trunk/proteinstructure/Graph.java

package proteinstructure;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.PrintStream;
import java.io.IOException;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.ArrayList;
import java.util.TreeMap;
import tools.MySQLConnection;


public class Graph {

        public final static String MYSQLSERVER="white";
        public final static String MYSQLUSER=getUserName();
        public final static String MYSQLPWD="nieve";

        ArrayList<Contact> contacts;
        // nodes is a TreeMap of residue serials to residue types (3 letter code)
        TreeMap<Integer,String> nodes;
        String sequence;
        String accode;
        String chain;
        double cutoff;
        String ct;
        boolean directed=false;
        
        // these 2 fields only used when reading from db
        int graphid=0;
        int sm_id=0;
        
        /**
         * Constructs Graph object by passing ArrayList with contacts and TreeMap with nodes (res serials and types)
         * Must also pass contact type, cutoff, accession code and chain
         * @param contacts
         * @param nodes
         * @param sequence
         * @param cutoff
         * @param ct
         * @param accode
         * @param chain
         */
        public Graph (ArrayList<Contact> contacts, TreeMap<Integer,String> nodes, String sequence, double cutoff,String ct, String accode, String chain) {
                this.contacts=contacts;
                this.cutoff=cutoff;
                this.nodes=nodes;
                this.sequence=sequence;
                this.accode=accode;
                this.chain=chain;
                this.ct=ct;
                if (ct.contains("/")){
                        directed=true;
                }
        }
        
        /**
         * Constructs Graph object from graph db, given the dbname, accode, chaincode (classic pdb chain code), ct and cutoff
         * @param dbname
         * @param accode
         * @param chaincode
         * @param cutoff
         * @param ct
         */
        public Graph(String dbname, String accode, String chaincode, double cutoff, String ct) throws GraphIdNotFoundError{
                this.cutoff=cutoff;
                this.accode=accode;
                this.ct=ct;
                //TODO graphs in db are never directed, so this doesn't really apply here. Must solve all this!
                if (ct.contains("/")){
                        directed=true;
                }
                MySQLConnection conn = new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD,dbname);
                getgraphid(conn, chaincode); // initialises graphid, sm_id and chain
                read_graph_from_db(conn); // gets contacts, nodes and sequence
                conn.close();
        }

        /**
         * Constructs Graph object by reading a file with contacts
         * An object created with this constructor will be missing the fields sequence and nodes
         * That means it's not possible to get a ContactMap from it using getCM because CM needs both sequence and nodes
         * @param contactsfile
         * @param cutoff
         * @param ct
         * @throws IOException
         * @throws FileNotFoundException
         */
        public Graph (String contactsfile, double cutoff,String ct) throws IOException, FileNotFoundException{
                this.cutoff=cutoff;
                this.ct=ct;
                if (ct.contains("/")){
                        directed=true;
                }
                read_contacts_from_file(contactsfile);
        }

        //TODO implement (from python) write_graph_to_db, do we really need it here??

        /** get user name from operating system (for use as database username) */
        private static String getUserName() {
                String user = null;
                user = System.getProperty("user.name");
                if(user == null) {
                        System.err.println("Could not get user name from operating system. Exiting");
                        System.exit(1);
                }
                return user;
        }

        public void read_contacts_from_file (String contactsfile) throws FileNotFoundException, IOException {
                contacts = new ArrayList<Contact>();
                System.out.println("Reading contacts from file "+contactsfile);
                BufferedReader fcont = new BufferedReader(new FileReader(new File(contactsfile)));
                String line;
                while ((line = fcont.readLine() ) != null ) {
                        int i = Integer.parseInt(line.split("\\s+")[0]);
                        int j = Integer.parseInt(line.split("\\s+")[1]);
                        contacts.add(new Contact(i,j));
                }
                fcont.close();
        }
        
        /**
         * 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 taken from nodes, thus it won't have unobserved or non standard aas.
         * @param conn
         */
        public void read_graph_from_db(MySQLConnection conn){
                contacts = new ArrayList<Contact>();
                nodes = new TreeMap<Integer, String>();
                sequence = "";
                try {
                        String sql="SELECT i_num,j_num FROM 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 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));
                                sequence+=res;
                        }
                        rsst.close();
                        stmt.close();
                } catch (SQLException e) {
                        e.printStackTrace();
                }

        }
        
        public void getgraphid (MySQLConnection conn, String chaincode) throws GraphIdNotFoundError{
                // input is chaincode i.e. pdb chain code
        // we take chain (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="='"+chaincode+"' ";
                if (chaincode.equals("NULL")){
                        chainstr=" IS NULL ";
                }
                try {
                        String sql="SELECT graph_id, pchain_code FROM chain_graph WHERE accession_code='"+accode+"' 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);
                                chain=rsst.getString(2);
                        }
                        if (check!=1){
                                System.err.println("No pgraph_id match or more than 1 match for accession_code="+accode+", chain_pdb_code="+chaincode+", 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 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);
                        }
                        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();
                }
                
        }
        
        public void write_contacts_to_file (String outfile) throws IOException {
                PrintStream Out = new PrintStream(new FileOutputStream(outfile));
                for (Contact pair:contacts){
                        int i_resser=pair.i;
                        int j_resser=pair.j;
                        Out.println(i_resser+"\t"+j_resser);
                }
                Out.close();            
        }
        
        public ContactMap getCM() {
                // residues is the map from residue nums to residue types used in ContactMap class, i.e. it is the same as Pdb.resser2restype or Graph.nodes
                TreeMap<Integer,String> residues = new TreeMap<Integer,String>();
                // we copy residues from nodes (deep copy) 
                for (int node:nodes.keySet()){
                        residues.put(node, nodes.get(node));
                }
                // check if we are in directed or undirected case. If undirected we fill the opposite contacts to pass a full list of contacts to ContactMap (which contains full matrix)
                ArrayList<Contact> contacts2pass = new ArrayList<Contact>();
                if (directed){
                        contacts2pass=contacts;
                } else {
                        for (Contact cont:contacts){
                                int i_resser = cont.i;
                                int j_resser = cont.j;
                                contacts2pass.add(new Contact(i_resser,j_resser));
                                contacts2pass.add(new Contact(j_resser,i_resser));
                        }
                }
                // construct the ContactMap object and return it
                ContactMap cm = new ContactMap(contacts2pass,residues,sequence);
                return cm;
                
        }
        
}
Revision:	141
Committed:	Mon May 14 15:51:54 2007 UTC (17 years, 4 months ago) by duarte
File size:	8536 byte(s)
Log Message:	Changed input in constructor for reading from db: chain->chaincode Now getgraphid initialises too the internal chain code (pchain_code from graph db)
Line	User	Rev	File contents
1	duarte	123	package proteinstructure;
2	duarte	134	import java.io.BufferedReader;
3			import java.io.File;
4			import java.io.FileNotFoundException;
5	duarte	123	import java.io.FileOutputStream;
6	duarte	134	import java.io.FileReader;
7	duarte	123	import java.io.PrintStream;
8			import java.io.IOException;
9	duarte	135	import java.sql.ResultSet;
10			import java.sql.SQLException;
11			import java.sql.Statement;
12	duarte	123	import java.util.ArrayList;
13	duarte	129	import java.util.TreeMap;
14	duarte	135	import tools.MySQLConnection;
15	duarte	123
16
17			public class Graph {
18
19	duarte	135	public final static String MYSQLSERVER="white";
20			public final static String MYSQLUSER=getUserName();
21			public final static String MYSQLPWD="nieve";
22
23	duarte	123	ArrayList<Contact> contacts;
24	duarte	135	// nodes is a TreeMap of residue serials to residue types (3 letter code)
25	duarte	129	TreeMap<Integer,String> nodes;
26			String sequence;
27			String accode;
28			String chain;
29	duarte	123	double cutoff;
30			String ct;
31	duarte	135	boolean directed=false;
32	duarte	123
33	duarte	135	// these 2 fields only used when reading from db
34			int graphid=0;
35			int sm_id=0;
36
37	duarte	134	/**
38			* Constructs Graph object by passing ArrayList with contacts and TreeMap with nodes (res serials and types)
39			* Must also pass contact type, cutoff, accession code and chain
40			* @param contacts
41			* @param nodes
42			* @param sequence
43			* @param cutoff
44			* @param ct
45			* @param accode
46			* @param chain
47			*/
48	duarte	129	public Graph (ArrayList<Contact> contacts, TreeMap<Integer,String> nodes, String sequence, double cutoff,String ct, String accode, String chain) {
49	duarte	123	this.contacts=contacts;
50			this.cutoff=cutoff;
51	duarte	129	this.nodes=nodes;
52			this.sequence=sequence;
53			this.accode=accode;
54			this.chain=chain;
55	duarte	123	this.ct=ct;
56	duarte	129	if (ct.contains("/")){
57			directed=true;
58			}
59	duarte	123	}
60	duarte	135
61			/**
62	duarte	141	* Constructs Graph object from graph db, given the dbname, accode, chaincode (classic pdb chain code), ct and cutoff
63	duarte	135	* @param dbname
64			* @param accode
65	duarte	141	* @param chaincode
66	duarte	135	* @param cutoff
67			* @param ct
68			*/
69	duarte	141	public Graph(String dbname, String accode, String chaincode, double cutoff, String ct) throws GraphIdNotFoundError{
70	duarte	135	this.cutoff=cutoff;
71			this.accode=accode;
72			this.ct=ct;
73			//TODO graphs in db are never directed, so this doesn't really apply here. Must solve all this!
74			if (ct.contains("/")){
75			directed=true;
76			}
77			MySQLConnection conn = new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD,dbname);
78	duarte	141	getgraphid(conn, chaincode); // initialises graphid, sm_id and chain
79			read_graph_from_db(conn); // gets contacts, nodes and sequence
80	duarte	135	conn.close();
81			}
82	duarte	129
83	duarte	134	/**
84			* Constructs Graph object by reading a file with contacts
85			* An object created with this constructor will be missing the fields sequence and nodes
86			* That means it's not possible to get a ContactMap from it using getCM because CM needs both sequence and nodes
87			* @param contactsfile
88			* @param cutoff
89			* @param ct
90			* @throws IOException
91			* @throws FileNotFoundException
92			*/
93			public Graph (String contactsfile, double cutoff,String ct) throws IOException, FileNotFoundException{
94			this.cutoff=cutoff;
95			this.ct=ct;
96			if (ct.contains("/")){
97			directed=true;
98			}
99			read_contacts_from_file(contactsfile);
100			}
101
102	duarte	135	//TODO implement (from python) write_graph_to_db, do we really need it here??
103
104			/** get user name from operating system (for use as database username) */
105			private static String getUserName() {
106			String user = null;
107			user = System.getProperty("user.name");
108			if(user == null) {
109			System.err.println("Could not get user name from operating system. Exiting");
110			System.exit(1);
111			}
112			return user;
113			}
114
115	duarte	134	public void read_contacts_from_file (String contactsfile) throws FileNotFoundException, IOException {
116			contacts = new ArrayList<Contact>();
117			System.out.println("Reading contacts from file "+contactsfile);
118			BufferedReader fcont = new BufferedReader(new FileReader(new File(contactsfile)));
119			String line;
120			while ((line = fcont.readLine() ) != null ) {
121			int i = Integer.parseInt(line.split("\\s+")[0]);
122			int j = Integer.parseInt(line.split("\\s+")[1]);
123			contacts.add(new Contact(i,j));
124			}
125			fcont.close();
126			}
127
128	duarte	135	/**
129			* Reads contacts and nodes from db.
130			* The db must be a graph db following our standard format, i.e. must have tables:
131			* chain_graph, single_model_graph, single_model_node, single_model_edge
132			* 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
133			* We read both edges and nodes from single_model_edge and single_model_node.
134			* The sequence is taken from nodes, thus it won't have unobserved or non standard aas.
135			* @param conn
136			*/
137			public void read_graph_from_db(MySQLConnection conn){
138			contacts = new ArrayList<Contact>();
139			nodes = new TreeMap<Integer, String>();
140			sequence = "";
141			try {
142			String sql="SELECT i_num,j_num FROM single_model_edge WHERE graph_id="+graphid+" AND j_num>i_num ORDER BY i_num,j_num ";
143			Statement stmt = conn.createStatement();
144			ResultSet rsst = stmt.executeQuery(sql);
145			while (rsst.next()) {
146			int i=rsst.getInt(1);
147			int j=rsst.getInt(2);
148			contacts.add(new Contact(i,j));
149			}
150			rsst.close();
151			stmt.close();
152			sql="SELECT num,res FROM single_model_node WHERE graph_id="+graphid+" ORDER BY num ";
153			stmt = conn.createStatement();
154			rsst = stmt.executeQuery(sql);
155			while (rsst.next()){
156			int num=rsst.getInt(1);
157			String res=rsst.getString(2);
158			nodes.put(num, AA.oneletter2threeletter(res));
159			sequence+=res;
160			}
161			rsst.close();
162			stmt.close();
163			} catch (SQLException e) {
164			e.printStackTrace();
165			}
166
167			}
168
169	duarte	141	public void getgraphid (MySQLConnection conn, String chaincode) throws GraphIdNotFoundError{
170			// input is chaincode i.e. pdb chain code
171			// we take chain (internal chain identifier, pchain_code for msdsd and asym_id for pdbase) from pchain_code field in chain_graph
172			// (in the chain_graph table the internal chain identifier is called 'pchain_code')
173	duarte	135	int pgraphid=0;
174	duarte	141	String chainstr="='"+chaincode+"' ";
175			if (chaincode.equals("NULL")){
176			chainstr=" IS NULL ";
177			}
178	duarte	135	try {
179	duarte	141	String sql="SELECT graph_id, pchain_code FROM chain_graph WHERE accession_code='"+accode+"' AND chain_pdb_code"+chainstr+" AND dist="+cutoff;
180	duarte	135	Statement stmt = conn.createStatement();
181			ResultSet rsst = stmt.executeQuery(sql);
182			int check=0;
183			while (rsst.next()) {
184			check++;
185			pgraphid=rsst.getInt(1);
186	duarte	141	chain=rsst.getString(2);
187	duarte	135	}
188			if (check!=1){
189	duarte	141	System.err.println("No pgraph_id match or more than 1 match for accession_code="+accode+", chain_pdb_code="+chaincode+", dist="+cutoff);
190	duarte	135	}
191			rsst.close();
192			stmt.close();
193			// we set the ctstr to the same as ct except in ALL case, where it is BB+SC+BB/SC
194			String ctstr=ct;
195			if (ct.equals("ALL")){
196			ctstr="BB+SC+BB/SC";
197			}
198			sql="SELECT graph_id,single_model_id FROM single_model_graph WHERE pgraph_id="+pgraphid+" AND CT='"+ctstr+"' AND dist="+cutoff+" AND CR='(true)' AND CW=1";
199			stmt = conn.createStatement();
200			rsst = stmt.executeQuery(sql);
201			check=0;
202			while (rsst.next()){
203			check++;
204			graphid=rsst.getInt(1);
205			sm_id=rsst.getInt(2);
206			}
207			if (check!=1){
208			System.err.println("No graph_id match or more than 1 match for pgraph_id="+pgraphid+", CT="+ctstr+" and cutoff="+cutoff);
209			throw new GraphIdNotFoundError("No graph_id match or more than 1 match for pgraph_id="+pgraphid+", CT="+ctstr+" and cutoff="+cutoff);
210			}
211			} catch (SQLException e) {
212			e.printStackTrace();
213			}
214
215			}
216
217	duarte	123	public void write_contacts_to_file (String outfile) throws IOException {
218			PrintStream Out = new PrintStream(new FileOutputStream(outfile));
219			for (Contact pair:contacts){
220			int i_resser=pair.i;
221			int j_resser=pair.j;
222			Out.println(i_resser+"\t"+j_resser);
223			}
224			Out.close();
225			}
226	duarte	129
227			public ContactMap getCM() {
228			// residues is the map from residue nums to residue types used in ContactMap class, i.e. it is the same as Pdb.resser2restype or Graph.nodes
229			TreeMap<Integer,String> residues = new TreeMap<Integer,String>();
230			// we copy residues from nodes (deep copy)
231			for (int node:nodes.keySet()){
232			residues.put(node, nodes.get(node));
233			}
234			// check if we are in directed or undirected case. If undirected we fill the opposite contacts to pass a full list of contacts to ContactMap (which contains full matrix)
235			ArrayList<Contact> contacts2pass = new ArrayList<Contact>();
236			if (directed){
237			contacts2pass=contacts;
238			} else {
239			for (Contact cont:contacts){
240			int i_resser = cont.i;
241			int j_resser = cont.j;
242			contacts2pass.add(new Contact(i_resser,j_resser));
243			contacts2pass.add(new Contact(j_resser,i_resser));
244			}
245			}
246			// construct the ContactMap object and return it
247			ContactMap cm = new ContactMap(contacts2pass,residues,sequence);
248			return cm;
249
250			}
251
252	duarte	123	}