owl/trunk/iterateUpperNbs.java

import tools.MySQLConnection;

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

public class iterateUpperNbs {

        /**
         *  
         * exchange of one neighbor at a time by a common neighbor 
         * @author lappe
         */
        static int maxRank = 31; // value to replace for non-existence of central redue in the resultvector (rank=0) 
        // higher values should penalize non-existence more
        static String user = "lappe"    ; // change user name!!
        static MySQLConnection conn;
        static double lastEntropy=0.0, lastFreq, lastAUC, lastavgk, lastdevk; 
        static double  orgEntropy=0.0, orgFreq, orgAUC, orgavgk, orgdevk; 
        static int lastRank, lastTotal;  
        static int orgRank, orgTotal;
        
        public static void main(String[] args) throws SQLException {
                
            if (args.length<2){
                        System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 9 28");
                        System.exit(1);
                }               
                int graphid = Integer.parseInt( args[0]);
                int resnr = Integer.parseInt( args[1]); 
                int n1=0, n2=0, ni=0, nj=0, j_num=0, j_shell, j_cnsize, i, j, sumdelta, j_num12=0, j_num21=0; 
                conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2"); // the UPPERCASE DB!  
                String sql, j_res, j_sec, restype="?", ressec="?", nbs, mymove; 
                Statement stmt, jst;  
                ResultSet rsst;
                
                try {
                        System.out.println("getting direct neighborhood ... "); 
                        stmt = conn.createStatement();
                        stmt.executeUpdate("drop table if exists temp_shell;"); 
                        stmt.close(); 
        
                        stmt = conn.createStatement();
                        stmt.executeUpdate("create table temp_shell as select i_num, i_res, j_num, j_res, j_sstype, 1 as shell from single_model_edge where graph_id="+graphid+" and i_num="+resnr+";");
                        stmt.close(); 
        
                        System.out.println("building the 2nd shell");  
                        sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        while (rsst.next()) {
                                n1++; 
                                j_num = rsst.getInt(1);
                                System.out.println(n1+":"+j_num); 
                                jst = conn.createStatement();
                                sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell from single_model_edge where graph_id="+graphid+" and i_num="+j_num+";";
                                // System.out.println(">"+sql); 
                                jst.executeUpdate( sql); 
                                jst.close(); 
                        } // end while 
                        rsst.close(); 
                        stmt.close(); 
                        
                        // percolate the environment  
                        System.out.println("moving a contact from shell1 -> shell2");  
                        sql = "select j_num, j_res, j_sstype, shell from temp_shell where i_num="+resnr+" and shell = 1 order by rand() limit 1;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        if (rsst.next()) {
                                j_num12 = rsst.getInt( 1); 
                                System.out.println(rsst.getInt( 4)+" -> 2 : ("+rsst.getString( 2)+":"+j_num12+":"+rsst.getString( 3)+")");
                        }
                        rsst.close();
                        stmt.close(); 
                        stmt = conn.createStatement();
                        stmt.executeUpdate("update temp_shell set shell=2 where j_num="+j_num12+";"); 
                        stmt.close(); 
                        
                        
                // and move an indirect nbor from shell2 -> shell 1; 
                        System.out.println("moving a contact from shell2 -> shell1");  
                        sql = "select j_num, j_res, j_sstype, shell from temp_shell where i_num!="+resnr+" and j_num!="+resnr+" and shell = 2 order by rand() limit 1;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        if (rsst.next()) {
                                j_num21 = rsst.getInt( 1); 
                                System.out.println(rsst.getInt( 4)+" -> 1 : ("+rsst.getString( 2)+":"+j_num21+":"+rsst.getString( 3)+")");
                        }
                        rsst.close();
                        stmt.close(); 
                        stmt = conn.createStatement();
                        stmt.executeUpdate("update temp_shell set shell=1 where j_num="+j_num21+";");
                        stmt.close(); 
                        
                        System.out.println("retrieving the entire 1st and 2nd shell");  
                        sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell group by j_num;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        // counting shell2
                        n2=0; 
                        while (rsst.next()) {
                                if ( rsst.getInt( 4)==2) { // count 2nd shell entry 
                                        n2++;
                                        if ( rsst.getInt( 1)==resnr) { // this is the central node -> get type and secondary structure 
                                                restype =  rsst.getString( 2).toUpperCase(); 
                                                ressec  =  rsst.getString( 3).toUpperCase();
                                        } // end if central residue 
                                } // end if 2nds shell 
                                System.out.println(n2+":"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)); 
                        } // end while 
                        System.out.println("SIZE 1st shell "+n1); 
                        System.out.println("SIZE 2nd shell "+n2);
                        System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec); 
                        
                        for (j=0; j<=n2; j++) { // outer loop through all indirect contacts
                                // System.out.print(i+" - "); 
                                sumdelta=0; 
                                for (i=0; i<=n1; i++) { // inner loop through all direct contacts
                                        mymove = "("+i+","+j+")";
                                        ni = 0; 
                                        nj = 0; 
                                        nbs="%";
                                        rsst.beforeFirst();
                                        while (rsst.next()) {
                                                j_num = rsst.getInt( 1); 
                                                j_res = rsst.getString(2);
                                                j_sec = rsst.getString(3);
                                                j_shell = rsst.getInt( 4);
                                                j_cnsize = rsst.getInt( 5);
                                          
                                                if (j_shell==1) { // a direct 1st shell neighbour 
                                                        ni++;
                                                        if (ni!=i) {// if this is NOT the one direct nb 2B dropped 
                                                                nbs+=j_res.toUpperCase()+"%";                                                           
                                                        } else { // this one IS dropped 
                                                                mymove += "(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")"; 
                                                        } // end if ni!=i 
                                                } else { // 2nd shell neighbour 
                                                        nj++; 
                                                        if (j_num==resnr) { // the central residue is part if the 2nd shell
                                                                if (nj!=j) { // drop x if marked for inclusion 
                                                                        nbs+="x%"; 
                                                                } else {
                                                                        mymove += " no x ..."; 
                                                                }
                                                        } else { // this is not x 
                                                                if (nj==j) { // this is the 2nd shell nb 2B included
                                                                        nbs+=j_res.toUpperCase()+"%";
                                                                        mymove += "(+"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")"; 
                                                                } // end if 
                                                        } // end if this is central residue x 
                                                } // end if 1st/2nd shell
                                        } // end while through the entire nbhood 
                                        
                                        getEntropy( nbs, restype); 
                                        if (i==0 && j==0) { // original nbhoodstring without any insertions/deletions 
                                                orgEntropy = lastEntropy;
                                                orgFreq = lastFreq;
                                                orgAUC  = lastAUC;
                                                orgavgk = lastavgk;
                                                orgdevk = lastdevk; 
                                                orgRank = lastRank;
                                                orgTotal= lastTotal; 
                                        } // end if 0/0 for defining org*
                                        if (lastRank > 0) { 
                                                sumdelta += (lastRank-orgRank);
                                        } else {
                                                sumdelta += (maxRank-orgRank);
                                        }
                                        
                                        // System.out.println(" t="+orgTotal+" \tentropy = "+String.format("%.5f", orgEntropy)+" \trank#"+String.format("%2d",orgRank)+" \tp("+restype+") = "+String.format("%.5f",orgFreq)+" \t\tAUC = "+String.format("%.5f",orgAUC)+" \t\tavg(k)="+String.format("%.2f",orgavgk)+"\tstddev="+String.format("%.2f",orgdevk));
                                        //if ((lastRank>0 && lastRank<orgRank) || (i==0 && j==0)) {
                                                System.out.print(mymove+"\t"+nbs);
                                                printValues();  
                                        //}
                                                                
                                        
                                        // System.out.println(".");
                                } // close inner loop (i)
                                System.out.println( "Summ "+j+":"+sumdelta);
                        } // next outerloop (j)
                        rsst.close(); 
                        stmt.close(); 
                        
                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                } // end try/catch 
                System.out.println("fin."); 
        }       // end main 
        
        public static void printValues() {
                System.out.print( "\t"+lastTotal+"("+(lastTotal-orgTotal)+")"); 
                System.out.print( "\t"+String.format("%.5f", lastEntropy) +" ("+String.format("%.5f", lastEntropy-orgEntropy)+")");
                System.out.print( "\t#"+String.format("%2d",lastRank) +" ("+String.format("%2d",(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.print( "\t"+String.format("%.2f", lastavgk) +" ("+String.format("%.2f", (lastavgk-orgavgk))+")");
                System.out.print( "\t"+String.format("%.2f", lastdevk) +" ("+String.format("%.2f", (lastdevk-orgdevk))+")");
                System.out.println("");
        }
        
        public static void getEntropy( String nbs, String centRes) {
                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, avg( k), stddev( k) 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 = 0.0; 
                        lastRank = 0; 
                        lastFreq = 0.0;
                        lastavgk = 0.0;
                        lastdevk = 0.0;
                        while (rsst.next()) {   
                                rank ++;
                                res = rsst.getString(1); // 1st column -- res
                                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; 
                                        lastavgk = rsst.getDouble(4);
                                        lastdevk = rsst.getDouble(5);
                                }
                                if (seenCentRes) lastAUC += p; 
                                // System.out.println("");
                        }
                        // System.out.println("Sum :"+lastTotal+"       : "+psum+"       : "+plogpsum);
                        rsst.close(); 
                        stmt.close(); 
                        lastEntropy = plogpsum; 
                        if (lastRank==0) lastRank = maxRank;  
                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                }
                
        } // end of getEntropy 

} // end class 
Revision:	202
Committed:	Thu Jun 21 17:18:11 2007 UTC (17 years, 3 months ago) by duarte
File size:	10295 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	166	import tools.MySQLConnection;
2
3			import java.sql.SQLException;
4			import java.sql.Statement;
5			import java.sql.ResultSet;
6
7	lappe	173	public class iterateUpperNbs {
8	lappe	166
9			/**
10			*
11			* exchange of one neighbor at a time by a common neighbor
12			* @author lappe
13			*/
14	lappe	180	static int maxRank = 31; // value to replace for non-existence of central redue in the resultvector (rank=0)
15	lappe	173	// higher values should penalize non-existence more
16	lappe	166	static String user = "lappe" ; // change user name!!
17			static MySQLConnection conn;
18	lappe	170	static double lastEntropy=0.0, lastFreq, lastAUC, lastavgk, lastdevk;
19			static double orgEntropy=0.0, orgFreq, orgAUC, orgavgk, orgdevk;
20			static int lastRank, lastTotal;
21			static int orgRank, orgTotal;
22	lappe	166
23	duarte	202	public static void main(String[] args) throws SQLException {
24	lappe	166
25			if (args.length<2){
26			System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 9 28");
27			System.exit(1);
28			}
29			int graphid = Integer.parseInt( args[0]);
30			int resnr = Integer.parseInt( args[1]);
31	lappe	173	int n1=0, n2=0, ni=0, nj=0, j_num=0, j_shell, j_cnsize, i, j, sumdelta, j_num12=0, j_num21=0;
32			conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2"); // the UPPERCASE DB!
33			String sql, j_res, j_sec, restype="?", ressec="?", nbs, mymove;
34	lappe	166	Statement stmt, jst;
35	lappe	173	ResultSet rsst;
36	lappe	166
37			try {
38			System.out.println("getting direct neighborhood ... ");
39			stmt = conn.createStatement();
40			stmt.executeUpdate("drop table if exists temp_shell;");
41			stmt.close();
42
43			stmt = conn.createStatement();
44			stmt.executeUpdate("create table temp_shell as select i_num, i_res, j_num, j_res, j_sstype, 1 as shell from single_model_edge where graph_id="+graphid+" and i_num="+resnr+";");
45			stmt.close();
46
47			System.out.println("building the 2nd shell");
48			sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;";
49			stmt = conn.createStatement();
50			rsst = stmt.executeQuery(sql);
51			while (rsst.next()) {
52			n1++;
53			j_num = rsst.getInt(1);
54			System.out.println(n1+":"+j_num);
55			jst = conn.createStatement();
56			sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell from single_model_edge where graph_id="+graphid+" and i_num="+j_num+";";
57			// System.out.println(">"+sql);
58			jst.executeUpdate( sql);
59			jst.close();
60			} // end while
61			rsst.close();
62			stmt.close();
63
64	lappe	180	// percolate the environment
65	lappe	173	System.out.println("moving a contact from shell1 -> shell2");
66			sql = "select j_num, j_res, j_sstype, shell from temp_shell where i_num="+resnr+" and shell = 1 order by rand() limit 1;";
67			stmt = conn.createStatement();
68			rsst = stmt.executeQuery(sql);
69			if (rsst.next()) {
70			j_num12 = rsst.getInt( 1);
71			System.out.println(rsst.getInt( 4)+" -> 2 : ("+rsst.getString( 2)+":"+j_num12+":"+rsst.getString( 3)+")");
72			}
73			rsst.close();
74			stmt.close();
75			stmt = conn.createStatement();
76			stmt.executeUpdate("update temp_shell set shell=2 where j_num="+j_num12+";");
77			stmt.close();
78
79
80			// and move an indirect nbor from shell2 -> shell 1;
81			System.out.println("moving a contact from shell2 -> shell1");
82			sql = "select j_num, j_res, j_sstype, shell from temp_shell where i_num!="+resnr+" and j_num!="+resnr+" and shell = 2 order by rand() limit 1;";
83			stmt = conn.createStatement();
84			rsst = stmt.executeQuery(sql);
85			if (rsst.next()) {
86			j_num21 = rsst.getInt( 1);
87			System.out.println(rsst.getInt( 4)+" -> 1 : ("+rsst.getString( 2)+":"+j_num21+":"+rsst.getString( 3)+")");
88			}
89			rsst.close();
90			stmt.close();
91			stmt = conn.createStatement();
92			stmt.executeUpdate("update temp_shell set shell=1 where j_num="+j_num21+";");
93			stmt.close();
94
95	lappe	170	System.out.println("retrieving the entire 1st and 2nd shell");
96	lappe	166	sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell group by j_num;";
97			stmt = conn.createStatement();
98			rsst = stmt.executeQuery(sql);
99			// counting shell2
100			n2=0;
101			while (rsst.next()) {
102	lappe	170	if ( rsst.getInt( 4)==2) { // count 2nd shell entry
103			n2++;
104			if ( rsst.getInt( 1)==resnr) { // this is the central node -> get type and secondary structure
105			restype = rsst.getString( 2).toUpperCase();
106			ressec = rsst.getString( 3).toUpperCase();
107			} // end if central residue
108			} // end if 2nds shell
109	lappe	166	System.out.println(n2+":"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5));
110			} // end while
111			System.out.println("SIZE 1st shell "+n1);
112			System.out.println("SIZE 2nd shell "+n2);
113	lappe	170	System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec);
114	lappe	166
115	lappe	173	for (j=0; j<=n2; j++) { // outer loop through all indirect contacts
116	lappe	170	// System.out.print(i+" - ");
117	lappe	173	sumdelta=0;
118			for (i=0; i<=n1; i++) { // inner loop through all direct contacts
119			mymove = "("+i+","+j+")";
120	lappe	170	ni = 0;
121			nj = 0;
122	lappe	173	nbs="%";
123	lappe	170	rsst.beforeFirst();
124			while (rsst.next()) {
125			j_num = rsst.getInt( 1);
126			j_res = rsst.getString(2);
127			j_sec = rsst.getString(3);
128			j_shell = rsst.getInt( 4);
129			j_cnsize = rsst.getInt( 5);
130
131			if (j_shell==1) { // a direct 1st shell neighbour
132			ni++;
133			if (ni!=i) {// if this is NOT the one direct nb 2B dropped
134	lappe	173	nbs+=j_res.toUpperCase()+"%";
135	lappe	170	} else { // this one IS dropped
136	lappe	173	mymove += "(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")";
137	lappe	170	} // end if ni!=i
138			} else { // 2nd shell neighbour
139			nj++;
140			if (j_num==resnr) { // the central residue is part if the 2nd shell
141			if (nj!=j) { // drop x if marked for inclusion
142	lappe	173	nbs+="x%";
143	lappe	170	} else {
144	lappe	173	mymove += " no x ...";
145	lappe	170	}
146			} else { // this is not x
147			if (nj==j) { // this is the 2nd shell nb 2B included
148	lappe	173	nbs+=j_res.toUpperCase()+"%";
149			mymove += "(+"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")";
150	lappe	170	} // end if
151			} // end if this is central residue x
152			} // end if 1st/2nd shell
153			} // end while through the entire nbhood
154	lappe	166
155	lappe	173	getEntropy( nbs, restype);
156	lappe	170	if (i==0 && j==0) { // original nbhoodstring without any insertions/deletions
157			orgEntropy = lastEntropy;
158			orgFreq = lastFreq;
159			orgAUC = lastAUC;
160			orgavgk = lastavgk;
161			orgdevk = lastdevk;
162			orgRank = lastRank;
163			orgTotal= lastTotal;
164	lappe	173	} // end if 0/0 for defining org*
165			if (lastRank > 0) {
166			sumdelta += (lastRank-orgRank);
167			} else {
168			sumdelta += (maxRank-orgRank);
169			}
170	lappe	166
171	lappe	173	// System.out.println(" t="+orgTotal+" \tentropy = "+String.format("%.5f", orgEntropy)+" \trank#"+String.format("%2d",orgRank)+" \tp("+restype+") = "+String.format("%.5f",orgFreq)+" \t\tAUC = "+String.format("%.5f",orgAUC)+" \t\tavg(k)="+String.format("%.2f",orgavgk)+"\tstddev="+String.format("%.2f",orgdevk));
172			//if ((lastRank>0 && lastRank<orgRank) \|\| (i==0 && j==0)) {
173			System.out.print(mymove+"\t"+nbs);
174			printValues();
175			//}
176
177
178	lappe	170	// System.out.println(".");
179	lappe	173	} // close inner loop (i)
180			System.out.println( "Summ "+j+":"+sumdelta);
181			} // next outerloop (j)
182	lappe	166	rsst.close();
183			stmt.close();
184
185	lappe	170	} catch (SQLException e) {
186			e.printStackTrace();
187			System.err.println("SQLException: " + e.getMessage());
188			System.err.println("SQLState: " + e.getSQLState());
189			} // end try/catch
190			System.out.println("fin.");
191			} // end main
192
193			public static void printValues() {
194			System.out.print( "\t"+lastTotal+"("+(lastTotal-orgTotal)+")");
195			System.out.print( "\t"+String.format("%.5f", lastEntropy) +" ("+String.format("%.5f", lastEntropy-orgEntropy)+")");
196			System.out.print( "\t#"+String.format("%2d",lastRank) +" ("+String.format("%2d",(lastRank-orgRank))+")");
197			System.out.print( "\t"+String.format("%.5f", lastFreq) +" ("+String.format("%.5f", (lastFreq-orgFreq))+")");
198			System.out.print( "\t"+String.format("%.5f", lastAUC) +" ("+String.format("%.5f", (lastAUC-orgAUC))+")");
199			System.out.print( "\t"+String.format("%.2f", lastavgk) +" ("+String.format("%.2f", (lastavgk-orgavgk))+")");
200			System.out.print( "\t"+String.format("%.2f", lastdevk) +" ("+String.format("%.2f", (lastdevk-orgdevk))+")");
201			System.out.println("");
202			}
203
204			public static void getEntropy( String nbs, String centRes) {
205			String sql, res;
206			Statement stmt;
207			ResultSet rsst;
208			double p, psum=0.0, logp, plogp, plogpsum=0.0;
209			try {
210			sql = "select count(*) from single_model_node where n like '"+nbs+"';";
211			// System.out.println( sql);
212			stmt = conn.createStatement();
213			rsst = stmt.executeQuery(sql);
214			if (rsst.next()) lastTotal = rsst.getInt( 1);
215			rsst.close();
216			stmt.close();
217	lappe	166
218	lappe	170	sql = "select res, count() as t, count()/"+lastTotal+" as p, avg( k), stddev( k) from single_model_node where n like '"+nbs+"' group by res order by p DESC;";
219			stmt = conn.createStatement();
220			rsst = stmt.executeQuery(sql);
221			// System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)");
222			int rank = 0;
223			boolean seenCentRes = false;
224			lastAUC = 0.0;
225			lastRank = 0;
226			lastFreq = 0.0;
227			lastavgk = 0.0;
228			lastdevk = 0.0;
229			while (rsst.next()) {
230			rank ++;
231			res = rsst.getString(1); // 1st column -- res
232			p = rsst.getDouble(3); // 3rd: fraction p
233			// System.out.print(rank+ " : " + res+" : "+num+ " : " + p);
234			logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits
235			// System.out.print(" : " + logp);
236			plogp = -1.0 * p * logp;
237			// System.out.print(" : " + plogp);
238			plogpsum += plogp;
239			psum += p;
240
241			if (res.equals(centRes)) {
242			// System.out.print(" <==" + centRes);
243			seenCentRes = true;
244			lastFreq = p;
245			lastRank = rank;
246			lastavgk = rsst.getDouble(4);
247			lastdevk = rsst.getDouble(5);
248			}
249			if (seenCentRes) lastAUC += p;
250			// System.out.println("");
251			}
252			// System.out.println("Sum :"+lastTotal+" : "+psum+" : "+plogpsum);
253			rsst.close();
254			stmt.close();
255			lastEntropy = plogpsum;
256	lappe	173	if (lastRank==0) lastRank = maxRank;
257	lappe	166	} catch (SQLException e) {
258			e.printStackTrace();
259			System.err.println("SQLException: " + e.getMessage());
260			System.err.println("SQLState: " + e.getSQLState());
261	lappe	170	}
262	lappe	166
263	lappe	170	} // end of getEntropy
264	lappe	166
265	lappe	170	} // end class