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/****************************************************************************
* Copyright (C) from 2009 to Present EPAM Systems.
*
* This file is part of Indigo toolkit.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
***************************************************************************/
package com.epam.indigo;
import com.sun.jna.Native;
import com.sun.jna.Platform;
import java.io.FileNotFoundException;
public class Bingo {
private final 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));
this.indigo = indigo;
}
public Bingo(Indigo indigo, String location, String options) {
loadLibrary(indigo.getUserSpecifiedPath());
this.indigo = indigo;
this.indigo.setSessionID();
id = Bingo.checkResult(indigo, lib.bingoLoadDatabaseFile(location, options));
}
protected void finalize() {
dispose();
}
private synchronized static void loadLibrary(String path) {
if (lib != null)
return;
try {
if (Platform.isLinux() || Platform.isSolaris())
lib = Native.load(IndigoUtils.getPathToBinary(Bingo.class, Indigo.getPlatformDependentPath(), path, "libbingo-nosql.so"), BingoLib.class);
else if (Platform.isMac())
lib = Native.load(IndigoUtils.getPathToBinary(Bingo.class, Indigo.getPlatformDependentPath(), path, "libbingo-nosql.dylib"), BingoLib.class);
else if (Platform.isWindows())
lib = Native.load(IndigoUtils.getPathToBinary(Bingo.class, Indigo.getPlatformDependentPath(), path, "bingo-nosql.dll"), BingoLib.class);
} catch (FileNotFoundException e) {
throw new RuntimeException(e.getMessage());
}
}
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(this.id, record.self, id));
}
/**
* Insert a structure into the database and returns id of this structure
*
* @param record Indigo object with a chemical structure (molecule or reaction)
* @param ext_fp Indigo object with a external similarity fingerprint (molecule or reaction)
* @return record id
*/
public int insertWithExtFP(IndigoObject record, IndigoObject ext_fp) {
indigo.setSessionID();
return Bingo.checkResult(indigo, lib.bingoInsertRecordObjWithExtFP(id, record.self, ext_fp.self));
}
/**
* Inserts a structure under a specified id
*
* @param record Indigo object with a chemical structure (molecule or reaction)
* @param id record id
* @param ext_fp Indigo object with a external similarity fingerprint (molecule or reaction)
* @return inserted record id
*/
public int insertWithExtFP(IndigoObject record, IndigoObject ext_fp, int id) {
indigo.setSessionID();
return Bingo.checkResult(indigo, lib.bingoInsertRecordObjWithIdAndExtFP(this.id, record.self, id, ext_fp.self));
}
/**
* Delete a record by id
*
* @param id Record id
*/
public void delete(int id) {
indigo.setSessionID();
Bingo.checkResult(indigo, lib.bingoDeleteRecord(this.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 similarity 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 similarity search operation
*
* @param query indigo object (molecule or reaction)
* @param min Minimum similarity value
* @param max Maximum similarity value
* @return Bingo search object instance
*/
public BingoObject searchSim(IndigoObject query, float min, float max) {
return searchSim(query, min, max, null);
}
/**
* Execute similarity search with external fingerprint
*
* @param query indigo object (molecule or reaction)
* @param min Minimum similarity value
* @param max Maximum similarity value
* @param ext_fp Indigo object with a external similarity fingerprint (molecule or reaction)
* @param metric Default value is "tanimoto"
* @return Bingo search object instance
*/
public BingoObject searchSimWithExtFP(IndigoObject query, float min, float max, IndigoObject ext_fp, String metric) {
if (metric == null) {
metric = "tanimoto";
}
indigo.setSessionID();
return new BingoObject(Bingo.checkResult(indigo, lib.bingoSearchSimWithExtFP(id, query.self, min, max, ext_fp.self, metric)), indigo, lib);
}
/**
* Execute similarity search with external fingerprint
*
* @param query indigo object (molecule or reaction)
* @param min Minimum similarity value
* @param max Maximum similarity value
* @param ext_fp Indigo object with a external similarity fingerprint (molecule or reaction)
* @return Bingo search object instance
*/
public BingoObject searchSimWithExtFP(IndigoObject query, float min, float max, IndigoObject ext_fp) {
return searchSimWithExtFP(query, min, max, ext_fp, null);
}
/**
* Execute similarity search for most similar structures (defined by limit)
*
* @param query indigo object (molecule or reaction)
* @param limit Number of structures
* @param minSim Minimum similarity value
* @param metric Default value is "tanimoto"
* @return Bingo search object instance
*/
public BingoObject searchSimTopN(IndigoObject query, int limit, float minSim, String metric) {
if (metric == null) {
metric = "tanimoto";
}
indigo.setSessionID();
return new BingoObject(Bingo.checkResult(indigo, lib.bingoSearchSimTopN(id, query.self, limit, minSim, metric)), indigo, lib);
}
/**
* Execute similarity search for most similar structures (defined by limit)
*
* @param query indigo object (molecule or reaction)
* @param limit Number of structures
* @param minSim Minimum similarity value
* @return Bingo search object instance
*/
public BingoObject searchSimTopN(IndigoObject query, int limit, float minSim) {
return searchSimTopN(query, limit, minSim, null);
}
/**
* Execute similarity search for most similar structures with external fingerprint
*
* @param query indigo object (molecule or reaction)
* @param limit Number of structures
* @param minSim Minimum similarity value
* @param metric Default value is "tanimoto"
* @param extFp Indigo object with a external similarity fingerprint (molecule or reaction)
* @return Bingo search object instance
*/
public BingoObject searchSimTopNWithExtFP(IndigoObject query, int limit, float minSim, IndigoObject extFp, String metric) {
if (metric == null) {
metric = "tanimoto";
}
indigo.setSessionID();
return new BingoObject(Bingo.checkResult(indigo, lib.bingoSearchSimTopNWithExtFP(id, query.self, limit, minSim, extFp.self, metric)), indigo, lib);
}
/**
* Execute similarity search for most similar structures with external fingerprint
*
* @param query indigo object (molecule or reaction)
* @param limit Number of structures
* @param minSim Minimum similarity value
* @param extFp Indigo object with a external similarity fingerprint (molecule or reaction)
* @return Bingo search object instance
*/
public BingoObject searchSimTopNWithExtFP(IndigoObject query, int limit, float minSim, IndigoObject extFp) {
return searchSimTopNWithExtFP(query, limit, minSim, extFp, null);
}
/**
* Execute enumerate id operation
*
* @return Bingo enumerate id object instance
*/
public BingoObject enumerateId() {
indigo.setSessionID();
return new BingoObject(Bingo.checkResult(indigo, lib.bingoEnumerateId(id)), indigo, lib);
}
/**
* 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(this.id, id)));
}
/**
* Returns Bingo version
*
* @return Bingo version
*/
public String version() {
indigo.setSessionID();
return Bingo.checkResult(indigo, lib.bingoVersion());
}
}
