Package com.im.ijcs.api.ddl

Interface JChemTableManager

  • All Superinterfaces:
    TableManager
    public interface JChemTableManager
extends TableManager
    Provides a central point for management of JChem tables and their associated artifacts. All tables and associated artifacts should be created through this class. This class should be remotable as all method arguments and return types are simple Objects that are Serializable and it does not use any DFItems.
    Author:
    Tim Dudgeon

    • Field Detail

      • DEFAULT_JCHEMPROPERTIES_TABLE_NAME

        @Deprecated
static final java.lang.String DEFAULT_JCHEMPROPERTIES_TABLE_NAME
        Deprecated.
        Use @{link com.im.commons.db.ddl.DBDatabaseInfo.DEFAULT_JCHEMPROPERTIES_TABLE_NAME}
        See Also:
        Constant Field Values

    • Method Detail

      • rebuildCartridgeIndex

        void rebuildCartridgeIndex​(com.im.commons.db.ddl.DBIndexInfo index,
                           boolean recalculate,
                           com.im.commons.progress.DFFeedback feedback)
        Rebuild the cartridge index in place. Usually done to repair an index that has been marked as invalid during a failed operation by setting recalculate to false.
        Parameters:
        index - The JChem cartridge index
        recalculate - Whether to recalualate the descriptors. If true the operation can be very slow. Usually false is sufficient to repair an index that has become invalid as a result of an exception.
        feedback - The feedback for reporting operation progress, etc.

      • updateChemicalTermsColumn

        com.im.commons.db.ddl.DBColInfo updateChemicalTermsColumn​(com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo desc,
                                                          com.im.commons.db.ddl.DBColInfo colInfo,
                                                          java.lang.String newChemicalTermsExpression,
                                                          com.im.commons.progress.DFFeedback feedback)

      • updateAbsoluteStereo

        com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo updateAbsoluteStereo​(com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo desc,
                                                                               boolean newValue,
                                                                               com.im.commons.progress.DFFeedback feedback)

      • updateStandardizer

        com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo updateStandardizer​(com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo desc,
                                                                             java.lang.String stndzr,
                                                                             com.im.commons.progress.DFFeedback feedback)

      • createJChemTableUpdater

        com.im.commons.db.JChemTableUpdater createJChemTableUpdater​(java.lang.String dbSchemaName,
                                                            java.lang.String propTableName)
                                                     throws java.sql.SQLException
        Throws:
        java.sql.SQLException

      • dropJChemPropertyTable

        void dropJChemPropertyTable​(java.lang.String dbSchemaName,
                            java.lang.String propTableName,
                            com.im.commons.progress.DFFeedback feedback)
        Drop the specified JChem property table
        Parameters:
        dbSchemaName - The DB schema
        propTableName - The name of the property table
        feedback - The feedback for reporting operation progress, etc.

      • setJChemPropertyTableProperties

        void setJChemPropertyTableProperties​(java.lang.String dbSchemaName,
                                     java.lang.String propTableName,
                                     java.util.Map<java.lang.String,​java.lang.String> props,
                                     com.im.commons.progress.DFFeedback feedback)
        Sets the specified properties into the JChem property table. throws an exception if the table does not exist

      • createJChemPropertyTable

        com.im.commons.db.ddl.tablesets.JChemPropertyTableSetInfo createJChemPropertyTable​(java.lang.String dbSchemaName,
                                                                                   java.lang.String propTableName,
                                                                                   java.util.Map<java.lang.String,​java.lang.String> props,
                                                                                   com.im.commons.progress.DFFeedback feedback)
        Creates the JChem property table. The table name is specified by the value of the jChemPropsTable property which is is initialized to JChemProperties if no value is specified
        Parameters:
        dbSchemaName - The schema for the table
        propTableName - The table name for the property table
        props - The p roperties that should be added to the table

      • addChemicalTermsColumn

        com.im.commons.db.ddl.DBColInfo addChemicalTermsColumn​(com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo desc,
                                                       java.lang.String columnName,
                                                       java.lang.String colClass,
                                                       java.lang.String nativeType,
                                                       java.lang.String columnDefinition,
                                                       java.lang.String chemicalTermsExpression,
                                                       com.im.commons.progress.DFFeedback feedback)

      • createJChemCartIndex

        com.im.commons.db.ddl.tablesets.JChemCartridgeAbstractTableSetInfo createJChemCartIndex​(com.im.commons.db.ddl.tablesets.StandardTableSetInfo desc,
                                                                                        java.lang.String structureColName,
                                                                                        java.lang.String schemaPlusIndexName,
                                                                                        java.lang.String schemaPlusProptable,
                                                                                        int tableType,
                                                                                        int numberOfInts,
                                                                                        int numberOfOnes,
                                                                                        int numberOfEdges,
                                                                                        java.lang.String standardizer,
                                                                                        boolean absoluteStereo,
                                                                                        boolean duplicateFiltering,
                                                                                        boolean tautomerDuplicateChecking,
                                                                                        com.im.commons.progress.DFFeedback feedback)
        Add a cartridge index to the standard table, replacing the StandardTableSetInfo for a JChemCartridgeStandardTableSetInfo
        Parameters:
        desc - The table description for the standard table
        structureColName - The name of the column with the structures. The index will be added to this column
        schemaPlusIndexName - The schema qualified name of the cart index
        schemaPlusProptable - The scheam qualified property table name
        tableType -
        numberOfInts -
        numberOfOnes -
        numberOfEdges -
        standardizer -
        absoluteStereo -
        duplicateFiltering -
        tautomerDuplicateChecking -
        feedback - The feedback for reporting operation progress, etc.
        Returns:
        The new table description

      • retrieveMolecularDescriptors

        java.util.List<chemaxon.descriptors.MolecularDescriptor> retrieveMolecularDescriptors​(com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo desc)

      • retrieveDissimilarityMetrics

        chemaxon.jchem.db.JChemSearch.DissimilarityMetrics retrieveDissimilarityMetrics​(com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo desc)

      • getTablesAssociatedWithPropertyTable

        @Deprecated
com.im.commons.util.CaseInsensitiveSet getTablesAssociatedWithPropertyTable​(java.lang.String schemaPlusProptable)
        Deprecated.
        Get all JChem tables belonging to this property table.
        Parameters:
        schemaPlusProptable - The schema qualified property table name
        Returns:
        The schema qualified table names of the tables used by this property table. The case cannot be relied on so this is returned as a case insensitive set

      • getPropertyTableForJChemBaseTable

        java.lang.String getPropertyTableForJChemBaseTable​(java.lang.String dbSchemaName,
                                                   java.lang.String table)

      • getTableSetInfoForJChemBaseTable

        com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo getTableSetInfoForJChemBaseTable​(java.lang.String dbSchemaName,
                                                                                           java.lang.String tableName,
                                                                                           java.lang.String schemaPlusProptable)

      • createJChemBaseTable

        com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo createJChemBaseTable​(java.lang.String dbSchemaName,
                                                                               java.lang.String tableName,
                                                                               java.lang.String schemaPlusProptable,
                                                                               int tableType,
                                                                               int numberOfInts,
                                                                               int numberOfOnes,
                                                                               int numberOfEdges,
                                                                               boolean absoluteStereo,
                                                                               boolean tautomerDuplicateChecking,
                                                                               java.lang.String standardizerConfig,
                                                                               com.im.commons.progress.DFFeedback feedback)

      • createJChemCartIndex

        com.im.commons.db.ddl.tablesets.JChemCartridgeAbstractTableSetInfo createJChemCartIndex​(com.im.commons.db.ddl.tablesets.JChemBaseTableSetInfo desc,
                                                                                        java.lang.String structureColName,
                                                                                        java.lang.String schemaPlusIndexName,
                                                                                        java.util.Map<java.lang.String,​java.lang.String> params,
                                                                                        com.im.commons.progress.DFFeedback feedback)
        Add a cartridge index to the JChem table, replacing the JChemBaseTableSetInfo for a JChemCartridgeJChemBaseTableSetInfo
        Parameters:
        desc - The table description for the JChemBase table
        structureColName - Should be CD_STRUCTURE
        schemaPlusIndexName - The schema qualified name of the cart index
        params - The cart creation params and name=value type pairs
        feedback - The feedback for reporting operation progress, etc.
        Returns:
        The new table dsescription

      • dropChemicalTermsColumn

        void dropChemicalTermsColumn​(com.im.commons.db.ddl.tablesets.AbstractJChemTableSetInfo desc,
                             java.lang.String columnName,
                             com.im.commons.progress.DFFeedback feedback)
        Delete a chemical terms column.
        Parameters:
        desc - The AbstractJChemTableSetInfo
        columnName - The name of the database column for a JChemBase table, or the name of the column in the index table for a cartridge index on a standard table
        feedback - The feedback for reporting operation progress, etc.