public String getResultTable()
      Getter for property resultTable.
      Returns:
      Value of property resultTable.

    • setNumberOfProcessingThreads

      public void setNumberOfProcessingThreads(int threads)
      Sets the number of processing threads.
      Parameters:
      threads - the number of threads.
      If set to 0, the number of threads will be equal to the number of logical processors available for the Java Vitual Machine (default).
      NOTE: Under Java Runtime Environment 1.3.1 or older the number of processors cannot be determined. In this case the default number of threads is 16.
      Since:
      JChem 3.0

    • getNumberOfProcessingThreads

      public int getNumberOfProcessingThreads()
      Gets the number of processing threads.
      Returns:
      number of threads executed the database search.

    • setThreadPriority

      public void setThreadPriority(int priority)
      Sets the priority of the processing threads. Only effective, if setRunMode(int) is set to either RUN_MODE_ASYNCH_COMPLETE or RUN_MODE_ASYNCH_PROGRESSIVE .
      Parameters:
      priority - the priority ranging 1 (Thread.MIN_PRIORITY) to 10 (Thread.MAX_PRIORITY).
      The default and recommended setting is 1 ( Thread.MIN_PRIORITY).
      NOTE: if all other threads are not constantly calculating, a low priority setting will not slow down the search process, and it will help user interfaces to be responsive.
      Since:
      JChem 3.0

    • getResult

      public int getResult(int index)
      Indexed getter for property results. Returns a cd_id value of the found compound specified by index. If result table is generated, getResult throws NullPointerException.
      Parameters:
      index - Index of the property.
      Returns:
      Value of the property at index.
      See Also:

    • getResultContext

      public chemaxon.jchem.db.SearchCoreReturnedValue getResultContext()
      For internal use only.
      Returns:
      the result

    • getResults

      public int[] getResults()
      Returns an int array containing the cd_id values of found compounds. If a result table is generated in the database, it returns null.
      Returns:
      an array of cd_ids

    • getExtraInformation

      public List<byte[]> getExtraInformation()
      For internal use only.
      Returns:
      extrainformation for all results

    • cleanResults

      public void cleanResults()
      Cleans stored search results. Can be called to save memory while keeping the JChemSearch object. since JChem 3.0

    • getDissimilarity

      public float getDissimilarity(int index)
      Indexed getter for property dissimilarity. Returns the calculated dissimilarity value of the found compound specified by index and the query structure. If searching has not been finished yet or if a result table is generated, getDissimilarity throws NullPointerException.
      Parameters:
      index - Index of the property.
      Returns:
      Value of the property at index.
      See Also:

    • getDissimilarity

      public float[] getDissimilarity()
      Getter for dissimilarity results. Returns the calculated dissimilarity values calculated for the last query strucutre. If searching has not been finished yet or if a result table is generated, getDissimilarity throws NullPointerException.
      Returns:
      the dissimilarity results.
      See Also:

    • getProgressMessage

      public String getProgressMessage()
      Getter for property progressMessage. It returns a message that shows the state of the search. It can be used for showing the progress of the search.
      Returns:
      Value of property progressMessage.

    • isMaxResultCountReached

      public boolean isMaxResultCountReached()
      Getter for property maxResultCountReached. It returns true if the search was stopped because the number of hits had reached the maximum value, false otherwise.
      Returns:
      Value of property maxResultCountReached.

    • isMaxTimeReached

      public boolean isMaxTimeReached()
      Getter for property maxTimeReached. It returns true if the search stopped because the time that passed since the start of the searched had reached the maximum value, false otherwise.
      Returns:
      Value of property maxTimeReached.

    • getResultCount

      public int getResultCount()
      Getter for property resultCount. It returns the number of hits found by the search.
      Returns:
      Value of property resultCount.

    • isRunning

      public boolean isRunning()
      Getter for property running.
      Returns:
      Value of property running.

    • setRunning

      public void setRunning(boolean run) throws SQLException, IOException, DatabaseSearchException
      Setter for property running. If it is set to true and the search has not been started yet, then searching is unleashed. If it is set to false and a search is running, the the process will be stopped. (Default: false)
      Parameters:
      run - New value of property run.
      Throws:
      IOException - if an io error is encountered
      DatabaseSearchException - if a search error occurs
      SQLException - if an sql exception is encountered

    • run

      public void run() throws IOException, DatabaseSearchException, SQLException
      Starts searching. Same as setRunning(true)
      Throws:
      IOException - if an io error is encountered
      DatabaseSearchException - if a search error occurs
      SQLException - if an sql exception is encountered

    • hasMoreHits

      public boolean hasMoreHits() throws InterruptedException
      Used with run mode = RUN_MODE_ASYNCH_PROGRESSIVE.
      Returns true if there are more hits to retrieve with getNextHit() or getAvailableNewHits(int), false otherwise.
      Returns:
      true if there are more hits to retrieve with getNextHit() or getAvailableNewHits(int), false otherwise.
      Throws:
      InterruptedException - if the thread is interrupted during waiting
      Since:
      JChem 5.0

    • getNextHit

      public int getNextHit() throws InterruptedException
      Used with run mode = RUN_MODE_ASYNCH_PROGRESSIVE.
      Returns the next available hit. Waits until at least one is available or throws NoSuchElementException, there are no more hits to return.
      Returns:
      the next available hit. Waits until at least one is available or throws NoSuchElementException, there are no more hits to return.
      Throws:
      InterruptedException - if the calling thread was interrupted while waiting for the next available hit.
      Since:
      JChem 5.0

    • getAvailableNewHits

      public int[] getAvailableNewHits(int minimumHitSize) throws InterruptedException, DatabaseSearchException
      Used with run mode = RUN_MODE_ASYNCH_PROGRESSIVE.
      Returns all new hits available at the time of return, but at least minimumHitSize new hits.
      Parameters:
      minimumHitSize - the minimum number of hits to return, which will be waited if not yet available.
      Returns:
      all new hits available at the time of return, but at least minimumHitSize new hits.
      Throws:
      InterruptedException - if the calling thread was interrupted while waiting.
      DatabaseSearchException - if there was an error during searching.
      Since:
      JChem 5.0

    • getAvailableExtraInformation

      public List<byte[]> getAvailableExtraInformation(int minimumHitSize) throws InterruptedException, DatabaseSearchException
      For internal use only.
      Parameters:
      minimumHitSize - minmum size of hits to collect
      Returns:
      list of extrainformation
      Throws:
      InterruptedException - if the thread is interrupted during waiting
      DatabaseSearchException - if the search ecountered a problem

    • waitUntilSearchComplete

      public void waitUntilSearchComplete() throws InterruptedException
      Used with run mode = RUN_MODE_ASYNCH_PROGRESSIVE.
      Waits until after the search has completed.
      Throws:
      InterruptedException - if the calling thread was interrupted while waiting.
      Since:
      JChem 5.0

    • getScreenedCount

      public int getScreenedCount()
      Gets the number of total screened structures.
      Returns:
      the number of total screened structures, or -1 if the screened count was not calculated
      Since:
      JChem 5.6

    • getScreenedCountUnique

      public int getScreenedCountUnique()
      Gets the number of unique screened structures.
      Returns:
      the number of unique screened structures, or -1 if the screened count was not calculated
      Since:
      JChem 5.6

    • getScreenedCountTotal

      public int getScreenedCountTotal()
      Gets the number of total screened structures.
      Returns:
      the number of total screened structures, or -1 if the screened count was not calculated
      Since:
      JChem 5.6

    • getScreenedResults

      public int[] getScreenedResults()
      Gets the screened unique structures' ids.
      Returns:
      the screened structures' ids
      Since:
      JChem 5.6

    • getScreeningTime

      public long getScreeningTime()
      Gets the screening time.
      Returns:
      the screening time in milliseconds

    • getFirstHitTime

      public long getFirstHitTime()
      Gets the first hit's retrieving time (measured from start of screening).
      Returns:
      the retrieving time of first hit in milliseconds

    • getSearchTime

      public long getSearchTime()
      Gets the total search time.
      Returns:
      the search time in milliseconds (includes screening time) If the returned value is -1 then the search time is invalid (e.g search hasn't finished yet).

    • isTargetMarkush

      public boolean isTargetMarkush()
      Gets whether target structure table is a Markush table
      Returns:
      true if target table is a Markush table, false if not

    • getEnumerationCount

      public int getEnumerationCount()
      Gets the number of enumerates used while screening the database
      Returns:
      the number of enumerates for the query

    • isLicensed

      public boolean isLicensed()
      Specified by:
      isLicensed in interface chemaxon.license.Licensable

    • setLicenseEnvironment

      public void setLicenseEnvironment(String env)
      Specified by:
      setLicenseEnvironment in interface chemaxon.license.Licensable

    • setProgressMessage

      public void setProgressMessage(String message)

    • getCacheLoadTime

      public long getCacheLoadTime() throws IllegalStateException
      Gets the time spent with cache loading for the target structure table. Returns
      Returns:
      duration for the last successful cache loading in milliseconds
      Throws:
      IllegalStateException - if no cache is loaded yet

    • getCacheSizeEstimate

      public double getCacheSizeEstimate() throws IllegalStateException
      Returns an estimate of the cache size for the target structure table.
      Returns:
      estimated size of the cache for the target structure table in MBs
      Throws:
      IllegalStateException - if no cache is loaded yet

    • getCacheSize

      public double getCacheSize() throws IllegalStateException
      Returns the size of the cache for the target structure table.

      Warning: the calculation performed by this function may be slow and may consume a large amount of memory. Consider to use getCacheSizeEstimate() to obtain an estimation of the cache size much faster.

      Returns:
      the size of the cache for the target structure table in MBs
      Throws:
      IllegalStateException - if no cache is loaded yet

    • getHitsAsRgDecomp

      public RgDecompResults getHitsAsRgDecomp(int[] hits, int attachmentType) throws SearchException, MolFormatException, SQLException
      Returns hits as result of r-group decomposition according to the original query. Various results are returned in one RgDecompResults object: More details about r-group decomposition can be found here. For more sophisticated usages (e.g. all hits of query in a specific target) see our RGroupDecomposition API documentation.
      Parameters:
      hits - cd_ids of target structures
      attachmentType - Type of visualization of attachment of ligands.
      Returns:
      An RGDecompResults object.
      Throws:
      SQLException - if an sql exception is encountered
      SearchException - Search failure
      MolFormatException - if the molecule can't be read
      Since:
      JChem 5.3
      See Also:

    • getHitsAsMolecules

      public Molecule[] getHitsAsMolecules(int[] idList, HitColoringAndAlignmentOptions options, List<String> dataFieldNames, List<Object[]> dataFieldValues) throws SQLException, IOException, SearchException, chemaxon.enumeration.supergraph.SupergraphException, DatabaseSearchException
      Returns hits ready for display. If hit alignment or coloring is needed, the graph search must be repeated for the selected structures to obtain the atom indexes of hits. (Storing this data would consume too much memory for large hit sets) If alignment mode has been set to rotate, and query has 0 dimension, it will be cleaned in 2d. If alignment mode has been set to partial clean, this option will be changed to rotate in this case.
      Parameters:
      idList - the cd_id list of hits to be retrieved.
      options - the options for coloring and alignment. If null the structures will be displayed in their original form.
      dataFieldNames - fields of the jchem table that should be fetched together with the structure or null.
      dataFieldValues - an empty List required or it can be null. The fetched values will be stored in this object as Object[] elements.
      Returns:
      the hits as Molecules, colored and aligned if needed. If coloring is specified in case of SearchConstants.SUPERSTRUCTURE search mode, always the query structure is returned, the target subgraph is colored. If there is no hit for a target then the appropriate element of the result array is null.
      Throws:
      SQLException - if the fetched row is deleted
      IOException - if an io error is encountered
      SearchException - Search failure during getting colored atoms
      chemaxon.enumeration.supergraph.SupergraphException - Search failure during getting colored atoms
      DatabaseSearchException - Search failure during getting colored atoms
      Since:
      JChem 5.0

    • getHitsAsHitDisplayTool

      public HitDisplayTool getHitsAsHitDisplayTool(int[] idList, HitColoringAndAlignmentOptions options, List<String> dataFieldNames, List<Object[]> dataFieldValues, List<? super Molecule> molecules, List<byte[]> sources) throws SQLException, IOException, SearchException, chemaxon.enumeration.supergraph.SupergraphException, DatabaseSearchException
      Gets a HitDisplayTool object from which the results can be retrieved. Parameters are similar to getHitsAsMolecules(int[], HitColoringAndAlignmentOptions, List, List) Additional parameters: molecules, sources Example usage: 
       List<Molecule> molecules = new ArrayList<Molecule>();
 List<byte[]> sources = new ArrayList<byte[]>();
 HitDisplayTool colorUtil = getHitsAsHitDisplayTool(idList, options,
         dataFieldNames, dataFieldValues, molecules, sources);
 for (int x = 0, n = molecules.size(); x < n; x++) {
     if (molecules.get(x) == null) { // not found
         continue;
     }
     colorUtil.setMoleculeMarkushSourceTarget(molecules.get(x), sources.get(x));
     // fetch the hits using colorUtil.getNextHit() or colorUtil.getHits(int)
     // ...
 }
      Parameters:
      idList - the cd_id list of hits to be retrieved.
      options - the options for coloring and alignment. If null the structures will be displayed in their original form.
      dataFieldNames - fields of the jchem table that should be fetched together with the structure or null.
      dataFieldValues - an empty List required or it can be null. The fetched values will be stored in this object as Object[] elements.
      molecules - An empty list that will contain the molecules to be set on the hitdisplaytool object. For not found IDs (e.g. deleted) null is set.
      sources - An empty list that will contain the byte array sources to be set on the hitdisplaytool object.
      Returns:
      the hitDisplayTool object
      Throws:
      SQLException - if an sql error encountered
      IOException - if an io exception is encountered
      SearchException - if there was an error during searching.
      chemaxon.enumeration.supergraph.SupergraphException - if there was an error during searching.
      DatabaseSearchException - if there was an error during searching.
      Since:
      version 5.4

    • setTargetCollection

      @Beta public void setTargetCollection(chemaxon.jchem.base.storage.search.CurrentTargetCollection targetCollection)
      For internal use only.
      Parameters:
      targetCollection - the targetcollection to use

    • toString

      public String toString()
      Overrides:
      toString in class Object