owl/trunk/hashIterNbhood.java

import tools.MySQLConnection;

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

public class hashIterNbhood {

        /**
         *  
         * iterating over all steps by exchange of one neighbor at a time by a common neighbor 
         * with subsequent scoring 
         * @author lappe
         */
        static int maxRank = 21; // 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 int lastRank, lastTotal;  
        static int graphid=0, resnr=0; 
        static int size1=0, size2=0; // the dimensions of the matrices = |shell1|x|shell2| = nr of direct(1) x indirect(2) nbs 
        static String rsideline[], rheadline[]={" -->\t(-)1st shell\t0"," |\t        \t-"," |\t(+)     \t0"," V\t2nd shell\t-"};
        static String sideline[], headline[]={"\t\t0","\t\t-","\t\t0","\t\t-","\t\tX"};
        static String restype="?", ressec="?", newnbhood=""; 
        static int cn1[], cn2[]; 
        static int sumdelta[][], rank[][], total[][], cnsize[][];
        static double entropy[][], freq[][], AUC[][]; 
        static String newnbs[][], nbstring[][], moveset[][];  
        
        static int printRank=1, 
        printTotal   = 2, 
        printEntropy = 3, 
        printFreq    = 4,    
        printAUC     = 5, 
        printNbstring= 6, 
        printMoveset = 7,
        printdeltaRank=8,
        printCNSize   =9, 
        printCNSxdelta=10;
        
        public static void main(String[] args) {
                
            if (args.length<2){
                        System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 7 110");
                        System.exit(1);
                }               
                graphid = Integer.parseInt( args[0]);
                resnr = Integer.parseInt( args[1]); 
                int j_num=0, oj_num=0, oj_shell, oj_cnsize, i, j, x, oi, oj, o1, o2, score=0;
                boolean overx = false;  
                String sql, oj_res, oj_sec;  
                Statement mstmt, mjst, nstmt;  
                ResultSet mrsst, nrsst;
                
                try {
                        conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2"); // the UPPERCASE DB!  
                        System.out.println("Hashed Iterating / Evaluating neighborhood v.0.2. "); 

                        sql = "select num, res, sstype from single_model_node where graph_id="+graphid+" and num="+resnr+";"; 
                        mstmt = conn.createStatement();
                        mrsst = mstmt.executeQuery(sql); 
                        if (mrsst.next()) {
                            // this is the central node -> get type and secondary structure 
                                restype =  mrsst.getString( 2).toUpperCase(); 
                                ressec  =  mrsst.getString( 3).toUpperCase();
                        } // end if central residue
                        mrsst.close();
                        mstmt.close(); 
                        System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec); 
                        
//                      retrieve the original nbhood into orig_shell
                        System.out.println("retrieving original first shell ... "); 
                        mstmt = conn.createStatement();
                        mstmt.executeUpdate("drop table if exists orig_shell;"); 
                        mstmt.close(); 
        
                        mstmt = conn.createStatement();
                        mstmt.executeUpdate("create table orig_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+";");
                        mstmt.close(); 
        
                        System.out.println("adding the original 2nd shell ...");  
                        sql = "select j_num from orig_shell where shell=1;";
                        mstmt = conn.createStatement();
                        mrsst = mstmt.executeQuery(sql);
                        i=0; 
                        while (mrsst.next()) {
                                i++; 
                                oj_num = mrsst.getInt(1);
                                System.out.println(i+":"+oj_num); 
                                mjst = conn.createStatement();
                                sql = "insert into orig_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="+oj_num+";";
                                // System.out.println(">"+sql); 
                                mjst.executeUpdate( sql); 
                                mjst.close(); 
                        } // end while 
                        mrsst.close(); 
                        mstmt.close(); 

                        System.out.println("gathering the original 1st and 2nd shell nbs.");  
                        sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from orig_shell where j_num!="+resnr+" group by j_num order by j_num;";
                        mstmt = conn.createStatement();
                        mrsst = mstmt.executeQuery(sql);
                        o1=0; 
                        o2=0;           
                        while (mrsst.next()) {
                                if ( mrsst.getInt( 4)==1) { // count 1st shell entry 
                                        o1++;
                                        System.out.print("1#"+o1);
                                        rheadline[0]+="\t"+o1; 
                                        rheadline[1]+="\t"+mrsst.getString(2); // res
                                        rheadline[2]+="\t"+mrsst.getInt(1); // resnum 
                                        rheadline[3]+="\t"+mrsst.getString(3); // SStype
                                } // end if 2st shell 
                                if ( mrsst.getInt( 4)==2) { // count 2nd shell entry 
                                        o2++;
                                        System.out.print("2#"+o2);
                                } // end if 2nd shell 
                                System.out.println(" :\t"+mrsst.getInt( 1)+"\t"+mrsst.getString( 2)+"\t"+mrsst.getString( 3)+"\t"+mrsst.getInt( 4)+"\t"+mrsst.getInt( 5)); 
                        } // end while
                        System.out.println("Orig.SIZE 1st shell "+o1); 
                        System.out.println("Orig.SIZE 2nd shell "+o2);
                        rsideline = new String[o2+1];
                        rsideline[0]="+0\tRnum:S(cn)"; 
                        sumdelta = new int[(o1+1)][(o2+1)];
                        newnbs = new String[(o1+1)][(o2+1)];
                        // creating the perturbed version of shell 1 into temp_shell
                        for (j=0; j<=o2; j++) { // <=o2 outer loop through all originally indirect contacts
                                
                                for (i=0; i<=o1; i++) { // inner loop through all originally direct contacts
                                        System.out.println("---------------------------------------------"); 
                                        System.out.println("Creating perturbed nbhood ("+i+","+j+")\t");
//                                      clear first 
                                        nstmt = conn.createStatement();
                                        nstmt.executeUpdate("drop table if exists temp_shell;"); 
                                        nstmt.close(); 
                                        nstmt = conn.createStatement();
                                        nstmt.executeUpdate("create table temp_shell select * from orig_shell limit 0;"); 
                                        nstmt.close();
                                        oi = 0; 
                                        oj = 0; 
                                        mrsst.beforeFirst();
                                        newnbhood=""; 
                                        overx = false;
                                        while (mrsst.next()) {
                                                oj_num = mrsst.getInt( 1); 
                                                oj_res = mrsst.getString(2);
                                                oj_sec = mrsst.getString(3);
                                                oj_shell = mrsst.getInt( 4);
                                                oj_cnsize = mrsst.getInt( 5);
                                                if (oj_num>resnr) { // we are over x 
                                                        if (!overx) {
                                                                newnbhood+="x"; 
                                                                overx=true; 
                                                        } // end if over x 
                                                } // END IF J > X 
                                                if (oj_shell==1) { // a direct 1st shell neighbour 
                                                        oi++;
                                                        if (oi!=i) {// if this is NOT the one direct nb 2B dropped
                                                                // include as 1st shell nbor into temp_shell    
                                                                nstmt = conn.createStatement();
                                                                sql = "insert into temp_shell values("+resnr+",\'"+restype+"\',"+oj_num+",\'"+oj_res+"\',\'"+oj_sec+"\', 1);"; 
                                                                // System.out.println("oi>"+ sql); 
                                                                nstmt.executeUpdate(sql);
                                                                nstmt.close();  
                                                                newnbhood+=oj_res;
                                                        } // end if ni!=i 
                                                } else { // 2nd shell neighbour 
                                                        oj++; 
                                                        if (oj==j) { // this is the 2nd shell nb 2B included
                                                                // put as new 1st shell nbor 
                                                                nstmt = conn.createStatement();
                                                                sql = "insert into temp_shell values("+resnr+",\'"+restype+"\',"+oj_num+",\'"+oj_res+"\',\'"+oj_sec+"\', 1);"; 
                                                                // System.out.println("oj>"+ sql);
                                                                nstmt.executeUpdate(sql);
                                                                nstmt.close();          
                                                                newnbhood+=oj_res; 
                                                        } // end if
                                                        if (j==0) { // creating the sideline ruler array for the output 
                                                                rsideline[oj] = "+"+oj+"\t"+oj_res+""+oj_num+":"+oj_sec+"("+oj_cnsize+")";
                                                        } // end if j==0 
                                                } // end if 1st/2nd shell
                                                
                                        } // end while through the entire nbhood
                                        if (!overx) { // we haven't seen a nb > x yet 
                                                newnbhood+="x"; // x sits at the end of the nbhoodstring 
                                                overx=true; 
                                        } // end if over x 
                                        System.out.println("new direct nbhood "+newnbhood); 
                                        // Now the "updated" / perturbed version of shell 1 is in temp_shell
                                        // we can build 2nd shell accordingly. 
                                        // System.out.println("building the 2nd shell");  
                                        sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;";
                                        nstmt = conn.createStatement();
                                        nrsst = nstmt.executeQuery(sql);
                                        x = 0; 
                                        while (nrsst.next()) {
                                                x++;
                                                j_num = nrsst.getInt( 1); 
                                                // System.out.println(x+":"+nrsst.getString( 2)+" "+j_num+" "+nrsst.getString( 3)); 
                                                mjst = 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); 
                                                mjst.executeUpdate( sql); 
                                                mjst.close(); 
                                        } // end while 
                                        nrsst.close(); 
                                        nstmt.close(); 
                                        // and score this move
                                        newnbs[i][j]= newnbhood; 
                                        System.out.println("Scoring ["+i+"]["+j+"] "+newnbs[i][j]);
                                        score = scoreCurrentNbhood();
                                        sumdelta[i][j] = score; 
                                        reportMatrix( printCNSize );
                                        reportMatrix( printdeltaRank ); 
                                        reportMatrix( printCNSxdelta ); 
                                        System.out.println("SumDeltaRank Score = \t"+score);            
                                        // reportMatrix( printNbstring ); 
                                } // next i
                                System.out.println("\t"); 
                        } // next j 
                        // report total matrix sumdelta  
                        reportResults( o1, o2, printRank); 
                        reportResults( o1, o2, printNbstring); 
                        // Cleanup ... 
                        mrsst.close(); 
                        mstmt.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 reportResults( int o1, int o2, int what2print) {
                System.out.println("Printing "+what2print); 
                if (what2print==printRank) System.out.println("Overall resulting SumDeltaRank Matrix" ); 
                if (what2print==printNbstring) System.out.println("Overall tested new nbhoodStrings" ); 
                /*if (what2print==printTotal) System.out.print("total[i][j]" ); 
                if (what2print==printEntropy) System.out.print("entropy[i][j]" );
                if (what2print==printFreq ) System.out.print("freq[i][j]" ); 
                if (what2print==printAUC) System.out.print("AUC[i][j]" ); 
                
                if (what2print==printMoveset) System.out.print("moveset[i][j]" );
                if (what2print==printdeltaRank) System.out.print("rank[i][j]-rank[0][0]" );) */ 
                
                // print headerline(s)
                System.out.println(rheadline[0]);
                System.out.println(rheadline[1]);
                System.out.println(rheadline[2]);
                System.out.println(rheadline[3]);
                for (int j=0; j<=o2; j++) {     
                        // print rsideline
                        System.out.print( rsideline[j]+"\t"); 
                        for ( int i=0; i<=o1; i++) {
                                if (what2print==printRank) System.out.print( sumdelta[i][j] ); 
                                if (what2print==printNbstring) System.out.print( newnbs[i][j] );
                                System.out.print("\t"); 
                        } // next i 
                        System.out.println(""); 
                } // next j     
        } // end of reportResults  
        

        public static int scoreCurrentNbhood() {
                int n1=0, n2=0, ni, nj, i, j, j_num, j_shell, j_cnsize, sumdeltarank=0;
                String sql, j_res, j_sec, nbs, mymove, precol;
                boolean overx = false;  
                Statement stmt;  
                ResultSet rsst;

                try {
                        headline[0]="\t\t0";
                        headline[1]="\t\t-";
                        headline[2]="\t\t0";
                        headline[3]="\t\t-";
                        headline[4]="\t\tX";
        
                        // System.out.println("retrieving the entire nbhood (1st and 2nd shell)");  
                        sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell where j_num!="+resnr+" group by j_num order by j_num;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        // counting shell2
                        n2=0;           
                        while (rsst.next()) {
                                if ( rsst.getInt( 4)==1) { // count 1st shell entry 
                                        n1++;
                                        System.out.print("1#"+n1);
                                        headline[0]+="\t"+n1; 
                                        headline[1]+="\t"+rsst.getString(2); // res
                                        headline[2]+="\t"+rsst.getInt(1); // resnum 
                                        headline[3]+="\t"+rsst.getString(3); // SStype
                                        headline[4]+="\t"+rsst.getInt(5); // CNSize
                                } // end if 2st shell 
                                if ( rsst.getInt( 4)==2) { // count 2nd shell entry 
                                        n2++;
                                        System.out.print("2#"+n2);
                                } // end if 2nd shell 
                                System.out.println(" :\t"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)); 
                        } // end while
                        size1 = n1; 
                        size2 = n2; 
                        System.out.println("SIZE 1st shell "+size1); 
                        System.out.println("SIZE 2nd shell "+size2);
                        headline[4]=headline[4].replace("X",(""+size1));
                        
                        // n1 and n2 are known, initialise matrices accordingly. 
                        // nbhood, move, rank, entropy, freq, AUC etc. (evtl.+ degree(?)) 
                        rank = new int[(n1+1)][(n2+1)];
                        rank[0][0]=maxRank;
                        total = new int[(n1+1)][(n2+1)];
                        entropy = new double[(n1+1)][(n2+1)];
                        freq = new double[(n1+1)][(n2+1)];        
                        AUC = new double[(n1+1)][(n2+1)];
                        nbstring = new String[(n1+1)][(n2+1)];
                        moveset = new String[(n1+1)][(n2+1)];
                        sideline = new String[n2+1];
                        cn1 = new int[n1+1]; 
                        cn2 = new int[n2+1]; 
                        cnsize = new int[(n1+1)][(n2+1)];
  
                        for (j=0; j<=n2; j++) { // outer loop through all indirect contacts
                                for (i=0; i<=n1; i++) { // inner loop through all direct contacts
                                        mymove = "";
                                        overx = false;
                                        System.out.print("("+i+","+j+")\t");
                                        ni = 0; 
                                        nj = 0; 
                                        sideline[0]="+0\tRnum:S("+n1+")";
                                        cn1[0]=n1; 
                                        cn2[0]=n1; 
                                        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_num>resnr) { // we are over x 
                                                        if (!overx) {
                                                                nbs+="x%"; 
                                                                overx=true; 
                                                        } // end if over x 
                                                } // END IF J > X 
                                                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()+"%"; // it is included                                                                 
                                                        } else { // this one IS dropped 
                                                                mymove += "(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")";
                                                                cn1[ni]=j_cnsize; 
                                                        } // end if ni!=i 
                                                } else { // 2nd shell neighbour 
                                                        nj++; 
                                                        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 
//                                                      // only once for building the sidelines
                                                        if (j==0) {
                                                                sideline[nj] = "+"+nj+"\t"+j_res+""+j_num+":"+j_sec+"("+j_cnsize+")";
                                                                cn2[nj] = j_cnsize; 
                                                        } // end if sideline                                            
                                                } // end if 1st/2nd shell
                                        } // end while through the entire nbhood
                                        if (!overx) { // in case x is the very last we haven't seen it yet  
                                                nbs+="x%"; // add it in the end 
                                                overx=true; 
                                        } // end if over x 
                                        System.out.print("("+nbs+")\t");
                                        nbstring[i][j] = nbs;
                                        moveset[i][j] = mymove;
                                        precol = nbstring[i][0]; 
                                        getEntropy( nbs, restype, precol);
                                        if (lastRank==0) lastRank = rank[0][0];
                                        rank[i][j] = lastRank;
                                        entropy[i][j] = lastEntropy; 
                                        freq[i][j] = lastFreq;
                                        AUC[i][j]  = lastAUC;
                                        total[i][j]= lastTotal; 
                                        cnsize[i][j]=cn1[i]*cn2[j]; 
                                        if (lastRank > 0) { 
                                                sumdeltarank += ((lastRank-(rank[0][0]))*(cnsize[i][j]));
                                        } else {
                                                sumdeltarank += ((maxRank-(rank[0][0]))*(cnsize[i][j]));
                                        } // end if lastRank was defined 
                                } // close inner loop (i)
                                System.out.println(".");
                        } // 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.");
                return sumdeltarank; 
        }       // end scoreCurrentNbhood


        public static void reportMatrix( int what2print) {
                System.out.println("Printing "+what2print); 
                if (what2print==printRank) System.out.print("rank[i][j]" ); 
                if (what2print==printTotal) System.out.print("total[i][j]" ); 
                if (what2print==printEntropy) System.out.print("entropy[i][j]" );
                if (what2print==printFreq ) System.out.print("freq[i][j]" ); 
                if (what2print==printAUC) System.out.print("AUC[i][j]" ); 
                if (what2print==printNbstring) System.out.print("nbstring[i][j]" ); 
                if (what2print==printMoveset) System.out.print("moveset[i][j]" );
                if (what2print==printdeltaRank) System.out.print("rank[i][j]-rank[0][0]" );
                if (what2print==printCNSize) System.out.print("cnsize[i][j]" );
                if (what2print==printCNSxdelta) System.out.print("cnsize[i][j]*(rank[i][j]-rank[0][0])" );
                
                System.out.println("..."); 
                // print headerline(s)
                System.out.println(headline[0]);
                System.out.println(headline[1]);
                System.out.println(headline[2]);
                System.out.println(headline[3]);
                System.out.println(headline[4]);
                for (int j=0; j<=size2; j++) {  
                        // print sideline
                        System.out.print( sideline[j]+"\t"); 
                        for ( int i=0; i<=size1; i++) {
                                if (what2print==printRank) System.out.print( rank[i][j] ); 
                                if (what2print==printTotal) System.out.print( total[i][j] ); 
                                if (what2print==printEntropy) System.out.print( entropy[i][j] );
                                if (what2print==printFreq ) System.out.print( freq[i][j] ); 
                                if (what2print==printAUC) System.out.print( AUC[i][j] ); 
                                if (what2print==printNbstring) System.out.print( nbstring[i][j] ); 
                                if (what2print==printMoveset) System.out.print( moveset[i][j] ); 
                                if (what2print==printdeltaRank) System.out.print( rank[i][j]-rank[0][0] );
                                if (what2print==printCNSize) System.out.print( cnsize[i][j] );
                                if (what2print==printCNSxdelta) System.out.print( cnsize[i][j]*(rank[i][j]-rank[0][0]) ); 
                                System.out.print("\t"); 
                        } // next i 
                        System.out.println(""); 
                } // next j     
        } // end of report 
        
        public static void getEntropy( String nbs, String centRes, String predec) {
                String sql, res, this_n, prec_n; 
                Statement stmt;  
                ResultSet rsst;
                double p, psum=0.0, logp, plogp, plogpsum=0.0; 
                try {
                        // Hashing first row tables comes first
                        // System.out.println("nbs   : "+nbs); 
                        // System.out.println("predec: "+predec);
                        this_n = nbs.replace("%",""); 
                        prec_n = predec.replace("%","");
                        // System.out.println("this_n: ["+this_n+"]"); 
                        // System.out.println("prec_n: ["+prec_n+"]");
                        if (prec_n.equals(this_n)) {
                                // System.out.println("have to create db for this "+prec_n);
                                sql = "create table IF NOT EXISTS nbhashtables."+prec_n+" as select res, n, k from single_model_node where n like '"+nbs+"';"; 
                                // System.out.println(" >> "+sql); 
                                stmt = conn.createStatement();
                                stmt.executeUpdate( sql); 
                                stmt.close(); 
                        } // else System.out.println("using preceding db of "+prec_n); 
                        
                        // now we can safely derive the estimates from the hashtable
                        sql = "select count(*) from nbhashtables."+prec_n+" 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 nbhashtables."+prec_n+" 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:	492
Committed:	Wed Jan 2 13:18:57 2008 UTC (16 years, 8 months ago) by duarte
File size:	20279 byte(s)
Log Message:	Copied the aglappe-jung branch into trunk.
Line	User	Rev	File contents
1	lappe	214	import tools.MySQLConnection;
2
3			import java.sql.SQLException;
4			import java.sql.Statement;
5			import java.sql.ResultSet;
6
7			public class hashIterNbhood {
8
9			/**
10			*
11			* iterating over all steps by exchange of one neighbor at a time by a common neighbor
12			* with subsequent scoring
13			* @author lappe
14			*/
15	lappe	267	static int maxRank = 21; // value to replace for non-existence of central redue in the resultvector (rank=0)
16	lappe	214	// higher values should penalize non-existence more
17			static String user = "lappe" ; // change user name!!
18			static MySQLConnection conn;
19			static double lastEntropy=0.0, lastFreq, lastAUC, lastavgk, lastdevk;
20			static int lastRank, lastTotal;
21			static int graphid=0, resnr=0;
22			static int size1=0, size2=0; // the dimensions of the matrices = \|shell1\|x\|shell2\| = nr of direct(1) x indirect(2) nbs
23			static String rsideline[], rheadline[]={" -->\t(-)1st shell\t0"," \|\t \t-"," \|\t(+) \t0"," V\t2nd shell\t-"};
24	lappe	267	static String sideline[], headline[]={"\t\t0","\t\t-","\t\t0","\t\t-","\t\tX"};
25	lappe	214	static String restype="?", ressec="?", newnbhood="";
26	lappe	267	static int cn1[], cn2[];
27			static int sumdelta[][], rank[][], total[][], cnsize[][];
28	lappe	214	static double entropy[][], freq[][], AUC[][];
29			static String newnbs[][], nbstring[][], moveset[][];
30
31			static int printRank=1,
32			printTotal = 2,
33			printEntropy = 3,
34			printFreq = 4,
35			printAUC = 5,
36			printNbstring= 6,
37			printMoveset = 7,
38	lappe	267	printdeltaRank=8,
39			printCNSize =9,
40			printCNSxdelta=10;
41	lappe	214
42			public static void main(String[] args) {
43
44			if (args.length<2){
45			System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 7 110");
46			System.exit(1);
47			}
48			graphid = Integer.parseInt( args[0]);
49			resnr = Integer.parseInt( args[1]);
50			int j_num=0, oj_num=0, oj_shell, oj_cnsize, i, j, x, oi, oj, o1, o2, score=0;
51			boolean overx = false;
52			String sql, oj_res, oj_sec;
53			Statement mstmt, mjst, nstmt;
54			ResultSet mrsst, nrsst;
55
56			try {
57			conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2"); // the UPPERCASE DB!
58			System.out.println("Hashed Iterating / Evaluating neighborhood v.0.2. ");
59
60			sql = "select num, res, sstype from single_model_node where graph_id="+graphid+" and num="+resnr+";";
61			mstmt = conn.createStatement();
62			mrsst = mstmt.executeQuery(sql);
63			if (mrsst.next()) {
64			// this is the central node -> get type and secondary structure
65			restype = mrsst.getString( 2).toUpperCase();
66			ressec = mrsst.getString( 3).toUpperCase();
67			} // end if central residue
68			mrsst.close();
69			mstmt.close();
70			System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec);
71
72			// retrieve the original nbhood into orig_shell
73			System.out.println("retrieving original first shell ... ");
74			mstmt = conn.createStatement();
75			mstmt.executeUpdate("drop table if exists orig_shell;");
76			mstmt.close();
77
78			mstmt = conn.createStatement();
79			mstmt.executeUpdate("create table orig_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+";");
80			mstmt.close();
81
82			System.out.println("adding the original 2nd shell ...");
83			sql = "select j_num from orig_shell where shell=1;";
84			mstmt = conn.createStatement();
85			mrsst = mstmt.executeQuery(sql);
86			i=0;
87			while (mrsst.next()) {
88			i++;
89			oj_num = mrsst.getInt(1);
90			System.out.println(i+":"+oj_num);
91			mjst = conn.createStatement();
92			sql = "insert into orig_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="+oj_num+";";
93			// System.out.println(">"+sql);
94			mjst.executeUpdate( sql);
95			mjst.close();
96			} // end while
97			mrsst.close();
98			mstmt.close();
99
100			System.out.println("gathering the original 1st and 2nd shell nbs.");
101			sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from orig_shell where j_num!="+resnr+" group by j_num order by j_num;";
102			mstmt = conn.createStatement();
103			mrsst = mstmt.executeQuery(sql);
104			o1=0;
105			o2=0;
106			while (mrsst.next()) {
107			if ( mrsst.getInt( 4)==1) { // count 1st shell entry
108			o1++;
109			System.out.print("1#"+o1);
110			rheadline[0]+="\t"+o1;
111			rheadline[1]+="\t"+mrsst.getString(2); // res
112			rheadline[2]+="\t"+mrsst.getInt(1); // resnum
113			rheadline[3]+="\t"+mrsst.getString(3); // SStype
114			} // end if 2st shell
115			if ( mrsst.getInt( 4)==2) { // count 2nd shell entry
116			o2++;
117			System.out.print("2#"+o2);
118			} // end if 2nd shell
119			System.out.println(" :\t"+mrsst.getInt( 1)+"\t"+mrsst.getString( 2)+"\t"+mrsst.getString( 3)+"\t"+mrsst.getInt( 4)+"\t"+mrsst.getInt( 5));
120			} // end while
121			System.out.println("Orig.SIZE 1st shell "+o1);
122			System.out.println("Orig.SIZE 2nd shell "+o2);
123			rsideline = new String[o2+1];
124			rsideline[0]="+0\tRnum:S(cn)";
125			sumdelta = new int[(o1+1)][(o2+1)];
126			newnbs = new String[(o1+1)][(o2+1)];
127			// creating the perturbed version of shell 1 into temp_shell
128			for (j=0; j<=o2; j++) { // <=o2 outer loop through all originally indirect contacts
129
130			for (i=0; i<=o1; i++) { // inner loop through all originally direct contacts
131			System.out.println("---------------------------------------------");
132			System.out.println("Creating perturbed nbhood ("+i+","+j+")\t");
133			// clear first
134			nstmt = conn.createStatement();
135			nstmt.executeUpdate("drop table if exists temp_shell;");
136			nstmt.close();
137			nstmt = conn.createStatement();
138			nstmt.executeUpdate("create table temp_shell select * from orig_shell limit 0;");
139			nstmt.close();
140			oi = 0;
141			oj = 0;
142			mrsst.beforeFirst();
143			newnbhood="";
144			overx = false;
145			while (mrsst.next()) {
146			oj_num = mrsst.getInt( 1);
147			oj_res = mrsst.getString(2);
148			oj_sec = mrsst.getString(3);
149			oj_shell = mrsst.getInt( 4);
150			oj_cnsize = mrsst.getInt( 5);
151			if (oj_num>resnr) { // we are over x
152			if (!overx) {
153			newnbhood+="x";
154			overx=true;
155			} // end if over x
156			} // END IF J > X
157			if (oj_shell==1) { // a direct 1st shell neighbour
158			oi++;
159			if (oi!=i) {// if this is NOT the one direct nb 2B dropped
160			// include as 1st shell nbor into temp_shell
161			nstmt = conn.createStatement();
162			sql = "insert into temp_shell values("+resnr+",\'"+restype+"\',"+oj_num+",\'"+oj_res+"\',\'"+oj_sec+"\', 1);";
163			// System.out.println("oi>"+ sql);
164			nstmt.executeUpdate(sql);
165			nstmt.close();
166			newnbhood+=oj_res;
167			} // end if ni!=i
168			} else { // 2nd shell neighbour
169			oj++;
170			if (oj==j) { // this is the 2nd shell nb 2B included
171			// put as new 1st shell nbor
172			nstmt = conn.createStatement();
173			sql = "insert into temp_shell values("+resnr+",\'"+restype+"\',"+oj_num+",\'"+oj_res+"\',\'"+oj_sec+"\', 1);";
174			// System.out.println("oj>"+ sql);
175			nstmt.executeUpdate(sql);
176			nstmt.close();
177			newnbhood+=oj_res;
178			} // end if
179			if (j==0) { // creating the sideline ruler array for the output
180			rsideline[oj] = "+"+oj+"\t"+oj_res+""+oj_num+":"+oj_sec+"("+oj_cnsize+")";
181			} // end if j==0
182			} // end if 1st/2nd shell
183
184			} // end while through the entire nbhood
185			if (!overx) { // we haven't seen a nb > x yet
186			newnbhood+="x"; // x sits at the end of the nbhoodstring
187			overx=true;
188			} // end if over x
189			System.out.println("new direct nbhood "+newnbhood);
190			// Now the "updated" / perturbed version of shell 1 is in temp_shell
191			// we can build 2nd shell accordingly.
192			// System.out.println("building the 2nd shell");
193			sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;";
194			nstmt = conn.createStatement();
195			nrsst = nstmt.executeQuery(sql);
196			x = 0;
197			while (nrsst.next()) {
198			x++;
199			j_num = nrsst.getInt( 1);
200			// System.out.println(x+":"+nrsst.getString( 2)+" "+j_num+" "+nrsst.getString( 3));
201			mjst = conn.createStatement();
202			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+";";
203			// System.out.println(">"+sql);
204			mjst.executeUpdate( sql);
205			mjst.close();
206			} // end while
207			nrsst.close();
208			nstmt.close();
209			// and score this move
210			newnbs[i][j]= newnbhood;
211			System.out.println("Scoring ["+i+"]["+j+"] "+newnbs[i][j]);
212			score = scoreCurrentNbhood();
213			sumdelta[i][j] = score;
214	lappe	267	reportMatrix( printCNSize );
215	lappe	214	reportMatrix( printdeltaRank );
216	lappe	267	reportMatrix( printCNSxdelta );
217	lappe	214	System.out.println("SumDeltaRank Score = \t"+score);
218			// reportMatrix( printNbstring );
219			} // next i
220			System.out.println("\t");
221			} // next j
222			// report total matrix sumdelta
223			reportResults( o1, o2, printRank);
224			reportResults( o1, o2, printNbstring);
225			// Cleanup ...
226			mrsst.close();
227			mstmt.close();
228
229			} catch (SQLException e) {
230			e.printStackTrace();
231			System.err.println("SQLException: " + e.getMessage());
232			System.err.println("SQLState: " + e.getSQLState());
233			} // end try/catch
234			System.out.println("fin.");
235			} // end main
236
237
238
239			public static void reportResults( int o1, int o2, int what2print) {
240			System.out.println("Printing "+what2print);
241			if (what2print==printRank) System.out.println("Overall resulting SumDeltaRank Matrix" );
242			if (what2print==printNbstring) System.out.println("Overall tested new nbhoodStrings" );
243			/*if (what2print==printTotal) System.out.print("total[i][j]" );
244			if (what2print==printEntropy) System.out.print("entropy[i][j]" );
245			if (what2print==printFreq ) System.out.print("freq[i][j]" );
246			if (what2print==printAUC) System.out.print("AUC[i][j]" );
247
248			if (what2print==printMoveset) System.out.print("moveset[i][j]" );
249			if (what2print==printdeltaRank) System.out.print("rank[i][j]-rank[0][0]" );) */
250
251			// print headerline(s)
252			System.out.println(rheadline[0]);
253			System.out.println(rheadline[1]);
254			System.out.println(rheadline[2]);
255			System.out.println(rheadline[3]);
256			for (int j=0; j<=o2; j++) {
257			// print rsideline
258			System.out.print( rsideline[j]+"\t");
259			for ( int i=0; i<=o1; i++) {
260			if (what2print==printRank) System.out.print( sumdelta[i][j] );
261			if (what2print==printNbstring) System.out.print( newnbs[i][j] );
262			System.out.print("\t");
263			} // next i
264			System.out.println("");
265			} // next j
266			} // end of reportResults
267
268
269
270			public static int scoreCurrentNbhood() {
271			int n1=0, n2=0, ni, nj, i, j, j_num, j_shell, j_cnsize, sumdeltarank=0;
272			String sql, j_res, j_sec, nbs, mymove, precol;
273			boolean overx = false;
274			Statement stmt;
275			ResultSet rsst;
276
277			try {
278			headline[0]="\t\t0";
279			headline[1]="\t\t-";
280			headline[2]="\t\t0";
281			headline[3]="\t\t-";
282	lappe	267	headline[4]="\t\tX";
283
284	lappe	214	// System.out.println("retrieving the entire nbhood (1st and 2nd shell)");
285			sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell where j_num!="+resnr+" group by j_num order by j_num;";
286			stmt = conn.createStatement();
287			rsst = stmt.executeQuery(sql);
288			// counting shell2
289			n2=0;
290			while (rsst.next()) {
291			if ( rsst.getInt( 4)==1) { // count 1st shell entry
292			n1++;
293			System.out.print("1#"+n1);
294			headline[0]+="\t"+n1;
295			headline[1]+="\t"+rsst.getString(2); // res
296			headline[2]+="\t"+rsst.getInt(1); // resnum
297			headline[3]+="\t"+rsst.getString(3); // SStype
298	lappe	267	headline[4]+="\t"+rsst.getInt(5); // CNSize
299	lappe	214	} // end if 2st shell
300			if ( rsst.getInt( 4)==2) { // count 2nd shell entry
301			n2++;
302			System.out.print("2#"+n2);
303			} // end if 2nd shell
304			System.out.println(" :\t"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5));
305			} // end while
306			size1 = n1;
307			size2 = n2;
308			System.out.println("SIZE 1st shell "+size1);
309			System.out.println("SIZE 2nd shell "+size2);
310	lappe	267	headline[4]=headline[4].replace("X",(""+size1));
311
312	lappe	214	// n1 and n2 are known, initialise matrices accordingly.
313			// nbhood, move, rank, entropy, freq, AUC etc. (evtl.+ degree(?))
314			rank = new int[(n1+1)][(n2+1)];
315	lappe	267	rank[0][0]=maxRank;
316	lappe	214	total = new int[(n1+1)][(n2+1)];
317			entropy = new double[(n1+1)][(n2+1)];
318			freq = new double[(n1+1)][(n2+1)];
319			AUC = new double[(n1+1)][(n2+1)];
320			nbstring = new String[(n1+1)][(n2+1)];
321			moveset = new String[(n1+1)][(n2+1)];
322	lappe	267	sideline = new String[n2+1];
323			cn1 = new int[n1+1];
324			cn2 = new int[n2+1];
325			cnsize = new int[(n1+1)][(n2+1)];
326
327	lappe	214	for (j=0; j<=n2; j++) { // outer loop through all indirect contacts
328			for (i=0; i<=n1; i++) { // inner loop through all direct contacts
329			mymove = "";
330			overx = false;
331			System.out.print("("+i+","+j+")\t");
332			ni = 0;
333			nj = 0;
334	lappe	267	sideline[0]="+0\tRnum:S("+n1+")";
335			cn1[0]=n1;
336			cn2[0]=n1;
337	lappe	214	nbs="%";
338			rsst.beforeFirst();
339			while (rsst.next()) {
340			j_num = rsst.getInt(1);
341			j_res = rsst.getString(2);
342			j_sec = rsst.getString(3);
343			j_shell = rsst.getInt(4);
344			j_cnsize = rsst.getInt(5);
345			if (j_num>resnr) { // we are over x
346			if (!overx) {
347			nbs+="x%";
348			overx=true;
349			} // end if over x
350			} // END IF J > X
351			if (j_shell==1) { // a direct 1st shell neighbour
352			ni++;
353			if (ni!=i) {// if this is NOT the one direct nb 2B dropped
354			nbs+=j_res.toUpperCase()+"%"; // it is included
355			} else { // this one IS dropped
356	lappe	267	mymove += "(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")";
357			cn1[ni]=j_cnsize;
358	lappe	214	} // end if ni!=i
359			} else { // 2nd shell neighbour
360			nj++;
361			if (nj==j) { // this is the 2nd shell nb 2B included
362			nbs+=j_res.toUpperCase()+"%";
363	lappe	267	mymove += "(+"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")";
364
365	lappe	214	} // end if
366			// // only once for building the sidelines
367			if (j==0) {
368	lappe	267	sideline[nj] = "+"+nj+"\t"+j_res+""+j_num+":"+j_sec+"("+j_cnsize+")";
369			cn2[nj] = j_cnsize;
370	lappe	214	} // end if sideline
371			} // end if 1st/2nd shell
372			} // end while through the entire nbhood
373			if (!overx) { // in case x is the very last we haven't seen it yet
374			nbs+="x%"; // add it in the end
375			overx=true;
376			} // end if over x
377			System.out.print("("+nbs+")\t");
378			nbstring[i][j] = nbs;
379			moveset[i][j] = mymove;
380			precol = nbstring[i][0];
381			getEntropy( nbs, restype, precol);
382	lappe	218	if (lastRank==0) lastRank = rank[0][0];
383			rank[i][j] = lastRank;
384	lappe	214	entropy[i][j] = lastEntropy;
385			freq[i][j] = lastFreq;
386			AUC[i][j] = lastAUC;
387			total[i][j]= lastTotal;
388	lappe	267	cnsize[i][j]=cn1[i]*cn2[j];
389	lappe	214	if (lastRank > 0) {
390	lappe	267	sumdeltarank += ((lastRank-(rank[0][0]))*(cnsize[i][j]));
391	lappe	214	} else {
392	lappe	267	sumdeltarank += ((maxRank-(rank[0][0]))*(cnsize[i][j]));
393	lappe	214	} // end if lastRank was defined
394			} // close inner loop (i)
395			System.out.println(".");
396			} // next outerloop (j)
397			rsst.close();
398			stmt.close();
399
400			} catch (SQLException e) {
401			e.printStackTrace();
402			System.err.println("SQLException: " + e.getMessage());
403			System.err.println("SQLState: " + e.getSQLState());
404			} // end try/catch
405			// System.out.println("fin.");
406			return sumdeltarank;
407			} // end scoreCurrentNbhood
408
409
410			public static void reportMatrix( int what2print) {
411			System.out.println("Printing "+what2print);
412			if (what2print==printRank) System.out.print("rank[i][j]" );
413			if (what2print==printTotal) System.out.print("total[i][j]" );
414			if (what2print==printEntropy) System.out.print("entropy[i][j]" );
415			if (what2print==printFreq ) System.out.print("freq[i][j]" );
416			if (what2print==printAUC) System.out.print("AUC[i][j]" );
417			if (what2print==printNbstring) System.out.print("nbstring[i][j]" );
418			if (what2print==printMoveset) System.out.print("moveset[i][j]" );
419			if (what2print==printdeltaRank) System.out.print("rank[i][j]-rank[0][0]" );
420	lappe	267	if (what2print==printCNSize) System.out.print("cnsize[i][j]" );
421			if (what2print==printCNSxdelta) System.out.print("cnsize[i][j]*(rank[i][j]-rank[0][0])" );
422
423	lappe	214	System.out.println("...");
424			// print headerline(s)
425			System.out.println(headline[0]);
426			System.out.println(headline[1]);
427			System.out.println(headline[2]);
428			System.out.println(headline[3]);
429	lappe	267	System.out.println(headline[4]);
430	lappe	214	for (int j=0; j<=size2; j++) {
431			// print sideline
432			System.out.print( sideline[j]+"\t");
433			for ( int i=0; i<=size1; i++) {
434			if (what2print==printRank) System.out.print( rank[i][j] );
435			if (what2print==printTotal) System.out.print( total[i][j] );
436			if (what2print==printEntropy) System.out.print( entropy[i][j] );
437			if (what2print==printFreq ) System.out.print( freq[i][j] );
438			if (what2print==printAUC) System.out.print( AUC[i][j] );
439			if (what2print==printNbstring) System.out.print( nbstring[i][j] );
440			if (what2print==printMoveset) System.out.print( moveset[i][j] );
441			if (what2print==printdeltaRank) System.out.print( rank[i][j]-rank[0][0] );
442	lappe	267	if (what2print==printCNSize) System.out.print( cnsize[i][j] );
443			if (what2print==printCNSxdelta) System.out.print( cnsize[i][j]*(rank[i][j]-rank[0][0]) );
444	lappe	214	System.out.print("\t");
445			} // next i
446			System.out.println("");
447			} // next j
448			} // end of report
449
450			public static void getEntropy( String nbs, String centRes, String predec) {
451			String sql, res, this_n, prec_n;
452			Statement stmt;
453			ResultSet rsst;
454			double p, psum=0.0, logp, plogp, plogpsum=0.0;
455			try {
456			// Hashing first row tables comes first
457			// System.out.println("nbs : "+nbs);
458			// System.out.println("predec: "+predec);
459			this_n = nbs.replace("%","");
460			prec_n = predec.replace("%","");
461			// System.out.println("this_n: ["+this_n+"]");
462			// System.out.println("prec_n: ["+prec_n+"]");
463			if (prec_n.equals(this_n)) {
464			// System.out.println("have to create db for this "+prec_n);
465			sql = "create table IF NOT EXISTS nbhashtables."+prec_n+" as select res, n, k from single_model_node where n like '"+nbs+"';";
466			// System.out.println(" >> "+sql);
467			stmt = conn.createStatement();
468			stmt.executeUpdate( sql);
469			stmt.close();
470			} // else System.out.println("using preceding db of "+prec_n);
471
472			// now we can safely derive the estimates from the hashtable
473			sql = "select count(*) from nbhashtables."+prec_n+" where n like '"+nbs+"';";
474			// System.out.println( sql);
475			stmt = conn.createStatement();
476			rsst = stmt.executeQuery(sql);
477			if (rsst.next()) lastTotal = rsst.getInt( 1);
478			rsst.close();
479			stmt.close();
480
481			sql = "select res, count() as t, count()/"+lastTotal+" as p, avg( k), stddev( k) from nbhashtables."+prec_n+" where n like '"+nbs+"' group by res order by p DESC;";
482			stmt = conn.createStatement();
483			rsst = stmt.executeQuery(sql);
484			// System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)");
485			int rank = 0;
486			boolean seenCentRes = false;
487			lastAUC = 0.0;
488			lastRank = 0;
489			lastFreq = 0.0;
490			lastavgk = 0.0;
491			lastdevk = 0.0;
492			while (rsst.next()) {
493			rank ++;
494			res = rsst.getString(1); // 1st column -- res
495			p = rsst.getDouble(3); // 3rd: fraction p
496			// System.out.print(rank+ " : " + res+" : "+num+ " : " + p);
497			logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits
498			// System.out.print(" : " + logp);
499			plogp = -1.0 * p * logp;
500			// System.out.print(" : " + plogp);
501			plogpsum += plogp;
502			psum += p;
503
504			if (res.equals(centRes)) {
505			// System.out.print(" <==" + centRes);
506			seenCentRes = true;
507			lastFreq = p;
508			lastRank = rank;
509			lastavgk = rsst.getDouble(4);
510			lastdevk = rsst.getDouble(5);
511			}
512			if (seenCentRes) lastAUC += p;
513			// System.out.println("");
514			}
515			// System.out.println("Sum :"+lastTotal+" : "+psum+" : "+plogpsum);
516			rsst.close();
517			stmt.close();
518			lastEntropy = plogpsum;
519			if (lastRank==0) lastRank = maxRank;
520			} catch (SQLException e) {
521			e.printStackTrace();
522			System.err.println("SQLException: " + e.getMessage());
523			System.err.println("SQLState: " + e.getSQLState());
524			}
525
526			} // end of getEntropy
527
528			} // end class