com.epam.indigo.Bingo Maven / Gradle / Ivy
/****************************************************************************
* Copyright (C) 2009-2015 EPAM Systems
*
* This file is part of Indigo toolkit.
*
* This file may be distributed and/or modified under the terms of the
* GNU General Public License version 3 as published by the Free Software
* Foundation and appearing in the file LICENSE.GPL included in the
* packaging of this file.
*
* This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
* WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
***************************************************************************/
package com.epam.indigo;
import com.sun.jna.Native;
import java.io.File;
import java.io.IOException;
public class Bingo {
private Indigo _indigo;
private static BingoLib _lib;
private int _id;
public Bingo (Indigo indigo, String location, String type, String options) {
loadLibrary(indigo.getUserSpecifiedPath());
_id = Bingo.checkResult(indigo, _lib.bingoCreateDatabaseFile(location, type, options));
_indigo = indigo;
}
public Bingo (Indigo indigo, String location, String options) {
loadLibrary(indigo.getUserSpecifiedPath());
_id = Bingo.checkResult(indigo, _lib.bingoLoadDatabaseFile(location, options));
_indigo = indigo;
}
protected void finalize() {
dispose();
}
private synchronized static void loadLibrary (String path) {
if (_lib != null)
return;
int os = Indigo.getOs();
if (os == Indigo.OS_LINUX || os == Indigo.OS_SOLARIS)
_lib = (BingoLib)Native.loadLibrary(getPathToBinary(path, "libbingo.so"), BingoLib.class);
else if (os == Indigo.OS_MACOS)
_lib = (BingoLib)Native.loadLibrary(getPathToBinary(path, "libbingo.dylib"), BingoLib.class);
else // os == OS_WINDOWS
_lib = (BingoLib)Native.loadLibrary(getPathToBinary(path, "bingo.dll"), BingoLib.class);
}
private static String getPathToBinary (String path, String filename) {
String dllpath = Indigo.getPlatformDependentPath();
if (path == null) {
String res = Indigo.extractFromJar(Bingo.class, "/" + dllpath, filename);
if (res != null)
return res;
path = "lib";
}
path = path + File.separator + dllpath + File.separator + filename;
try {
return (new File(path)).getCanonicalPath();
} catch (IOException e) {
return path;
}
}
public void dispose() {
if (_id >= 0) {
_indigo.setSessionID();
Bingo.checkResult(_indigo, _lib.bingoCloseDatabase(_id));
_id = -1;
}
}
public void close() {
dispose();
}
public static int checkResult(Indigo indigo, int result) {
if (result < 0) {
throw new BingoException(indigo, indigo.getLibrary().indigoGetLastError());
}
return result;
}
public static float checkResult(Indigo indigo, float result) {
if (result < 0.0) {
throw new BingoException(indigo, indigo.getLibrary().indigoGetLastError());
}
return result;
}
public static String checkResult(Indigo indigo, String result) {
if (result == null) {
throw new BingoException(indigo, indigo.getLibrary().indigoGetLastError());
}
return result;
}
/**
Creates a chemical storage of a specified type in a specified location
@param indigo Indigo instance
@param location Directory with the files location
@param type molecule" or "reaction"
@param options additional options separated with a semicolon. See the Bingo documentation for more detail
@return Bingo database instance
*/
public static Bingo createDatabaseFile(Indigo indigo, String location, String type, String options) {
indigo.setSessionID();
if (options == null)
{
options = "";
}
return new Bingo(indigo, location, type, options);
}
/**
Creates a chemical storage of a specified type in a specified location
@param indigo Indigo instance
@param location Directory with the files location
@param type molecule" or "reaction"
@return Bingo database instance
*/
public static Bingo createDatabaseFile(Indigo indigo, String location, String type) {
return createDatabaseFile(indigo, location, type, null);
}
/**
Loads a chemical storage of a specified type from a specified location
@param indigo Indigo instance
@param location Directory with the files location
@param options Additional options separated with a semicolon. See the Bingo documentation for more details
@return Bingo database instance
*/
public static Bingo loadDatabaseFile(Indigo indigo, String location, String options) {
if (options == null) {
options = "";
}
return new Bingo(indigo, location, options);
}
/**
Loads a chemical storage of a specified type from a specified location
@param indigo Indigo instance
@param location Directory with the files location
@return Bingo database instance
*/
public static Bingo loadDatabaseFile(Indigo indigo, String location) {
return loadDatabaseFile(indigo, location, null);
}
/**
Insert a structure into the database and returns id of this structure
@param record Indigo object with a chemical structure (molecule or reaction)
@return record id
*/
public int insert(IndigoObject record) {
_indigo.setSessionID();
return Bingo.checkResult(_indigo, _lib.bingoInsertRecordObj(_id, record.self));
}
/**
Inserts a structure under a specified id
@param record Indigo object with a chemical structure (molecule or reaction)
@param id record id
@return inserted record id
*/
public int insert(IndigoObject record, int id) {
_indigo.setSessionID();
return Bingo.checkResult(_indigo, _lib.bingoInsertRecordObjWithId(_id, record.self, id));
}
/**
Delete a record by id
@param id Record id
*/
public void delete(int id) {
_indigo.setSessionID();
Bingo.checkResult(_indigo, _lib.bingoDeleteRecord(_id, id));
}
/**
Execute substructure search operation
@param query Indigo query object (molecule or reaction)
@param options Search options
@return Bingo search object instance
*/
public BingoObject searchSub(IndigoObject query, String options) {
if (options == null) {
options = "";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(_indigo, _lib.bingoSearchSub(_id, query.self, options)), _indigo, _lib);
}
/**
Execute substructure search operation
@param query Indigo query object (molecule or reaction)
@return Bingo search object instance
*/
public BingoObject searchSub(IndigoObject query) {
return searchSub(query, null);
}
/**
Execute similarity search operation
@param query indigo object (molecule or reaction)
@param min Minimum similarity value
@param max Maximum similairy value
@param metric Default value is "tanimoto"
@return Bingo search object instance
*/
public BingoObject searchSim(IndigoObject query, float min, float max, String metric) {
if (metric == null) {
metric = "tanimoto";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(_indigo, _lib.bingoSearchSim(_id, query.self, min, max, metric)), _indigo, _lib);
}
/**
Execute Tanimoto similarity search operation
@param query indigo object (molecule or reaction)
@param min Minimum similarity value
@param max Maximum similairy value
@return Bingo search object instance
*/
public BingoObject searchSim(IndigoObject query, float min, float max) {
return searchSim(query, min, max, null);
}
/**
Perform exact search operation
@param query indigo object (molecule or reaction)
@param options search options
@return Bingo search object instance
*/
public BingoObject searchExact(IndigoObject query, String options) {
if (options == null) {
options = "";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(_indigo, _lib.bingoSearchExact(_id, query.self, options)), _indigo, _lib);
}
/**
Perform exact search operation
@param query indigo object (molecule or reaction)
@return Bingo search object instance
*/
public BingoObject searchExact(IndigoObject query) {
return searchExact(query, null);
}
/**
Perform search by molecular formula
@param query string with formula to search. For example, "C22 H23 N3 O2"
@param options search options
@return Bingo search object instance
*/
public BingoObject searchMolFormula(String query, String options) {
if (options == null) {
options = "";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(_indigo, _lib.bingoSearchMolFormula(_id, query, options)), _indigo, _lib);
}
/**
Perform search by molecular formula
@param query string with formula to search. For example, "C22 H23 N3 O2"
@return Bingo search object instance
*/
public BingoObject searchMolFormula(String query) {
return searchMolFormula(query, null);
}
/**
Post-process index optimization
*/
public void optimize () {
_indigo.setSessionID();
Bingo.checkResult(_indigo, _lib.bingoOptimize(_id));
}
/**
Returns an IndigoObject for the record with the specified id
@param id record id
@return Indigo object
*/
public IndigoObject getRecordById(int id) {
_indigo.setSessionID();
return new IndigoObject(_indigo, Bingo.checkResult(_indigo, _lib.bingoGetRecordObj(_id, id)));
}
/**
Returns Bingo version
@return Bingo version
*/
public String version() {
_indigo.setSessionID();
return Bingo.checkResult(_indigo, _lib.bingoVersion());
}
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