owl/trunk/minInfoGain.java

import tools.MySQLConnection;

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

public class minInfoGain {

        /**
         * "Hello World" for entropy calculations given a nbhoodstring 
         * 
         * @author lappe
         */
        
        static String user = "lappe"    ; // change user name!!
        static MySQLConnection conn;
        
        public static void main(String[] args) throws SQLException {
                double entropy = 0.0, newentropy=0.0, gain, mingain=99999999.9; 
                String nbhood = "", front, middle, tail, newhood="";
                if (args.length<1){
                        System.err.println("The starting neighborhood-string needs to be given .... i.e. %K%D%L%I%x%D%C%");
                        System.exit(1);
                }               
                nbhood = args[0];
                
                conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2"); 
                int l = (int)((nbhood.length()-1)/2); 
                
                while (l>=2) {
                        System.out.println("MinInfoGain");
                        System.out.print("0 - ("+nbhood+")("+l+") "); 
                        entropy = getEntropy( nbhood); 
                        System.out.println( entropy + " bits."); 
                        System.out.println("Symbols in nbhood :"+l); 
                        mingain = 99999999.9; 
                        for (int i = 0; i<l; i++) {
                                front = nbhood.substring(0,i*2); 
                                middle = nbhood.substring(i*2, i*2+2); 
                                tail = nbhood.substring(i*2+2);
                                System.out.print((i+1)+" - "+front+"("+middle+")"+tail);
                                newentropy = getEntropy( (front+tail)); 
                                gain = newentropy-entropy; 
                                System.out.print( " : "+newentropy +"bits, gain="+gain);
                                if (gain<mingain && !(middle.equals("%x"))) {
                                        mingain = gain;  
                                        newhood = front+tail; 
                                        System.out.println(" <<-"); 
                                } else {
                                        System.out.println(" ."); 
                                }
                        } // next symbol in nbhood; 
                        
                        if (newhood.equals(nbhood)) { // in case we got stcuk with the same string 
                                l=0; // - exit loop 
                        } else {        // continue with new nbhoodstring 
                                nbhood = newhood; 
                                l = (int)((nbhood.length()-1)/2);
                        }       
                        System.out.println("-->> "+nbhood+"("+l+")"); 
                
                } // 
                System.out.println("fin."); 
        }       

                
        
        public static double getEntropy( String nbs) {
                int total = 0; 
                String sql; 
                Statement stmt;  
                ResultSet rsst;
                double p, psum=0.0, logp, plogp, plogpsum=0.0; 
                
                try {
                        sql = "select count(*) from single_model_node where n like '"+nbs+"';";
                        // System.out.println( sql); 
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        if (rsst.next()) total = rsst.getInt( 1); 
                        rsst.close(); 
                        stmt.close(); 
                        
                        sql = "select res, count(*) as t, count(*)/"+total+" as p from single_model_node where n like '"+nbs+"' group by res order by res;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        // System.out.println("res : total t : fraction p : log2(p) : -p*log2(p)");
                        while (rsst.next()) {                           
                                //res = rsst.getString(1); // 1st column -- res
                                //num = rsst.getInt(2); // 2nd column -- num
                                p = rsst.getDouble(3); // 3rd: fraction p 
                                // System.out.print(res+"   : "+num+ " : " + p);
                                logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits 
                                // System.out.print(" : " + logp); 
                                plogp = -1.0 * p * logp;  
                                // System.out.print(" : " + plogp);
                                plogpsum += plogp;  
                                psum += p; 
                                // System.out.println("");
                        }
                        // System.out.println("Sum :"+total+"       : "+psum+"       : "+plogpsum);
                        rsst.close(); 
                        stmt.close(); 
                        
                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                }
                return plogpsum; 
        } // end of getEntropy 

}
Revision:	202
Committed:	Thu Jun 21 17:18:11 2007 UTC (17 years, 4 months ago) by duarte
File size:	3509 byte(s)
Log Message:	MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
Line	User	Rev	File contents
1	lappe	147	import tools.MySQLConnection;
2
3			import java.sql.SQLException;
4			import java.sql.Statement;
5			import java.sql.ResultSet;
6
7	lappe	149	public class minInfoGain {
8	lappe	147
9			/**
10			* "Hello World" for entropy calculations given a nbhoodstring
11			*
12			* @author lappe
13			*/
14
15			static String user = "lappe" ; // change user name!!
16			static MySQLConnection conn;
17
18	duarte	202	public static void main(String[] args) throws SQLException {
19	lappe	147	double entropy = 0.0, newentropy=0.0, gain, mingain=99999999.9;
20			String nbhood = "", front, middle, tail, newhood="";
21			if (args.length<1){
22			System.err.println("The starting neighborhood-string needs to be given .... i.e. %K%D%L%I%x%D%C%");
23			System.exit(1);
24			}
25			nbhood = args[0];
26
27			conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2");
28			int l = (int)((nbhood.length()-1)/2);
29
30			while (l>=2) {
31	lappe	149	System.out.println("MinInfoGain");
32	lappe	147	System.out.print("0 - ("+nbhood+")("+l+") ");
33			entropy = getEntropy( nbhood);
34			System.out.println( entropy + " bits.");
35			System.out.println("Symbols in nbhood :"+l);
36	lappe	149	mingain = 99999999.9;
37	lappe	147	for (int i = 0; i<l; i++) {
38			front = nbhood.substring(0,i*2);
39			middle = nbhood.substring(i2, i2+2);
40			tail = nbhood.substring(i*2+2);
41			System.out.print((i+1)+" - "+front+"("+middle+")"+tail);
42			newentropy = getEntropy( (front+tail));
43			gain = newentropy-entropy;
44			System.out.print( " : "+newentropy +"bits, gain="+gain);
45			if (gain<mingain && !(middle.equals("%x"))) {
46			mingain = gain;
47			newhood = front+tail;
48			System.out.println(" <<-");
49			} else {
50			System.out.println(" .");
51			}
52			} // next symbol in nbhood;
53	lappe	149
54			if (newhood.equals(nbhood)) { // in case we got stcuk with the same string
55			l=0; // - exit loop
56			} else { // continue with new nbhoodstring
57			nbhood = newhood;
58			l = (int)((nbhood.length()-1)/2);
59			}
60	lappe	147	System.out.println("-->> "+nbhood+"("+l+")");
61	lappe	149
62	lappe	147	} //
63			System.out.println("fin.");
64			}
65
66
67
68			public static double getEntropy( String nbs) {
69	duarte	202	int total = 0;
70			String sql;
71	lappe	147	Statement stmt;
72			ResultSet rsst;
73			double p, psum=0.0, logp, plogp, plogpsum=0.0;
74
75			try {
76			sql = "select count(*) from single_model_node where n like '"+nbs+"';";
77			// System.out.println( sql);
78			stmt = conn.createStatement();
79			rsst = stmt.executeQuery(sql);
80			if (rsst.next()) total = rsst.getInt( 1);
81			rsst.close();
82			stmt.close();
83
84			sql = "select res, count() as t, count()/"+total+" as p from single_model_node where n like '"+nbs+"' group by res order by res;";
85			stmt = conn.createStatement();
86			rsst = stmt.executeQuery(sql);
87			// System.out.println("res : total t : fraction p : log2(p) : -p*log2(p)");
88			while (rsst.next()) {
89	duarte	202	//res = rsst.getString(1); // 1st column -- res
90			//num = rsst.getInt(2); // 2nd column -- num
91	lappe	147	p = rsst.getDouble(3); // 3rd: fraction p
92			// System.out.print(res+" : "+num+ " : " + p);
93			logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits
94			// System.out.print(" : " + logp);
95			plogp = -1.0 * p * logp;
96			// System.out.print(" : " + plogp);
97			plogpsum += plogp;
98			psum += p;
99			// System.out.println("");
100			}
101			// System.out.println("Sum :"+total+" : "+psum+" : "+plogpsum);
102			rsst.close();
103			stmt.close();
104
105			} catch (SQLException e) {
106			e.printStackTrace();
107			System.err.println("SQLException: " + e.getMessage());
108			System.err.println("SQLState: " + e.getSQLState());
109			}
110			return plogpsum;
111			} // end of getEntropy
112
113			}