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 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 
         */
        public DbGraph(String dbname, MySQLConnection conn, String pdbCode, String pdbChainCode, double cutoff, String ct) throws GraphIdNotFoundError {
                this.dbname=dbname;
                this.conn=conn;
                this.cutoff=cutoff;
                this.pdbCode=pdbCode;
                this.ct=ct;
                // 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 
         */
        public DbGraph(String dbname, MySQLConnection conn, int graphid) throws GraphIdNotFoundError {
                this.dbname=dbname;
                this.conn=conn;
                this.graphid=graphid;
                // 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
         */
        private void read_graph_from_db(){
                contacts = new ContactList();
                nodes = new TreeMap<Integer, String>();
                try {
                        // 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 Contact(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();
                } catch (SQLException e) {
                        e.printStackTrace();
                }

        }
        
        private void getgraphid () throws GraphIdNotFoundError{
                // 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 ";
                }
                try {
                        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='(true)' AND CW=1";
                        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);
                        }
                } catch (SQLException e) {
                        e.printStackTrace();
                }
                
        }
        
        private void get_db_graph_info() throws GraphIdNotFoundError {
                try {
                        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();
                } catch (SQLException e) {
                        e.printStackTrace();
                }

        }

}
Revision:	207
Committed:	Wed Jun 27 11:06:34 2007 UTC (17 years, 3 months ago) by duarte
File size:	9820 byte(s)
Log Message:	Restructured construction of Pdb and Graph objects: now subclasses for each case Cleaned up and made consistent database connections Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection) PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively Updated following this changes testPdb and compareCMs
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			private int graphid=0;
25			//private int sm_id=0; // for future use
26
27			private String dbname;
28			private MySQLConnection conn;
29
30			/**
31			* Constructs Graph object from graph db, given the dbname, pdbCode, pdbChainCode (classic pdb chain code), ct and cutoff
32			* and passing a MySQLConnection
33			* @param dbname
34			* @param conn
35			* @param pdbCode
36			* @param pdbChainCode
37			* @param cutoff
38			* @param ct
39			* @throws GraphIdNotFoundError
40			*/
41			public DbGraph(String dbname, MySQLConnection conn, String pdbCode, String pdbChainCode, double cutoff, String ct) throws GraphIdNotFoundError {
42			this.dbname=dbname;
43			this.conn=conn;
44			this.cutoff=cutoff;
45			this.pdbCode=pdbCode;
46			this.ct=ct;
47			// we set the sequence to empty when we read from graph db. We don't have the full sequence in graph db
48			// 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
49			this.sequence="";
50			//TODO graphs in db are never directed, so this doesn't really apply here. Must solve all this!
51			if (ct.contains("/")){
52			directed=true;
53			}
54
55			getgraphid(); // initialises graphid, sm_id and chainCode
56			read_graph_from_db(); // gets contacts, nodes and sequence
57
58			this.obsLength=nodes.size();
59			if (!sequence.equals("")){
60			this.fullLength=sequence.length();
61			} else {
62			// if nodes TreeMap has correct residue numbering then this should get the right full length,
63			// we will only miss: gaps (unobserved residues) at the end of the sequence. Those we can't know unless full sequence is given
64			this.fullLength=Collections.max(nodes.keySet());
65			}
66			this.numContacts=contacts.size();
67			this.modified=false;
68			}
69
70			/**
71			* Constructs Graph object from graph db, given the dbname, pdbCode, pdbChainCode (classic pdb chain code), ct and cutoff
72			* MySQLConnection is taken from defaults in DbGraph class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
73			* @param dbname
74			* @param pdbCode
75			* @param pdbChainCode
76			* @param cutoff
77			* @param ct
78			* @throws GraphIdNotFoundError
79			* @throws SQLException
80			*/
81			public DbGraph(String dbname, String pdbCode, String pdbChainCode, double cutoff, String ct) throws GraphIdNotFoundError, SQLException{
82			this(dbname,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD),pdbCode,pdbChainCode,cutoff,ct);
83			}
84
85
86			/**
87			* Constructs Graph object from graph db, given the graphid and passing a MySQLConnection
88			* @param dbname
89			* @param conn
90			* @param graphid
91			* @throws GraphIdNotFoundError
92			*/
93			public DbGraph(String dbname, MySQLConnection conn, int graphid) throws GraphIdNotFoundError {
94			this.dbname=dbname;
95			this.conn=conn;
96			this.graphid=graphid;
97			// we set the sequence to empty when we read from graph db. We don't have the full sequence in graph db
98			// 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
99			this.sequence="";
100
101			read_graph_from_db(); // gets contacts, nodes and sequence
102			get_db_graph_info(); // gets pdbCode, pdbChainCode, chainCode, ct and cutoff from db (from graph_id)
103
104			//TODO graphs in db are never directed, so this doesn't really apply here. Must solve all this!
105			if (ct.contains("/")){
106			directed=true;
107			}
108			this.obsLength=nodes.size();
109			if (!sequence.equals("")){
110			this.fullLength=sequence.length();
111			} else {
112			// if nodes TreeMap has correct residue numbering then this should get the right full length,
113			// we will only miss: gaps (unobserved residues) at the end of the sequence. Those we can't know unless full sequence is given
114			this.fullLength=Collections.max(nodes.keySet());
115			}
116			this.numContacts=contacts.size();
117			this.modified=false;
118			}
119
120			/**
121			* Constructs Graph object from graph db, given the graphid
122			* MySQLConnection is taken from defaults in DbGraph class: MYSQLSERVER, MYSQLUSER, MYSQLPWD
123			* @param dbname
124			* @param graphid
125			* @throws GraphIdNotFoundError
126			* @throws SQLException
127			*/
128			public DbGraph(String dbname, int graphid) throws GraphIdNotFoundError, SQLException{
129			this(dbname,new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD), graphid);
130			}
131
132			/**
133			* Reads contacts and nodes from db.
134			* The db must be a graph db following our standard format, i.e. must have tables:
135			* chain_graph, single_model_graph, single_model_node, single_model_edge
136			* 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
137			* We read both edges and nodes from single_model_edge and single_model_node.
138			* The sequence is set to blank, as we can't get the full sequence from graph db
139			* @param conn
140			*/
141			private void read_graph_from_db(){
142			contacts = new ContactList();
143			nodes = new TreeMap<Integer, String>();
144			try {
145			// 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
146			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 ";
147			Statement stmt = conn.createStatement();
148			ResultSet rsst = stmt.executeQuery(sql);
149			while (rsst.next()) {
150			int i=rsst.getInt(1);
151			int j=rsst.getInt(2);
152			contacts.add(new Contact(i,j));
153			}
154			rsst.close();
155			stmt.close();
156			sql="SELECT num,res FROM "+dbname+".single_model_node WHERE graph_id="+graphid+" ORDER BY num ";
157			stmt = conn.createStatement();
158			rsst = stmt.executeQuery(sql);
159			while (rsst.next()){
160			int num=rsst.getInt(1);
161			String res=rsst.getString(2);
162			nodes.put(num, AA.oneletter2threeletter(res));
163			}
164			rsst.close();
165			stmt.close();
166			} catch (SQLException e) {
167			e.printStackTrace();
168			}
169
170			}
171
172			private void getgraphid () throws GraphIdNotFoundError{
173			// input is pdbChainCode i.e. pdb chain code
174			// we take chainCode (internal chain identifier, pchain_code for msdsd and asym_id for pdbase) from pchain_code field in chain_graph
175			// (in the chain_graph table the internal chain identifier is called 'pchain_code')
176			int pgraphid=0;
177			String chainstr="='"+pdbChainCode+"' ";
178			if (pdbChainCode.equals("NULL")){
179			chainstr=" IS NULL ";
180			}
181			try {
182			String sql="SELECT graph_id, pchain_code FROM "+dbname+".chain_graph WHERE accession_code='"+pdbCode+"' AND chain_pdb_code"+chainstr+" AND dist="+cutoff;
183			Statement stmt = conn.createStatement();
184			ResultSet rsst = stmt.executeQuery(sql);
185			int check=0;
186			while (rsst.next()) {
187			check++;
188			pgraphid=rsst.getInt(1);
189			chainCode=rsst.getString(2);
190			}
191			if (check!=1){
192			System.err.println("No pgraph_id match or more than 1 match for accession_code="+pdbCode+", chain_pdb_code="+pdbChainCode+", dist="+cutoff);
193			}
194			rsst.close();
195			stmt.close();
196			// we set the ctstr to the same as ct except in ALL case, where it is BB+SC+BB/SC
197			String ctstr=ct;
198			if (ct.equals("ALL")){
199			ctstr="BB+SC+BB/SC";
200			}
201			sql="SELECT graph_id,single_model_id FROM "+dbname+".single_model_graph WHERE pgraph_id="+pgraphid+" AND CT='"+ctstr+"' AND dist="+cutoff+" AND CR='(true)' AND CW=1";
202			stmt = conn.createStatement();
203			rsst = stmt.executeQuery(sql);
204			check=0;
205			while (rsst.next()){
206			check++;
207			graphid=rsst.getInt(1);
208			//sm_id=rsst.getInt(2); // we might want to use it in the future
209			}
210			if (check!=1){
211			System.err.println("No graph_id match or more than 1 match for pgraph_id="+pgraphid+", CT="+ctstr+" and cutoff="+cutoff);
212			throw new GraphIdNotFoundError("No graph_id match or more than 1 match for pgraph_id="+pgraphid+", CT="+ctstr+" and cutoff="+cutoff);
213			}
214			} catch (SQLException e) {
215			e.printStackTrace();
216			}
217
218			}
219
220			private void get_db_graph_info() throws GraphIdNotFoundError {
221			try {
222			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			System.err.println("No pgraph_id match or more than 1 match for graph_id="+graphid);
236			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			} catch (SQLException e) {
258			e.printStackTrace();
259			}
260
261			}
262
263			}