trunk/proteinstructure/DbGraph.java

package proteinstructure;

import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.Collections;
import java.util.TreeMap;

import tools.MySQLConnection;

/**
 * A residue interaction graph derived from a single chain pdb protein structure loaded from a graph database in aglappe's format 
 * 
 * @author              Jose Duarte
 * Class:               DbGraph
 * Package:             proteinstructure
 */
public class DbGraph extends Graph {

        private final static String MYSQLSERVER="white";
        private final static String MYSQLUSER=MySQLConnection.getUserName();
        private final static String MYSQLPWD="nieve";
        
        private final static String DEFAULT_CR ="(true)"; // default contact range (CR field in graph db)
        private final static String DEFAULT_CW ="1";      // default contact weight (CW field in graph db)
        
        private int graphid=0;
        //private int sm_id=0; // for future use
        
        private String dbname;
        private MySQLConnection conn;

        /**
         * Constructs Graph object from graph db, given the dbname, pdbCode, pdbChainCode (classic pdb chain code), ct and cutoff
         * and passing a MySQLConnection
         * @param dbname
         * @param conn
         * @param pdbCode
         * @param pdbChainCode
         * @param cutoff
         * @param ct
         * @throws GraphIdNotFoundError 
         * @throws SQLException 
         */
        public DbGraph(String dbname, MySQLConnection conn, String pdbCode, String pdbChainCode, double cutoff, String ct) throws GraphIdNotFoundError, SQLException {
                this.dbname=dbname;
                this.conn=conn;
                this.cutoff=cutoff;
                this.pdbCode=pdbCode.toLowerCase();                             // our convention: pdb codes are lower case
                this.pdbChainCode=pdbChainCode.toUpperCase();   // our convention: chain codes are upper case
                this.ct=ct;
                this.directed=false;
                // we set the sequence to empty when we read from graph db. We don't have the full sequence in graph db
                // when we pass the sequence in getCM to the ContactMap constructor we want to have either a full sequence (with unobserveds) or a blank in case we don't have the info
                this.sequence=""; 
                //TODO graphs in db are never directed, so this doesn't really apply here. Must solve all this!
                if (ct.contains("/")){
                        directed=true;
                }
                
                getgraphid(); // initialises graphid, sm_id and chainCode
                read_graph_from_db(); // gets contacts, nodes and sequence
                
                this.obsLength=nodes.size();
                if (!sequence.equals("")){
                        this.fullLength=sequence.length();
                } else {
                        // if nodes TreeMap has correct residue numbering then this should get the right full length,
                        // we will only miss: gaps (unobserved residues) at the end of the sequence. Those we can't know unless full sequence is given
                        this.fullLength=Collections.max(nodes.keySet());
                }
                this.numContacts=contacts.size();
                this.modified=false;
        }
        
        /**
         * Constructs Graph object from graph db, given the dbname, pdbCode, pdbChainCode (classic pdb chain code), ct and cutoff
         * MySQLConnection is taken from defaults in DbGraph class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
         * @param dbname
         * @param pdbCode
         * @param pdbChainCode
         * @param cutoff
         * @param ct
         * @throws GraphIdNotFoundError
         * @throws SQLException
         */
        public DbGraph(String dbname, String pdbCode, String pdbChainCode, double cutoff, String ct) throws GraphIdNotFoundError, SQLException{ 
                this(dbname,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD),pdbCode,pdbChainCode,cutoff,ct);
        }
        
        
        /**
         * Constructs Graph object from graph db, given the graphid and passing a MySQLConnection
         * @param dbname
         * @param conn
         * @param graphid
         * @throws GraphIdNotFoundError 
         * @throws SQLException 
         */
        public DbGraph(String dbname, MySQLConnection conn, int graphid) throws GraphIdNotFoundError, SQLException {
                this.dbname=dbname;
                this.conn=conn;
                this.graphid=graphid;
                this.directed=false;
                // we set the sequence to empty when we read from graph db. We don't have the full sequence in graph db
                // when we pass the sequence in getCM to the ContactMap constructor we want to have either a full sequence (with unobserveds) or a blank in case we don't have the info
                this.sequence="";
                
                read_graph_from_db(); // gets contacts, nodes and sequence
                get_db_graph_info(); // gets pdbCode, pdbChainCode, chainCode, ct and cutoff from db (from graph_id)
                
                //TODO graphs in db are never directed, so this doesn't really apply here. Must solve all this!
                if (ct.contains("/")){
                        directed=true;
                }
                this.obsLength=nodes.size();
                if (!sequence.equals("")){
                        this.fullLength=sequence.length();
                } else {
                        // if nodes TreeMap has correct residue numbering then this should get the right full length,
                        // we will only miss: gaps (unobserved residues) at the end of the sequence. Those we can't know unless full sequence is given
                        this.fullLength=Collections.max(nodes.keySet());
                }
                this.numContacts=contacts.size();
                this.modified=false;
        }

        /**
         * Constructs Graph object from graph db, given the graphid
         * MySQLConnection is taken from defaults in DbGraph class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
         * @param dbname
         * @param graphid
         * @throws GraphIdNotFoundError
         * @throws SQLException
         */
        public DbGraph(String dbname, int graphid) throws GraphIdNotFoundError, SQLException{
                this(dbname,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD), graphid);
        }
        
        /**
         * Reads contacts and nodes from db.
         * The db must be a graph db following our standard format, i.e. must have tables: 
         * chain_graph, single_model_graph, single_model_node, single_model_edge
         * We don't care here about the origin of the data (msdsd, pdbase, predicted) for the generation of the graph as long as it follows our data format
         * We read both edges and nodes from single_model_edge and single_model_node.
         * The sequence is set to blank, as we can't get the full sequence from graph db
         * @param conn
         * @throws SQLException 
         */
        private void read_graph_from_db() throws SQLException{
                contacts = new EdgeSet();
                nodes = new TreeMap<Integer, String>();

                // we read only half of the matrix (contacts in one direction only) so that we have the same type of contacts as when creating Graph from Pdb object
                String sql="SELECT i_num,j_num FROM "+dbname+".single_model_edge WHERE graph_id="+graphid+" AND j_num>i_num ORDER BY i_num,j_num ";
                Statement stmt = conn.createStatement();
                ResultSet rsst = stmt.executeQuery(sql);
                while (rsst.next()) {
                        int i=rsst.getInt(1);
                        int j=rsst.getInt(2);
                        contacts.add(new Edge(i,j));
                }
                rsst.close();
                stmt.close();
                sql="SELECT num,res FROM "+dbname+".single_model_node WHERE graph_id="+graphid+" ORDER BY num ";
                stmt = conn.createStatement();
                rsst = stmt.executeQuery(sql);
                while (rsst.next()){
                        int num=rsst.getInt(1);
                        String res=rsst.getString(2);
                        nodes.put(num, AA.oneletter2threeletter(res));
                }
                rsst.close();
                stmt.close();
        }
        
        private void getgraphid () throws GraphIdNotFoundError, SQLException{
                // input is pdbChainCode i.e. pdb chain code
        // we take chainCode (internal chain identifier, pchain_code for msdsd and asym_id for pdbase) from pchain_code field in chain_graph 
        // (in the chain_graph table the internal chain identifier is called 'pchain_code')
                int pgraphid=0;
                String chainstr="='"+pdbChainCode+"' ";
                if (pdbChainCode.equals("NULL")){
                        chainstr=" IS NULL ";
                }

                String sql="SELECT graph_id, pchain_code FROM "+dbname+".chain_graph WHERE accession_code='"+pdbCode+"' AND chain_pdb_code"+chainstr+" AND dist="+cutoff;
                Statement stmt = conn.createStatement();
                ResultSet rsst = stmt.executeQuery(sql);
                int check=0;
                while (rsst.next()) {
                        check++;
                        pgraphid=rsst.getInt(1);
                        chainCode=rsst.getString(2);
                }
                if (check!=1){
                        System.err.println("No pgraph_id match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode+", dist="+cutoff);
                }
                rsst.close();
                stmt.close();
                // we set the ctstr to the same as ct except in ALL case, where it is BB+SC+BB/SC
                String ctstr=ct;
                if (ct.equals("ALL")){
                        ctstr="BB+SC+BB/SC";
                }
                sql="SELECT graph_id,single_model_id FROM "+dbname+".single_model_graph WHERE pgraph_id="+pgraphid+" AND CT='"+ctstr+"' AND dist="+cutoff+" AND CR='"+DEFAULT_CR+"' AND CW="+DEFAULT_CW;
                stmt = conn.createStatement();
                rsst = stmt.executeQuery(sql);
                check=0;
                while (rsst.next()){
                        check++;
                        graphid=rsst.getInt(1);
                        //sm_id=rsst.getInt(2); // we might want to use it in the future
                }
                if (check!=1){
                        //System.err.println("No graph_id match or more than 1 match for pgraph_id="+pgraphid+", CT="+ctstr+" and cutoff="+cutoff);
                        throw new GraphIdNotFoundError("No graph_id match or more than 1 match for pgraph_id="+pgraphid+", CT="+ctstr+" and cutoff="+cutoff);
                }
        }
        
        private void get_db_graph_info() throws GraphIdNotFoundError, SQLException {
                        int pgraphid=0;
                        String sql="SELECT pgraph_id,CT,dist FROM "+dbname+".single_model_graph WHERE graph_id="+graphid;
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        int check=0;
                        while (rsst.next()) {
                                check++;
                                pgraphid=rsst.getInt(1);
                                ct=rsst.getString(2);
                                if (ct.equals("BB+SC+BB/SC")) ct="ALL";
                                cutoff=rsst.getDouble(3);
                        }
                        if (check!=1){
                                //System.err.println("No pgraph_id match or more than 1 match for graph_id="+graphid);
                                throw new GraphIdNotFoundError("No pgraph_id match or more than 1 match for graph_id="+graphid+" in db"+conn.getDbname());
                        }
                        rsst.close();
                        stmt.close();
                        sql="SELECT accession_code, chain_pdb_code, pchain_code FROM "+dbname+".chain_graph WHERE graph_id="+pgraphid;
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        check=0;
                        while (rsst.next()){
                                check++;
                                pdbCode=rsst.getString(1);
                                pdbChainCode=rsst.getString(2);
                                // java returns a null if the field is a database null, we want actually the "NULL" string in that case
                                if (pdbChainCode==null) pdbChainCode="NULL";
                                chainCode=rsst.getString(3);
                        }
                        if (check!=1){
                                System.err.println("No accession_code+chain_pdb_code+pchain_code match or more than 1 match for graph_id="+pgraphid+" in chain_graph table");
                        }
                        rsst.close();
                        stmt.close();
        }

}
Revision:	234
Committed:	Tue Jul 10 14:14:58 2007 UTC (17 years, 2 months ago) by duarte
File size:	10140 byte(s)
Log Message:	Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear) REFACTORING: ContactList -> EdgeSet Contact -> Edge
Line	User	Rev	File contents
1	duarte	207	package proteinstructure;
2
3			import java.sql.ResultSet;
4			import java.sql.SQLException;
5			import java.sql.Statement;
6			import java.util.Collections;
7			import java.util.TreeMap;
8
9			import tools.MySQLConnection;
10
11			/**
12			* A residue interaction graph derived from a single chain pdb protein structure loaded from a graph database in aglappe's format
13			*
14			* @author Jose Duarte
15			* Class: DbGraph
16			* Package: proteinstructure
17			*/
18			public class DbGraph extends Graph {
19
20			private final static String MYSQLSERVER="white";
21			private final static String MYSQLUSER=MySQLConnection.getUserName();
22			private final static String MYSQLPWD="nieve";
23
24	duarte	208	private final static String DEFAULT_CR ="(true)"; // default contact range (CR field in graph db)
25			private final static String DEFAULT_CW ="1"; // default contact weight (CW field in graph db)
26
27	duarte	207	private int graphid=0;
28			//private int sm_id=0; // for future use
29
30			private String dbname;
31			private MySQLConnection conn;
32
33			/**
34			* Constructs Graph object from graph db, given the dbname, pdbCode, pdbChainCode (classic pdb chain code), ct and cutoff
35			* and passing a MySQLConnection
36			* @param dbname
37			* @param conn
38			* @param pdbCode
39			* @param pdbChainCode
40			* @param cutoff
41			* @param ct
42			* @throws GraphIdNotFoundError
43	duarte	210	* @throws SQLException
44	duarte	207	*/
45	duarte	210	public DbGraph(String dbname, MySQLConnection conn, String pdbCode, String pdbChainCode, double cutoff, String ct) throws GraphIdNotFoundError, SQLException {
46	duarte	207	this.dbname=dbname;
47			this.conn=conn;
48			this.cutoff=cutoff;
49	stehr	217	this.pdbCode=pdbCode.toLowerCase(); // our convention: pdb codes are lower case
50			this.pdbChainCode=pdbChainCode.toUpperCase(); // our convention: chain codes are upper case
51	duarte	207	this.ct=ct;
52	duarte	208	this.directed=false;
53	duarte	207	// we set the sequence to empty when we read from graph db. We don't have the full sequence in graph db
54			// when we pass the sequence in getCM to the ContactMap constructor we want to have either a full sequence (with unobserveds) or a blank in case we don't have the info
55			this.sequence="";
56			//TODO graphs in db are never directed, so this doesn't really apply here. Must solve all this!
57			if (ct.contains("/")){
58			directed=true;
59			}
60
61			getgraphid(); // initialises graphid, sm_id and chainCode
62			read_graph_from_db(); // gets contacts, nodes and sequence
63
64			this.obsLength=nodes.size();
65			if (!sequence.equals("")){
66			this.fullLength=sequence.length();
67			} else {
68			// if nodes TreeMap has correct residue numbering then this should get the right full length,
69			// we will only miss: gaps (unobserved residues) at the end of the sequence. Those we can't know unless full sequence is given
70			this.fullLength=Collections.max(nodes.keySet());
71			}
72			this.numContacts=contacts.size();
73			this.modified=false;
74			}
75
76			/**
77			* Constructs Graph object from graph db, given the dbname, pdbCode, pdbChainCode (classic pdb chain code), ct and cutoff
78			* MySQLConnection is taken from defaults in DbGraph class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
79			* @param dbname
80			* @param pdbCode
81			* @param pdbChainCode
82			* @param cutoff
83			* @param ct
84			* @throws GraphIdNotFoundError
85			* @throws SQLException
86			*/
87			public DbGraph(String dbname, String pdbCode, String pdbChainCode, double cutoff, String ct) throws GraphIdNotFoundError, SQLException{
88			this(dbname,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD),pdbCode,pdbChainCode,cutoff,ct);
89			}
90
91
92			/**
93			* Constructs Graph object from graph db, given the graphid and passing a MySQLConnection
94			* @param dbname
95			* @param conn
96			* @param graphid
97			* @throws GraphIdNotFoundError
98	duarte	210	* @throws SQLException
99	duarte	207	*/
100	duarte	210	public DbGraph(String dbname, MySQLConnection conn, int graphid) throws GraphIdNotFoundError, SQLException {
101	duarte	207	this.dbname=dbname;
102			this.conn=conn;
103			this.graphid=graphid;
104	duarte	210	this.directed=false;
105	duarte	207	// we set the sequence to empty when we read from graph db. We don't have the full sequence in graph db
106			// when we pass the sequence in getCM to the ContactMap constructor we want to have either a full sequence (with unobserveds) or a blank in case we don't have the info
107			this.sequence="";
108
109			read_graph_from_db(); // gets contacts, nodes and sequence
110			get_db_graph_info(); // gets pdbCode, pdbChainCode, chainCode, ct and cutoff from db (from graph_id)
111
112			//TODO graphs in db are never directed, so this doesn't really apply here. Must solve all this!
113			if (ct.contains("/")){
114			directed=true;
115			}
116			this.obsLength=nodes.size();
117			if (!sequence.equals("")){
118			this.fullLength=sequence.length();
119			} else {
120			// if nodes TreeMap has correct residue numbering then this should get the right full length,
121			// we will only miss: gaps (unobserved residues) at the end of the sequence. Those we can't know unless full sequence is given
122			this.fullLength=Collections.max(nodes.keySet());
123			}
124			this.numContacts=contacts.size();
125			this.modified=false;
126			}
127
128			/**
129			* Constructs Graph object from graph db, given the graphid
130			* MySQLConnection is taken from defaults in DbGraph class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
131			* @param dbname
132			* @param graphid
133			* @throws GraphIdNotFoundError
134			* @throws SQLException
135			*/
136			public DbGraph(String dbname, int graphid) throws GraphIdNotFoundError, SQLException{
137			this(dbname,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD), graphid);
138			}
139
140			/**
141			* Reads contacts and nodes from db.
142			* The db must be a graph db following our standard format, i.e. must have tables:
143			* chain_graph, single_model_graph, single_model_node, single_model_edge
144			* We don't care here about the origin of the data (msdsd, pdbase, predicted) for the generation of the graph as long as it follows our data format
145			* We read both edges and nodes from single_model_edge and single_model_node.
146			* The sequence is set to blank, as we can't get the full sequence from graph db
147			* @param conn
148	duarte	210	* @throws SQLException
149	duarte	207	*/
150	duarte	210	private void read_graph_from_db() throws SQLException{
151	duarte	234	contacts = new EdgeSet();
152	duarte	207	nodes = new TreeMap<Integer, String>();
153
154	duarte	210	// we read only half of the matrix (contacts in one direction only) so that we have the same type of contacts as when creating Graph from Pdb object
155			String sql="SELECT i_num,j_num FROM "+dbname+".single_model_edge WHERE graph_id="+graphid+" AND j_num>i_num ORDER BY i_num,j_num ";
156			Statement stmt = conn.createStatement();
157			ResultSet rsst = stmt.executeQuery(sql);
158			while (rsst.next()) {
159			int i=rsst.getInt(1);
160			int j=rsst.getInt(2);
161	duarte	234	contacts.add(new Edge(i,j));
162	duarte	210	}
163			rsst.close();
164			stmt.close();
165			sql="SELECT num,res FROM "+dbname+".single_model_node WHERE graph_id="+graphid+" ORDER BY num ";
166			stmt = conn.createStatement();
167			rsst = stmt.executeQuery(sql);
168			while (rsst.next()){
169			int num=rsst.getInt(1);
170			String res=rsst.getString(2);
171			nodes.put(num, AA.oneletter2threeletter(res));
172			}
173			rsst.close();
174			stmt.close();
175	duarte	207	}
176
177	duarte	210	private void getgraphid () throws GraphIdNotFoundError, SQLException{
178	duarte	207	// input is pdbChainCode i.e. pdb chain code
179			// we take chainCode (internal chain identifier, pchain_code for msdsd and asym_id for pdbase) from pchain_code field in chain_graph
180			// (in the chain_graph table the internal chain identifier is called 'pchain_code')
181			int pgraphid=0;
182			String chainstr="='"+pdbChainCode+"' ";
183			if (pdbChainCode.equals("NULL")){
184			chainstr=" IS NULL ";
185			}
186	duarte	210
187			String sql="SELECT graph_id, pchain_code FROM "+dbname+".chain_graph WHERE accession_code='"+pdbCode+"' AND chain_pdb_code"+chainstr+" AND dist="+cutoff;
188			Statement stmt = conn.createStatement();
189			ResultSet rsst = stmt.executeQuery(sql);
190			int check=0;
191			while (rsst.next()) {
192			check++;
193			pgraphid=rsst.getInt(1);
194			chainCode=rsst.getString(2);
195	duarte	207	}
196	duarte	210	if (check!=1){
197			System.err.println("No pgraph_id match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode+", dist="+cutoff);
198			}
199			rsst.close();
200			stmt.close();
201			// we set the ctstr to the same as ct except in ALL case, where it is BB+SC+BB/SC
202			String ctstr=ct;
203			if (ct.equals("ALL")){
204			ctstr="BB+SC+BB/SC";
205			}
206			sql="SELECT graph_id,single_model_id FROM "+dbname+".single_model_graph WHERE pgraph_id="+pgraphid+" AND CT='"+ctstr+"' AND dist="+cutoff+" AND CR='"+DEFAULT_CR+"' AND CW="+DEFAULT_CW;
207			stmt = conn.createStatement();
208			rsst = stmt.executeQuery(sql);
209			check=0;
210			while (rsst.next()){
211			check++;
212			graphid=rsst.getInt(1);
213			//sm_id=rsst.getInt(2); // we might want to use it in the future
214			}
215			if (check!=1){
216	stehr	215	//System.err.println("No graph_id match or more than 1 match for pgraph_id="+pgraphid+", CT="+ctstr+" and cutoff="+cutoff);
217	duarte	210	throw new GraphIdNotFoundError("No graph_id match or more than 1 match for pgraph_id="+pgraphid+", CT="+ctstr+" and cutoff="+cutoff);
218			}
219	duarte	207	}
220
221	duarte	210	private void get_db_graph_info() throws GraphIdNotFoundError, SQLException {
222	duarte	207	int pgraphid=0;
223			String sql="SELECT pgraph_id,CT,dist FROM "+dbname+".single_model_graph WHERE graph_id="+graphid;
224			Statement stmt = conn.createStatement();
225			ResultSet rsst = stmt.executeQuery(sql);
226			int check=0;
227			while (rsst.next()) {
228			check++;
229			pgraphid=rsst.getInt(1);
230			ct=rsst.getString(2);
231			if (ct.equals("BB+SC+BB/SC")) ct="ALL";
232			cutoff=rsst.getDouble(3);
233			}
234			if (check!=1){
235	stehr	215	//System.err.println("No pgraph_id match or more than 1 match for graph_id="+graphid);
236	duarte	207	throw new GraphIdNotFoundError("No pgraph_id match or more than 1 match for graph_id="+graphid+" in db"+conn.getDbname());
237			}
238			rsst.close();
239			stmt.close();
240			sql="SELECT accession_code, chain_pdb_code, pchain_code FROM "+dbname+".chain_graph WHERE graph_id="+pgraphid;
241			stmt = conn.createStatement();
242			rsst = stmt.executeQuery(sql);
243			check=0;
244			while (rsst.next()){
245			check++;
246			pdbCode=rsst.getString(1);
247			pdbChainCode=rsst.getString(2);
248			// java returns a null if the field is a database null, we want actually the "NULL" string in that case
249			if (pdbChainCode==null) pdbChainCode="NULL";
250			chainCode=rsst.getString(3);
251			}
252			if (check!=1){
253			System.err.println("No accession_code+chain_pdb_code+pchain_code match or more than 1 match for graph_id="+pgraphid+" in chain_graph table");
254			}
255			rsst.close();
256			stmt.close();
257			}
258
259			}