owl/trunk/rewriteNBHood_parallel.java

import tools.MySQLConnection;

import java.sql.SQLException;
import java.sql.Statement;
import java.sql.ResultSet;

public class rewriteNBHood_parallel {

        /**
         * reriting the nbhoodstring such that BB dominated nbs are represented by SSType 
         * 
         * @author lappe
         */

        static String user = "lappe"    ; // change user name!!
        static MySQLConnection conn;
        static int k=0, k_sc=0, k_bb=0; 
        static String process,  cid, res, sectype, fullnbs;
        static int graph_id=0, node_id=0, resnr=0;


        public static void main(String[] args) throws SQLException {
                String nbhood = "", isql; 
                Statement istmt; 

                System.out.println("rewriteNBHood");
                if (args.length!=1){
                        System.err.println("The processname has to be given .... i.e. tla01");
                        System.exit(1);
                }               
                process = args[0];
                System.out.println("processID="+process);

                try {

                        conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2"); 
                        node_id = getNextNode(); 
                        while (node_id>0) {
                                System.out.print(graph_id); // graph
                                System.out.print("\t"+node_id); // node 
                                System.out.print("\t"+cid); // cid
                                System.out.print("\t"+resnr); // num
                                System.out.print("\t"+res); // res
                                System.out.print("\t"+sectype); // sstype 
                                fullnbs = "";
                                nbhood= getSSNbHoodString( graph_id, node_id, resnr); 

                                System.out.println("\t"+nbhood+"\t"+fullnbs);
                                istmt = conn.createStatement();
                                isql = "update single_model_cofull set k="+k+", k_bb="+k_bb+", k_sc="+k_sc+", n=\'"+nbhood+"\', nf=\'"+fullnbs+"\'" +
                                                " where ( graph_id="+graph_id+" and node_id="+node_id+");";
                                // System.out.println("i>"+isql); 
                                istmt.executeUpdate( isql);

                                node_id = getNextNode(); 
                        } // end while we have another node 

                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                }

                System.out.println("fin."); 
        }       

        public static int getNextNode() {
                String sql; 
                Statement stmt;  
                ResultSet rsst;

                graph_id=0;  
                node_id =0; 
                try {
                        sql = "update single_model_cofull set n=\'>"+process+"\' where length(n)=0 limit 1;";
                        stmt = conn.createStatement();
                        stmt.executeUpdate(sql);
                        sql = "select graph_id, node_id, cid, num, res, sstype from single_model_cofull where n=\'>"+process+"\';";
                        // System.out.println("node> "+ sql); 
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);

                        if (rsst.next()) {      
                                // System.out.print(">"); 
                                graph_id=rsst.getInt(1);  
                                node_id =rsst.getInt(2); 
                                cid     =rsst.getString(3); 
                                resnr   =rsst.getInt(4);
                                res     =rsst.getString(5);
                                sectype =rsst.getString(6); 
                        }
                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                }
                return node_id; 
        } // end of getnbhoodstring 


        public static String getSSNbHoodString( int gid, int nid, int num ) {
                int j_num, j_bb, j_sc;
                boolean overx=false; 
                String sql, nbs="", j_res, j_ss, nextnb; 
                Statement stmt;  
                ResultSet rsst;

                try {
                        k=0; k_sc=0; k_bb=0; 
                        sql = "select j_num, j_res, j_sstype, BB, SC from chain_edge where graph_id="+gid+" and i_node_id="+nid+" order by j_num;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        fullnbs=""; 
                        while (rsst.next()) {   
                                j_num = rsst.getInt(1); 
                                j_res = rsst.getString(2);                              
                                j_ss = rsst.getString(3); 
                                j_bb = rsst.getInt(4); 
                                j_sc = rsst.getInt(5);
                                nextnb="?"; 
                                if (!overx && j_num>num) { 
                                        overx=true; 
                                        nbs+="x";
                                        fullnbs+="x"; 
                                }
                                if ( (j_bb>j_sc) ) { // bb dominated -> only symbol for sstype
                                        k_bb++; 
                                        nextnb="o"; // for "other" 
                                        if (j_ss.equals("H")) nextnb="z"; // Helix 
                                        if (j_ss.equals("S")) nextnb="b"; // beta strand 
                                } else { // sc dominated contact
                                        k_sc++; 
                                        nextnb=j_res; 
                                } // end if bb dominated
                                nbs+= nextnb;
                                fullnbs+= j_res; 
                                k++; 
                                // System.out.print( nextnb);
                        }
                        rsst.close(); 
                        stmt.close();
                        if (!overx) {
                                nbs+="x"; // add if last in string == not seen yet
                                fullnbs+="x"; 
                        }

                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                }
                return nbs; 
        } // end of getnbhoodstring 
}
Revision:	492
Committed:	Wed Jan 2 13:18:57 2008 UTC (16 years, 9 months ago) by duarte
File size:	4388 byte(s)
Log Message:	Copied the aglappe-jung branch into trunk.
Line	User	Rev	File contents
1	lappe	291	import tools.MySQLConnection;
2
3			import java.sql.SQLException;
4			import java.sql.Statement;
5			import java.sql.ResultSet;
6
7			public class rewriteNBHood_parallel {
8
9			/**
10			* reriting the nbhoodstring such that BB dominated nbs are represented by SSType
11			*
12			* @author lappe
13			*/
14
15			static String user = "lappe" ; // change user name!!
16			static MySQLConnection conn;
17			static int k=0, k_sc=0, k_bb=0;
18			static String process, cid, res, sectype, fullnbs;
19			static int graph_id=0, node_id=0, resnr=0;
20
21
22			public static void main(String[] args) throws SQLException {
23			String nbhood = "", isql;
24			Statement istmt;
25
26			System.out.println("rewriteNBHood");
27			if (args.length!=1){
28			System.err.println("The processname has to be given .... i.e. tla01");
29			System.exit(1);
30			}
31			process = args[0];
32			System.out.println("processID="+process);
33
34			try {
35
36			conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2");
37			node_id = getNextNode();
38			while (node_id>0) {
39			System.out.print(graph_id); // graph
40			System.out.print("\t"+node_id); // node
41			System.out.print("\t"+cid); // cid
42			System.out.print("\t"+resnr); // num
43			System.out.print("\t"+res); // res
44			System.out.print("\t"+sectype); // sstype
45			fullnbs = "";
46			nbhood= getSSNbHoodString( graph_id, node_id, resnr);
47
48			System.out.println("\t"+nbhood+"\t"+fullnbs);
49			istmt = conn.createStatement();
50			isql = "update single_model_cofull set k="+k+", k_bb="+k_bb+", k_sc="+k_sc+", n=\'"+nbhood+"\', nf=\'"+fullnbs+"\'" +
51			" where ( graph_id="+graph_id+" and node_id="+node_id+");";
52			// System.out.println("i>"+isql);
53			istmt.executeUpdate( isql);
54
55			node_id = getNextNode();
56			} // end while we have another node
57
58			} catch (SQLException e) {
59			e.printStackTrace();
60			System.err.println("SQLException: " + e.getMessage());
61			System.err.println("SQLState: " + e.getSQLState());
62			}
63
64			System.out.println("fin.");
65			}
66
67			public static int getNextNode() {
68			String sql;
69			Statement stmt;
70			ResultSet rsst;
71
72			graph_id=0;
73			node_id =0;
74			try {
75			sql = "update single_model_cofull set n=\'>"+process+"\' where length(n)=0 limit 1;";
76			stmt = conn.createStatement();
77			stmt.executeUpdate(sql);
78			sql = "select graph_id, node_id, cid, num, res, sstype from single_model_cofull where n=\'>"+process+"\';";
79			// System.out.println("node> "+ sql);
80			stmt = conn.createStatement();
81			rsst = stmt.executeQuery(sql);
82
83			if (rsst.next()) {
84			// System.out.print(">");
85			graph_id=rsst.getInt(1);
86			node_id =rsst.getInt(2);
87			cid =rsst.getString(3);
88			resnr =rsst.getInt(4);
89			res =rsst.getString(5);
90			sectype =rsst.getString(6);
91			}
92			} catch (SQLException e) {
93			e.printStackTrace();
94			System.err.println("SQLException: " + e.getMessage());
95			System.err.println("SQLState: " + e.getSQLState());
96			}
97			return node_id;
98			} // end of getnbhoodstring
99
100
101			public static String getSSNbHoodString( int gid, int nid, int num ) {
102			int j_num, j_bb, j_sc;
103			boolean overx=false;
104			String sql, nbs="", j_res, j_ss, nextnb;
105			Statement stmt;
106			ResultSet rsst;
107
108			try {
109			k=0; k_sc=0; k_bb=0;
110			sql = "select j_num, j_res, j_sstype, BB, SC from chain_edge where graph_id="+gid+" and i_node_id="+nid+" order by j_num;";
111			stmt = conn.createStatement();
112			rsst = stmt.executeQuery(sql);
113			fullnbs="";
114			while (rsst.next()) {
115			j_num = rsst.getInt(1);
116			j_res = rsst.getString(2);
117			j_ss = rsst.getString(3);
118			j_bb = rsst.getInt(4);
119			j_sc = rsst.getInt(5);
120			nextnb="?";
121			if (!overx && j_num>num) {
122			overx=true;
123			nbs+="x";
124			fullnbs+="x";
125			}
126			if ( (j_bb>j_sc) ) { // bb dominated -> only symbol for sstype
127			k_bb++;
128			nextnb="o"; // for "other"
129			if (j_ss.equals("H")) nextnb="z"; // Helix
130			if (j_ss.equals("S")) nextnb="b"; // beta strand
131			} else { // sc dominated contact
132			k_sc++;
133			nextnb=j_res;
134			} // end if bb dominated
135			nbs+= nextnb;
136			fullnbs+= j_res;
137			k++;
138			// System.out.print( nextnb);
139			}
140			rsst.close();
141			stmt.close();
142			if (!overx) {
143			nbs+="x"; // add if last in string == not seen yet
144			fullnbs+="x";
145			}
146
147			} catch (SQLException e) {
148			e.printStackTrace();
149			System.err.println("SQLException: " + e.getMessage());
150			System.err.println("SQLState: " + e.getSQLState());
151			}
152			return nbs;
153			} // end of getnbhoodstring
154			}