owl/trunk/listInfoLoss.java

import tools.MySQLConnection;

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

public class listInfoLoss {

        /**
         * info loss / entropy calculations given a nbhoodstring 
         * dropping one neighbor at a time 
         * @author lappe
         */
        
        static String user = "lappe"    ; // change user name!!
        static MySQLConnection conn;
        static double orgFreq, lastFreq, orgAUC, lastAUC; 
        static int orgRank, lastRank, orgTotal, lastTotal; 
        
        public static void main(String[] args) {
                double entropy = 0.0, newentropy=0.0, gain; 
                String nbhood = "", front, middle, tail, newhood="", central ="I";
                if (args.length<2){
                        System.err.println("The starting neighborhood-string and central residue type needs to be given .... i.e. %K%D%L%I%x%D%C% I");
                        System.exit(1);
                }               
                nbhood = args[0];
                central = args[1]; 
                
                conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2_a"); 
                int l = (int)((nbhood.length()-1)/2); 
                
                        System.out.println("ListInfoLoss");
                        System.out.print("0 - ("+nbhood+")("+l+") "); 
                        entropy = getEntropy( nbhood, central); 
                        
                        // System.out.println("Symbols in nbhood :"+l); 
                        orgFreq = lastFreq;
                        orgAUC = lastAUC; 
                        orgRank = lastRank; 
                        orgTotal = lastTotal; 
                        System.out.println("central "+central+". \tt="+orgTotal+" \tentropy = "+String.format("%.5f", entropy)+" \trank#"+lastRank+" \tp("+central+") = "+String.format("%.5f",lastFreq)+" \t\tAUC = "+String.format("%.5f",lastAUC));
//                       System.out.println("Symbols in nbhood :"+l);
                        
                        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);
                                
                                newhood = front+tail; 
                                
                                System.out.print( " -> " + newhood); 
                                newentropy = getEntropy( newhood, central); 
                                gain = newentropy-entropy; 
                                System.out.print( "\t"+lastTotal+"("+(lastTotal-orgTotal)+")"); 
                                System.out.print( "\t"+String.format("%.5f", newentropy) +" ("+String.format("%.5f", gain)+")");
                                System.out.print( "\t#"+lastRank +" ("+(lastRank-orgRank)+")");
                                System.out.print( "\t"+String.format("%.5f", lastFreq) +" ("+String.format("%.5f", (lastFreq-orgFreq))+")");
                                System.out.print( "\t"+String.format("%.5f", lastAUC) +" ("+String.format("%.5f", (lastAUC-orgAUC))+")");
                                
                                System.out.println( ".");  
                        } // next symbol in nbhood;  
                
                System.out.println("fin."); 
        }       

                
        
        public static double getEntropy( String nbs, String centRes) {
                int num; 
                String sql, res; 
                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()) lastTotal = rsst.getInt( 1); 
                        rsst.close(); 
                        stmt.close(); 
                        
                        sql = "select res, count(*) as t, count(*)/"+lastTotal+" as p from single_model_node where n like '"+nbs+"' group by res order by p DESC;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        // System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)");
                        int rank = 0; 
                        boolean seenCentRes = false;  
                        lastAUC= 0; 
                        while (rsst.next()) {   
                                rank ++;
                                res = rsst.getString(1); // 1st column -- res
                                num = rsst.getInt(2); // 2nd column -- num
                                p = rsst.getDouble(3); // 3rd: fraction p 
                                // System.out.print(rank+ " : " + 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; 
                                
                                if (res.equals(centRes)) { 
                                        // System.out.print(" <==" + centRes);
                                        seenCentRes = true;
                                        lastFreq = p;
                                        lastRank = rank; 
                                }
                                if (seenCentRes) lastAUC += p; 
                                // System.out.println("");
                        }
                        // System.out.println("Sum :"+lastTotal+"       : "+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:	160
Committed:	Thu May 24 09:52:22 2007 UTC (17 years, 5 months ago) by lappe
File size:	4341 byte(s)
Log Message:	tab-Formatted output added
Line	User	Rev	File contents
1	lappe	160	import tools.MySQLConnection;
2
3			import java.sql.SQLException;
4			import java.sql.Statement;
5			import java.sql.ResultSet;
6
7			public class listInfoLoss {
8
9			/**
10			* info loss / entropy calculations given a nbhoodstring
11			* dropping one neighbor at a time
12			* @author lappe
13			*/
14
15			static String user = "lappe" ; // change user name!!
16			static MySQLConnection conn;
17			static double orgFreq, lastFreq, orgAUC, lastAUC;
18			static int orgRank, lastRank, orgTotal, lastTotal;
19
20			public static void main(String[] args) {
21			double entropy = 0.0, newentropy=0.0, gain;
22			String nbhood = "", front, middle, tail, newhood="", central ="I";
23			if (args.length<2){
24			System.err.println("The starting neighborhood-string and central residue type needs to be given .... i.e. %K%D%L%I%x%D%C% I");
25			System.exit(1);
26			}
27			nbhood = args[0];
28			central = args[1];
29
30			conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2_a");
31			int l = (int)((nbhood.length()-1)/2);
32
33			System.out.println("ListInfoLoss");
34			System.out.print("0 - ("+nbhood+")("+l+") ");
35			entropy = getEntropy( nbhood, central);
36
37			// System.out.println("Symbols in nbhood :"+l);
38			orgFreq = lastFreq;
39			orgAUC = lastAUC;
40			orgRank = lastRank;
41			orgTotal = lastTotal;
42			System.out.println("central "+central+". \tt="+orgTotal+" \tentropy = "+String.format("%.5f", entropy)+" \trank#"+lastRank+" \tp("+central+") = "+String.format("%.5f",lastFreq)+" \t\tAUC = "+String.format("%.5f",lastAUC));
43			// System.out.println("Symbols in nbhood :"+l);
44
45			for (int i = 0; i<l; i++) {
46			front = nbhood.substring(0,i*2);
47			middle = nbhood.substring(i2, i2+2);
48			tail = nbhood.substring(i*2+2);
49			System.out.print((i+1)+" - "+front+"("+middle+")"+tail);
50
51			newhood = front+tail;
52
53			System.out.print( " -> " + newhood);
54			newentropy = getEntropy( newhood, central);
55			gain = newentropy-entropy;
56			System.out.print( "\t"+lastTotal+"("+(lastTotal-orgTotal)+")");
57			System.out.print( "\t"+String.format("%.5f", newentropy) +" ("+String.format("%.5f", gain)+")");
58			System.out.print( "\t#"+lastRank +" ("+(lastRank-orgRank)+")");
59			System.out.print( "\t"+String.format("%.5f", lastFreq) +" ("+String.format("%.5f", (lastFreq-orgFreq))+")");
60			System.out.print( "\t"+String.format("%.5f", lastAUC) +" ("+String.format("%.5f", (lastAUC-orgAUC))+")");
61
62			System.out.println( ".");
63			} // next symbol in nbhood;
64
65			System.out.println("fin.");
66			}
67
68
69
70			public static double getEntropy( String nbs, String centRes) {
71			int num;
72			String sql, res;
73			Statement stmt;
74			ResultSet rsst;
75			double p, psum=0.0, logp, plogp, plogpsum=0.0;
76
77			try {
78			sql = "select count(*) from single_model_node where n like '"+nbs+"';";
79			// System.out.println( sql);
80			stmt = conn.createStatement();
81			rsst = stmt.executeQuery(sql);
82			if (rsst.next()) lastTotal = rsst.getInt( 1);
83			rsst.close();
84			stmt.close();
85
86			sql = "select res, count() as t, count()/"+lastTotal+" as p from single_model_node where n like '"+nbs+"' group by res order by p DESC;";
87			stmt = conn.createStatement();
88			rsst = stmt.executeQuery(sql);
89			// System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)");
90			int rank = 0;
91			boolean seenCentRes = false;
92			lastAUC= 0;
93			while (rsst.next()) {
94			rank ++;
95			res = rsst.getString(1); // 1st column -- res
96			num = rsst.getInt(2); // 2nd column -- num
97			p = rsst.getDouble(3); // 3rd: fraction p
98			// System.out.print(rank+ " : " + res+" : "+num+ " : " + p);
99			logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits
100			// System.out.print(" : " + logp);
101			plogp = -1.0 * p * logp;
102			// System.out.print(" : " + plogp);
103			plogpsum += plogp;
104			psum += p;
105
106			if (res.equals(centRes)) {
107			// System.out.print(" <==" + centRes);
108			seenCentRes = true;
109			lastFreq = p;
110			lastRank = rank;
111			}
112			if (seenCentRes) lastAUC += p;
113			// System.out.println("");
114			}
115			// System.out.println("Sum :"+lastTotal+" : "+psum+" : "+plogpsum);
116			rsst.close();
117			stmt.close();
118
119			} catch (SQLException e) {
120			e.printStackTrace();
121			System.err.println("SQLException: " + e.getMessage());
122			System.err.println("SQLState: " + e.getSQLState());
123			}
124			return plogpsum;
125			} // end of getEntropy
126
127			}