org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

Class Database

java.lang.Object

org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

public class Database
extends Object

This database singleton class implements methods to work with a SQLite database while doing similarity search.

Author:

bueltel

Method Summary

Modifier and Type	Method and Description
void	addColumn(String url, String tablename, String columnname) Adds a new column to a given table of a database.
void	createTable(String url, String tableName, String column1, String column2) Method creates a table with two columns (int, text) for ID and HELM in a database.
void	deleteContentFromDB(String url) Method deletes content from a database in order to be able to overwrite it with new content.
void	fillHELMTable(String url, String infilename, CreateDatabaseTask createDatabase) Fills the table with CID and HELM from an inputfile.
void	fillHELMTanimotoTable(String url, String tablename, List<Integer> idList, List<Double> tanimotoList) Method fills table with tanimoto value at the corresponding ID.
double	getBiggestTanimoto(String url) Returns the maximum similarity value that is found of a notation to the query.
static Database	getInstance() This is the static instance method.
List<Map<String,Object>>	getMostSimilarNotations(String url, String tablename, String columnname) Method selects ten notations with the highest similarity to the query.
List<Map<String,Object>>	getNotationsWithSpecificTanimoto(String url, String tablename, String columnname, double desiredTanimoto) Selects the helm notations with a tanimoto bigger than or equal to the desired similarity.
List<Map<String,Object>>	getNotationsWithSubset(String url, String tablename, String columnname) Selects the helm notations that the query notation is a subset of.
void	insertFingerprints(String url, List<BitSet> fingerprints, List<BitSet> naturalFingerprints, List<Integer> idList, String tablename) Fill table with HELM fingerprint at the corresponding ID.
void	loadDriver(String drivername) Method loads the database's driver dynamically once for entire application's lifetime.
Map<Integer,String>	readIDandHELMRecords(String url, String tablename) Method reads ID and HELM from table.
void	setSubset(String url, BitSet queryFingerprint, List<Integer> idList, List<BitSet> fingerprints) Method checks for a list of fingerprints if the query notation is a subset of it and stores true or false in the database for the corresponding fingerprint.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getInstance

public static Database getInstance()

This is the static instance method.

Returns:

Database

loadDriver

public void loadDriver(String drivername)
                throws ClassNotFoundException

Method loads the database's driver dynamically once for entire application's lifetime.

Parameters:

drivername - the drivername

Throws:

ClassNotFoundException - if anything goes wrong

createTable

public void createTable(String url,
                        String tableName,
                        String column1,
                        String column2)
                 throws SQLException

Method creates a table with two columns (int, text) for ID and HELM in a database.

Parameters:

url - the url of the database

tableName - the name of the table

column1 - the name of the first column

column2 - the name of the second column

Throws:

SQLException - if the sql statement goes wrong

addColumn

public void addColumn(String url,
                      String tablename,
                      String columnname)
               throws SQLException

Adds a new column to a given table of a database.

Parameters:

url - the url of the database

tablename - the name of the table

columnname - the name of the first column

Throws:

SQLException - if the sql statement goes wrong

deleteContentFromDB

public void deleteContentFromDB(String url)
                         throws SQLException

Method deletes content from a database in order to be able to overwrite it with new content.

Parameters:

url - the url of the database

Throws:

SQLException - if the sql statement goes wrong

fillHELMTable

public void fillHELMTable(String url,
                          String infilename,
                          CreateDatabaseTask createDatabase)
                   throws SQLException,
                          IOException

Fills the table with CID and HELM from an inputfile.

Parameters:

url - the url of the database

infilename - the input filename

createDatabase - createDatabaseTask

Throws:

SQLException - if the sql statement goes wrong

IOException - if anything goes wrong

insertFingerprints

public void insertFingerprints(String url,
                               List<BitSet> fingerprints,
                               List<BitSet> naturalFingerprints,
                               List<Integer> idList,
                               String tablename)
                        throws SQLException

Fill table with HELM fingerprint at the corresponding ID.

Parameters:

url - the url of the database

fingerprints - fingerprint of a HELM notation

naturalFingerprints - natural fingerprint of HELM notation

idList - the list of iDs of HELM

tablename - the name of the table

Throws:

SQLException - if anything goes wrong

fillHELMTanimotoTable

public void fillHELMTanimotoTable(String url,
                                  String tablename,
                                  List<Integer> idList,
                                  List<Double> tanimotoList)
                           throws SQLException

Method fills table with tanimoto value at the corresponding ID.

Parameters:

url - the url of the database

tablename - the name of the table

idList - the list of iDs of HELM

tanimotoList - the list of tanimoto values

Throws:

SQLException - if the sql statement goes wrong

readIDandHELMRecords

public Map<Integer,String> readIDandHELMRecords(String url,
                                                String tablename)
                                         throws SQLException

Method reads ID and HELM from table.

Parameters:

url - the url of the database

tablename - the name of the table

Returns:

Map with ID and HELM

Throws:

SQLException - if the sql statement goes wrong

getMostSimilarNotations

public List<Map<String,Object>> getMostSimilarNotations(String url,
                                                        String tablename,
                                                        String columnname)
                                                 throws SQLException

Method selects ten notations with the highest similarity to the query.

Parameters:

url - the url of the database

tablename - the name of the table

columnname - the name of the column

Returns:

List similar notations

Throws:

SQLException - if the sql statement goes wrong

getNotationsWithSpecificTanimoto

public List<Map<String,Object>> getNotationsWithSpecificTanimoto(String url,
                                                                 String tablename,
                                                                 String columnname,
                                                                 double desiredTanimoto)
                                                          throws SQLException

Selects the helm notations with a tanimoto bigger than or equal to the desired similarity.

Parameters:

url - the url of the database

tablename - the name of the table

columnname - the name of the column

desiredTanimoto - the desired minimum tanimoto value

Returns:

List HELM notation with minimum tanimoto value

Throws:

SQLException - if the sql statement goes wrong

getNotationsWithSubset

public List<Map<String,Object>> getNotationsWithSubset(String url,
                                                       String tablename,
                                                       String columnname)
                                                throws SQLException

Selects the helm notations that the query notation is a subset of.

Parameters:

url - the url of the database

tablename - the name of the table

columnname - the name of the column

Returns:

List subset notations

Throws:

SQLException - if the sql statement goes wrong

setSubset

public void setSubset(String url,
                      BitSet queryFingerprint,
                      List<Integer> idList,
                      List<BitSet> fingerprints)
               throws SQLException

Method checks for a list of fingerprints if the query notation is a subset of it and stores true or false in the database for the corresponding fingerprint.

Parameters:

url - the url of the database

queryFingerprint - the query fingerprint

idList - the list of ids

fingerprints - the list of fingerprints

Throws:

SQLException - if the sql statement goes wrong

getBiggestTanimoto

public double getBiggestTanimoto(String url)
                          throws SQLException

Returns the maximum similarity value that is found of a notation to the query.

Parameters:

url - the url of the database

Returns:

double the biggest found tanimoto value

Throws:

SQLException - if the sql statement goes wrong