Importer (JChem Base API documentation (c) 1998-2019 ChemAxon Ltd.)

java.lang.Object
- java.lang.Thread
- - chemaxon.jchem.db.Importer

All Implemented Interfaces:

chemaxon.jchem.db.Transfer, java.lang.Runnable
```
@PublicAPI
public class Importer
extends java.lang.Thread
implements chemaxon.jchem.db.Transfer
```
Tool for importing molecules to database tables from a File or InputStream object. Example of usage: File Import/Export Tools.

Author:

JChem Base team, Szilard Dorant, Edvard Buki, Nora Mate, Robert Wagner

Nested Class Summary
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary
- Fields inherited from class java.lang.Thread
  MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY
- Fields inherited from interface chemaxon.jchem.db.Transfer
  CXSMARTS, CXSMILES, INCHI, MOL2FILE, MOLFILE, MRV, RDFILE, RXNFILE, SDFILE, SMARTS, SMILES

Constructor Summary

Constructors
Constructor and Description

Importer()
Constructor.

Constructors
Constructor and Description
`Importer()` Constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`cancel()` Stops the importing progress.
`ConnectionHandler`	`getConnectionHandler()` Getter for property connectionHandler.
`java.lang.String`	`getConnections()` Deprecated. since 2.2 replaced by `getFieldConnections()`.
`java.util.List<java.lang.Integer>`	`getDuplicateIDList()` Returns the IDs (cd_id column in database table) of duplicate structures.
`int`	`getDuplicates()` Returns the number of molecules that were not imported, because they are duplicates.
`int`	`getEmptyStructures()` Returns the number of molecules that were not imported, because they are empty strucures.
`boolean`	`getEmptyStructuresAllowed()` Gets whether empty structures are allowed.
`java.lang.Throwable`	`getErrorCause()` Retrieves Throwable caught in `run()` method.
`java.lang.String`	`getErrorMessage()` If error occurs this function returns the error message.
`java.lang.String`	`getFieldConnections()` Returns the specified table field - file field pairs.
`java.util.List<java.lang.String>`	`getFieldNameList()` Returns field names in an SDfile.
`static java.util.List<java.lang.String>`	`getFieldNameList(java.io.InputStream is, int linesToCheck)` Returns field names in an SDfile.
`java.util.List<java.lang.Integer>`	`getImportedIDList()` Returns the IDs (cd_id column in database table) of imported structures.
`int`	`getImportedNumber()` Returns the number of imported molecules.
`java.lang.Object`	`getInput()` Gets the source object.
`java.lang.String`	`getNameFieldInDB()`
`java.lang.String`	`getNote()` Returns the note of the progresswriter.
`long`	`getProgress()` Gets the status of the importing progress.
`ProgressWriter`	`getProgressWriter()` Gets the ProgressWriter object used for monitoring.
`int`	`getRecordsToCheck()` Gets the number of records to check for file format.
`boolean`	`getSetChiralFlag()` Gets whether chiral flag is set on import.
`int`	`getSkip()` Gets the number of molecules to skip from the beginning ogf file.
`int`	`getStructCount()` Returns the current count of structures which were examined by the import process.
`java.lang.String`	`getTableName()` Gets the name of the table to import into.
`int`	`importMols()` Imports molecules.
`void`	`init()` Initialization, checking given number of lines for file format and fields.
`boolean`	`isDuplicateImportAllowed()` Gets whether duplicate structures are allowed.
`boolean`	`isFinished()` Checks whenver the import has been finished.
`boolean`	`isHaltOnError()` Gets if import should stop when an error occurs.
`void`	`run()` Starts execution as a thread.
`void`	`setConnectionHandler(ConnectionHandler conh)` Setter for property connectionHandler.
`void`	`setConnections(java.lang.String connections)` Deprecated. since 2.2 replaced by `setFieldConnections(String)`.
`void`	`setDuplicateImportAllowed(boolean b)` Deprecated. since JChem 5.4. This import option has been table option, instead of this use `setDuplicateImportAllowed(int)` method
`void`	`setDuplicateImportAllowed(int duplicateFilteringOption)` Sets the duplicate filtering option on import.
`void`	`setEmptyStructuresAllowed(boolean b)` If set to `false` does not import empty molecules.
`void`	`setFieldConnections(java.lang.String connections)` Specifies which data fields correspond to which table fieds.
`void`	`setHaltOnError(boolean b)` Sets if import should stop when an error occurs.
`void`	`setInfoStream(java.io.PrintStream st)` Sets the stream where information about the import prorcess will be written (e.g.
`void`	`setInput(java.io.File inputFile)` Sets the source object as a file.
`void`	`setInput(java.io.InputStream is)` Sets the source object as a stream.
`void`	`setInput(java.lang.String fileName)` Sets the source object as a file, specifying the name of the file.
`void`	`setNameFieldInDB(java.lang.String fieldName)` Set a DB field to contain the structure name.
`void`	`setOutputOptions(boolean printDuplicates, boolean printNonDuplicates, java.io.OutputStream os, boolean doNotImport)` With this option one can print duplicate or non-duplicate molecules to a stream.
`void`	`setProgressWriter(ProgressWriter pwriter)` Sets the `ProgressWriter` object to track the progress the actual importing.
`void`	`setRecordsToCheck(int recordsToCheck)` Sets the number of records to check for file format.
`void`	`setSetChiralFlag(boolean setChiralFlag)` Sets if chiral flag should be set to `true` during import.
`void`	`setSkip(int skip)` Sets the number of molecules to skip from the beginning ogf file.
`void`	`setStoreDuplicates(boolean value)` Specifies whether the ID's of duplicate structures should be stored.
`void`	`setStoreImportedIDs(boolean value)` Specifies whether the ID's of imported structures should be stored.
`void`	`setTableName(java.lang.String tname)` Sets the name of the table to import into.
`void`	`skip(int offset)` Skips the given number of molecules.

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Importer
```
public Importer()
```
    Constructor.
- Method Detail
  - setConnectionHandler
```
public void setConnectionHandler(ConnectionHandler conh)
```
    Setter for property connectionHandler. The ConnectionHandler must represent an open connection to the database.
    
    Parameters:
    
    conh - the connection handler
  - getConnectionHandler
```
public ConnectionHandler getConnectionHandler()
```
    Getter for property connectionHandler.
    
    Returns:
    
    the connection handler
  - setInput
```
public void setInput(java.io.File inputFile)
```
    Sets the source object as a file.
    
    Parameters:
    
    inputFile - the source file
  - setInput
```
public void setInput(java.io.InputStream is)
```
    Sets the source object as a stream.
    
    Parameters:
    
    is - the source stream
  - setInput
```
public void setInput(java.lang.String fileName)
```
    Sets the source object as a file, specifying the name of the file.
    
    Parameters:
    
    fileName - the source file name
  - getInput
```
public java.lang.Object getInput()
```
    Gets the source object. The object may be File or InputStream.
    
    Returns:
    
    the source object
  - setTableName
```
public void setTableName(java.lang.String tname)
```
    Sets the name of the table to import into.
    
    Parameters:
    
    tname - the table name
  - getTableName
```
public java.lang.String getTableName()
```
    Gets the name of the table to import into.
    
    Returns:
    
    the table name
  - setConnections
```
@Deprecated
public void setConnections(java.lang.String connections)
```
    Deprecated. since 2.2 replaced by setFieldConnections(String).
    Specifies which data fields correspond to which table fields.
    The fields are given in pair in the following format: "databaseField1=dataField1;databaseField2=dataField2"
    - If empty String, no connections are made to extra fields.
    - If null, the fields are automatically connected by equal names (default).
    Parameters:
    
    connections - the connection string
  - setFieldConnections
```
public void setFieldConnections(java.lang.String connections)
```
    Specifies which data fields correspond to which table fieds.
    The fields are given in pair in the following format: "databaseField1=dataField1;databaseField2=dataField2"
    - If empty String, no connections are made to extra fields.
    - If null, the fields are automatically connected by equal names (default).
    Parameters:
    
    connections - the connection string
  - getConnections
```
@Deprecated
public java.lang.String getConnections()
```
    Deprecated. since 2.2 replaced by getFieldConnections().
    
    Returns the specified table field - file field pairs.
    
    Returns:
    
    the connection string
  - getFieldConnections
```
public java.lang.String getFieldConnections()
```
    Returns the specified table field - file field pairs.
    
    Returns:
    
    the connection string
  - setRecordsToCheck
```
public void setRecordsToCheck(int recordsToCheck)
```
    Sets the number of records to check for file format. The same number of records will be checked for field names in the case of SDfiles.
    Default value is 500 records.
    Note: In the case of using InputStream as source, these records are buffered in memory. Make sure java has enough memory when setting this value very high. (-Xmx parameter)
    Using File as input recommended if it's feasible, since it doesn't need buffering.
    
    Parameters:
    
    recordsToCheck - the number of records to check for file format
  - getRecordsToCheck
```
public int getRecordsToCheck()
```
    Gets the number of records to check for file format.
    
    Returns:
    
    the number of records to check for file format
  - setProgressWriter
```
public void setProgressWriter(ProgressWriter pwriter)
```
    Sets the ProgressWriter object to track the progress the actual importing. (Format checking and skipping not monitored by this object.)
    It can be null if no monitoring is necessary.
    
    Parameters:
    
    pwriter - the progress writer
  - getProgressWriter
```
public ProgressWriter getProgressWriter()
```
    Gets the ProgressWriter object used for monitoring.
    
    Returns:
    
    the progress writer
  - setHaltOnError
```
public void setHaltOnError(boolean b)
```
    Sets if import should stop when an error occurs.
    
    Parameters:
    
    b - true if halt on error
  - isHaltOnError
```
public boolean isHaltOnError()
```
    Gets if import should stop when an error occurs.
    
    Returns:
    
    true if halt on error
  - setDuplicateImportAllowed
```
@Deprecated
public void setDuplicateImportAllowed(boolean b)
```
    Deprecated. since JChem 5.4. This import option has been table option, instead of this use setDuplicateImportAllowed(int) method
    
    If set to false does not import molecules that already exist in the table with the same topology. This checking may slow down the import progress.
    
    Parameters:
    
    b - new value for duplicateFiltering
    
    See Also:
    
    DatabaseProperties.setDuplicateFilteringOption(String, boolean), StructureTableOptions.isDuplicateFiltering()
  - setDuplicateImportAllowed
```
public void setDuplicateImportAllowed(int duplicateFilteringOption)
```
    Sets the duplicate filtering option on import. It can be banned, allowed or specified by the table option.
    Parameters:
    duplicateFilteringOption -
    
    If set to DUPLICATE_FILTERING_ON does not import molecules that already exist in the table with the same topology. Forces switching ON duplicate filtering regardless of table setting. This checking may slow down the import progress.
    
    If set to DUPLICATE_FILTERING_OFF duplicates are allowed. Forces switching OFF duplicate filtering regardless of table setting.
    
    If set to DUPLICATE_FILTERING_TABLE_OPTION the value of the table option (StructureTableOptions.isDuplicateFiltering()) controls the filtering of duplicates.
    
    Warning: switching duplicate filtering upon import to a different option than the table duplicate filtering option may result in table content not consistent with the table option.
    See Also:
    
    UpdateHandler.DUPLICATE_FILTERING_ON, UpdateHandler.DUPLICATE_FILTERING_OFF, UpdateHandler.DUPLICATE_FILTERING_TABLE_OPTION, StructureTableOptions.isDuplicateFiltering()
  - isDuplicateImportAllowed
```
public boolean isDuplicateImportAllowed()
```
    Gets whether duplicate structures are allowed.
    
    Returns:
    
    true if duplicates are allowed
    
    Throws:
    
    java.lang.IllegalArgumentException - if duplicate filtering option of the table cannot be determined.
  - setEmptyStructuresAllowed
```
public void setEmptyStructuresAllowed(boolean b)
```
    If set to false does not import empty molecules.
    
    Parameters:
    
    b - set to true if empty structures are allowed
  - getEmptyStructuresAllowed
```
public boolean getEmptyStructuresAllowed()
```
    Gets whether empty structures are allowed.
    
    Returns:
    
    true if empty structures are allowed
  - setSetChiralFlag
```
public void setSetChiralFlag(boolean setChiralFlag)
```
    Sets if chiral flag should be set to true during import.
    
    Parameters:
    
    setChiralFlag - if set to true, chiral flag is set to true for imported molecules. The default setting is false. since 2.3
  - getSetChiralFlag
```
public boolean getSetChiralFlag()
```
    Gets whether chiral flag is set on import.
    
    Returns:
    
    the current state
  - setNameFieldInDB
```
public void setNameFieldInDB(java.lang.String fieldName)
```
    Set a DB field to contain the structure name.
    
    Parameters:
    
    fieldName - the name of the column in the database
  - getNameFieldInDB
```
public java.lang.String getNameFieldInDB()
```
  - isFinished
```
public boolean isFinished()
```
    Checks whenver the import has been finished.
    
    Returns:
    
    true if importing has finished, else returns false.
  - getErrorMessage
```
public java.lang.String getErrorMessage()
```
    If error occurs this function returns the error message.
    
    Returns:
    
    the error message
  - getErrorCause
```
public java.lang.Throwable getErrorCause()
```
    Retrieves Throwable caught in run() method. WARNING This mechanism is expected to be revised in the near future, use with extreme caution!
    
    Returns:
    
    the error cause or null
  - getStructCount
```
public int getStructCount()
```
    Returns the current count of structures which were examined by the import process.
    
    Returns:
    
    the number of molecules imported so far
  - getImportedNumber
```
public int getImportedNumber()
```
    Returns the number of imported molecules.
    
    Returns:
    
    the number of molecules imported
  - getDuplicates
```
public int getDuplicates()
```
    Returns the number of molecules that were not imported, because they are duplicates.
    
    Returns:
    
    the number of duplicates encountered
  - getEmptyStructures
```
public int getEmptyStructures()
```
    Returns the number of molecules that were not imported, because they are empty strucures.
    
    Returns:
    
    the count of empty structures skipped
  - getNote
```
public java.lang.String getNote()
```
    Returns the note of the progresswriter.
    
    Returns:
    
    the note
  - setSkip
```
public void setSkip(int skip)
```
    Sets the number of molecules to skip from the beginning ogf file.
    
    Parameters:
    
    skip - the number of molecule to skip
  - getSkip
```
public int getSkip()
```
    Gets the number of molecules to skip from the beginning ogf file.
    
    Returns:
    
    the number of molecules to skip
  - getProgress
```
public long getProgress()
```
    Gets the status of the importing progress.
    
    Returns:
    
    the position of the ProgressWriter, -1 if the object is not set (null)
  - run
```
public void run()
```
    Starts execution as a thread. Calls init(),skip(), and importMols. Exceptions are caught and printed to stderr.
    
    Specified by:
    
    run in interface java.lang.Runnable
    
    Overrides:
    
    run in class java.lang.Thread
  - setInfoStream
```
public void setInfoStream(java.io.PrintStream st)
```
    Sets the stream where information about the import prorcess will be written (e.g. skipped duplicates and empty structures).
    
    Parameters:
    
    st - the stream. The default is null (no info is written).
  - setOutputOptions
```
public void setOutputOptions(boolean printDuplicates,
                             boolean printNonDuplicates,
                             java.io.OutputStream os,
                             boolean doNotImport)
```
    With this option one can print duplicate or non-duplicate molecules to a stream. Will print only if duplicate filtering is allowed.
    
    Parameters:
    
    printDuplicates - prints indexes of duplicate structures
    
    printNonDuplicates - prints indexes of imported structures
    
    os - outputStream to write information, if null stdout is used.
    
    doNotImport - disables the real importing, just generates the index entry.
  - setStoreDuplicates
```
public void setStoreDuplicates(boolean value)
```
    Specifies whether the ID's of duplicate structures should be stored.
    
    Parameters:
    
    value - enable/disable storing of duplicates
    
    See Also:
    
    getDuplicateIDList()
  - setStoreImportedIDs
```
public void setStoreImportedIDs(boolean value)
```
    Specifies whether the ID's of imported structures should be stored.
    
    Parameters:
    
    value - enable/disable storing of ids
    
    Since:
    
    JChem 3.1.7
    
    See Also:
    
    getImportedIDList()
  - getDuplicateIDList
```
public java.util.List<java.lang.Integer> getDuplicateIDList()
```
    Returns the IDs (cd_id column in database table) of duplicate structures.
    
    Returns:
    
    the IDs as a list containing Integer objects.
    
    See Also:
    
    setStoreDuplicates(boolean)
  - getImportedIDList
```
public java.util.List<java.lang.Integer> getImportedIDList()
```
    Returns the IDs (cd_id column in database table) of imported structures.
    
    Returns:
    
    the IDs as a list containing Integer objects.
    
    See Also:
    
    setStoreImportedIDs(boolean)
  - importMols
```
public int importMols()
               throws TransferException
```
    Imports molecules.
    
    Returns:
    
    the number of molecules imported
    
    Throws:
    
    TransferException - if the settings are invalid
  - cancel
```
public void cancel()
```
    Stops the importing progress.
  - skip
```
public void skip(int offset)
          throws TransferException
```
    Skips the given number of molecules.
    
    Parameters:
    
    offset - the number of molecules to be skipped
    
    Throws:
    
    TransferException - if the settings are invalid
  - init
```
public void init()
          throws TransferException
```
    Initialization, checking given number of lines for file format and fields. If not called explicitly, automatically called by skip or importMols if necessary.
    
    Throws:
    
    TransferException - if the settings are invalid
  - getFieldNameList
```
public java.util.List<java.lang.String> getFieldNameList()
                                                  throws TransferException,
                                                         java.io.IOException
```
    Returns field names in an SDfile. The file may come from an InputStream, import may follow without reopening the stream. Calls int if initialization is necessary.
    
    Returns:
    
    a vector of String objects, the names of the SDfile fields.
    
    Throws:
    
    TransferException - in case of failure
    
    java.io.IOException - if an IOException occurs
  - getFieldNameList
```
public static java.util.List<java.lang.String> getFieldNameList(java.io.InputStream is,
                                                                int linesToCheck)
                                                         throws java.io.IOException,
                                                                MRecordParseException
```
    Returns field names in an SDfile. NOTE: in order to return to the initial position, the InputStream has to reopened or repositioned (BufferedInputStream)
    
    Parameters:
    
    is - inputStream to read from
    
    linesToCheck - read ahead this many lines during field name identification
    
    Returns:
    
    a vector of String objects, the names of the SDfile fields.
    
    Throws:
    
    java.io.IOException - if the inputstream encounters a problem
    
    MRecordParseException - if a record could not be read.

Class Importer

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class java.lang.Thread

Fields inherited from interface chemaxon.jchem.db.Transfer

Constructor Summary

Method Summary

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Constructor Detail

Importer

Method Detail

setConnectionHandler

getConnectionHandler

setInput

setInput

setInput

getInput

setTableName

getTableName

setConnections

setFieldConnections

getConnections

getFieldConnections

setRecordsToCheck

getRecordsToCheck

setProgressWriter

getProgressWriter

setHaltOnError

isHaltOnError

setDuplicateImportAllowed

setDuplicateImportAllowed

isDuplicateImportAllowed

setEmptyStructuresAllowed

getEmptyStructuresAllowed

setSetChiralFlag

getSetChiralFlag

setNameFieldInDB

getNameFieldInDB

isFinished

getErrorMessage

getErrorCause

getStructCount

getImportedNumber

getDuplicates

getEmptyStructures

getNote

setSkip

getSkip

getProgress

run

setInfoStream

setOutputOptions

setStoreDuplicates

setStoreImportedIDs

getDuplicateIDList

getImportedIDList

importMols

cancel

skip

init

getFieldNameList

getFieldNameList