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
         * ATTENTION!! chain is the internal database identifier, NOT! the pdb chain code
         * TODO: we should also have a method to construct Graph from db using a pdb chain code 
         * @param dbname
         * @param accode
         * @param chain
         * @param cutoff
         * @param ct
         */
        public Graph(String dbname, String accode, String chain, double cutoff, String ct) throws GraphIdNotFoundError{
                this.cutoff=cutoff;
                this.accode=accode;
                this.chain=chain;
                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); // initialises graphid and sm_id
                read_graph_from_db(conn);
                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) throws GraphIdNotFoundError{
        // NOTE: as chain we are using our internal identifier, which is the pchain_code in msdsd or the asym_id in pdbase
        // in the chain_graph table the internal chain identifier is called 'pchain_code'
                int pgraphid=0;
                try {
                        String sql="SELECT graph_id FROM chain_graph WHERE accession_code='"+accode+"' AND pchain_code='"+chain+"' AND dist="+cutoff;
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        int check=0;
                        while (rsst.next()) {
                                check++;
                                pgraphid=rsst.getInt(1);
                        }
                        if (check!=1){
                                System.err.println("No pgraph_id match or more than 1 match for accession_code="+accode+", pchain_code="+chain+", 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:	135
Committed:	Mon May 14 09:49:04 2007 UTC (17 years, 9 months ago) by duarte
File size:	8357 byte(s)
Log Message:	NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd) Reading chain also in Pdb in read_pdb_data_from_file Not reading chain anymore in read_atomData of PdbaseInfo Added oneletter2threeletter and getoneletter2threeletter to AA class Changes in Graph: - added db static vars and getUserName method - new member variables graphid and sm_id - new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db - new method getgraphid New Exception class GraphIdNotFoundError
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			* Constructs Graph object from graph db
63			* ATTENTION!! chain is the internal database identifier, NOT! the pdb chain code
64			* TODO: we should also have a method to construct Graph from db using a pdb chain code
65			* @param dbname
66			* @param accode
67			* @param chain
68			* @param cutoff
69			* @param ct
70			*/
71			public Graph(String dbname, String accode, String chain, double cutoff, String ct) throws GraphIdNotFoundError{
72			this.cutoff=cutoff;
73			this.accode=accode;
74			this.chain=chain;
75			this.ct=ct;
76			//TODO graphs in db are never directed, so this doesn't really apply here. Must solve all this!
77			if (ct.contains("/")){
78			directed=true;
79			}
80			MySQLConnection conn = new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD,dbname);
81			getgraphid(conn); // initialises graphid and sm_id
82			read_graph_from_db(conn);
83			conn.close();
84			}
85	duarte	129
86	duarte	134	/**
87			* Constructs Graph object by reading a file with contacts
88			* An object created with this constructor will be missing the fields sequence and nodes
89			* That means it's not possible to get a ContactMap from it using getCM because CM needs both sequence and nodes
90			* @param contactsfile
91			* @param cutoff
92			* @param ct
93			* @throws IOException
94			* @throws FileNotFoundException
95			*/
96			public Graph (String contactsfile, double cutoff,String ct) throws IOException, FileNotFoundException{
97			this.cutoff=cutoff;
98			this.ct=ct;
99			if (ct.contains("/")){
100			directed=true;
101			}
102			read_contacts_from_file(contactsfile);
103			}
104
105	duarte	135	//TODO implement (from python) write_graph_to_db, do we really need it here??
106
107			/** get user name from operating system (for use as database username) */
108			private static String getUserName() {
109			String user = null;
110			user = System.getProperty("user.name");
111			if(user == null) {
112			System.err.println("Could not get user name from operating system. Exiting");
113			System.exit(1);
114			}
115			return user;
116			}
117
118	duarte	134	public void read_contacts_from_file (String contactsfile) throws FileNotFoundException, IOException {
119			contacts = new ArrayList<Contact>();
120			System.out.println("Reading contacts from file "+contactsfile);
121			BufferedReader fcont = new BufferedReader(new FileReader(new File(contactsfile)));
122			String line;
123			while ((line = fcont.readLine() ) != null ) {
124			int i = Integer.parseInt(line.split("\\s+")[0]);
125			int j = Integer.parseInt(line.split("\\s+")[1]);
126			contacts.add(new Contact(i,j));
127			}
128			fcont.close();
129			}
130
131	duarte	135	/**
132			* Reads contacts and nodes from db.
133			* The db must be a graph db following our standard format, i.e. must have tables:
134			* chain_graph, single_model_graph, single_model_node, single_model_edge
135			* 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
136			* We read both edges and nodes from single_model_edge and single_model_node.
137			* The sequence is taken from nodes, thus it won't have unobserved or non standard aas.
138			* @param conn
139			*/
140			public void read_graph_from_db(MySQLConnection conn){
141			contacts = new ArrayList<Contact>();
142			nodes = new TreeMap<Integer, String>();
143			sequence = "";
144			try {
145			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 ";
146			Statement stmt = conn.createStatement();
147			ResultSet rsst = stmt.executeQuery(sql);
148			while (rsst.next()) {
149			int i=rsst.getInt(1);
150			int j=rsst.getInt(2);
151			contacts.add(new Contact(i,j));
152			}
153			rsst.close();
154			stmt.close();
155			sql="SELECT num,res FROM single_model_node WHERE graph_id="+graphid+" ORDER BY num ";
156			stmt = conn.createStatement();
157			rsst = stmt.executeQuery(sql);
158			while (rsst.next()){
159			int num=rsst.getInt(1);
160			String res=rsst.getString(2);
161			nodes.put(num, AA.oneletter2threeletter(res));
162			sequence+=res;
163			}
164			rsst.close();
165			stmt.close();
166			} catch (SQLException e) {
167			e.printStackTrace();
168			}
169
170			}
171
172			public void getgraphid (MySQLConnection conn) throws GraphIdNotFoundError{
173			// NOTE: as chain we are using our internal identifier, which is the pchain_code in msdsd or the asym_id in pdbase
174			// in the chain_graph table the internal chain identifier is called 'pchain_code'
175			int pgraphid=0;
176			try {
177			String sql="SELECT graph_id FROM chain_graph WHERE accession_code='"+accode+"' AND pchain_code='"+chain+"' AND dist="+cutoff;
178			Statement stmt = conn.createStatement();
179			ResultSet rsst = stmt.executeQuery(sql);
180			int check=0;
181			while (rsst.next()) {
182			check++;
183			pgraphid=rsst.getInt(1);
184			}
185			if (check!=1){
186			System.err.println("No pgraph_id match or more than 1 match for accession_code="+accode+", pchain_code="+chain+", dist="+cutoff);
187			}
188			rsst.close();
189			stmt.close();
190			// we set the ctstr to the same as ct except in ALL case, where it is BB+SC+BB/SC
191			String ctstr=ct;
192			if (ct.equals("ALL")){
193			ctstr="BB+SC+BB/SC";
194			}
195			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";
196			stmt = conn.createStatement();
197			rsst = stmt.executeQuery(sql);
198			check=0;
199			while (rsst.next()){
200			check++;
201			graphid=rsst.getInt(1);
202			sm_id=rsst.getInt(2);
203			}
204			if (check!=1){
205			System.err.println("No graph_id match or more than 1 match for pgraph_id="+pgraphid+", CT="+ctstr+" and cutoff="+cutoff);
206			throw new GraphIdNotFoundError("No graph_id match or more than 1 match for pgraph_id="+pgraphid+", CT="+ctstr+" and cutoff="+cutoff);
207			}
208			} catch (SQLException e) {
209			e.printStackTrace();
210			}
211
212			}
213
214	duarte	123	public void write_contacts_to_file (String outfile) throws IOException {
215			PrintStream Out = new PrintStream(new FileOutputStream(outfile));
216			for (Contact pair:contacts){
217			int i_resser=pair.i;
218			int j_resser=pair.j;
219			Out.println(i_resser+"\t"+j_resser);
220			}
221			Out.close();
222			}
223	duarte	129
224			public ContactMap getCM() {
225			// 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
226			TreeMap<Integer,String> residues = new TreeMap<Integer,String>();
227			// we copy residues from nodes (deep copy)
228			for (int node:nodes.keySet()){
229			residues.put(node, nodes.get(node));
230			}
231			// 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)
232			ArrayList<Contact> contacts2pass = new ArrayList<Contact>();
233			if (directed){
234			contacts2pass=contacts;
235			} else {
236			for (Contact cont:contacts){
237			int i_resser = cont.i;
238			int j_resser = cont.j;
239			contacts2pass.add(new Contact(i_resser,j_resser));
240			contacts2pass.add(new Contact(j_resser,i_resser));
241			}
242			}
243			// construct the ContactMap object and return it
244			ContactMap cm = new ContactMap(contacts2pass,residues,sequence);
245			return cm;
246
247			}
248
249	duarte	123	}