branches/aglappe-jung/iterEvalNbhood.java

import tools.MySQLConnection;

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

public class iterEvalNbhood {

        /**
         *  
         * iterating over all steps by exchange of one neighbor at a time by a common neighbor 
         * with subsequent scoring 
         * @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 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-"};
        static String restype="?", ressec="?", newnbhood=""; 
        
        static int sumdelta[][], rank[][], total[][];
        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; 
        
        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. 9 28");
                        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;
                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("Iterating and 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=""; 
                                        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_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
                                        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( printRank );
                                        reportMatrix( printdeltaRank ); 
                                        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;
                boolean overx = false;  
                Statement stmt;  
                ResultSet rsst;

                try {
                        headline[0]="\t\t0";
                        headline[1]="\t\t-";
                        headline[2]="\t\t0";
                        headline[3]="\t\t-";
                        // 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
                                } // 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);

                        // n1 and n2 are known, initialise matrices accordingly. 
                        // nbhood, move, rank, entropy, freq, AUC etc. (evtl.+ degree(?)) 
                        rank = new int[(n1+1)][(n2+1)];
                        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];                    

                        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"; 
                                        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+")"; 
                                                        } // 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;
                                                        } // end if sideline                                            
                                                } // end if 1st/2nd shell
                                        } // end while through the entire nbhood 
                                        System.out.print("("+nbs+")\t");
                                        getEntropy( nbs, restype);
                                        rank[i][j] = lastRank; 
                                        nbstring[i][j] = nbs;
                                        moveset[i][j] = mymove;
                                        entropy[i][j] = lastEntropy; 
                                        freq[i][j] = lastFreq;
                                        AUC[i][j]  = lastAUC;
                                        total[i][j]= lastTotal; 

                                        if (lastRank > 0) { 
                                                sumdeltarank += (lastRank-(rank[0][0]));
                                        } else {
                                                sumdeltarank += (maxRank-(rank[0][0]));
                                        } // 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]" );
                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]);
                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] );
                                System.out.print("\t"); 
                        } // next i 
                        System.out.println(""); 
                } // next j     
        } // end of report 
        
        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:	213
Committed:	Thu Jun 28 09:38:49 2007 UTC (17 years, 3 months ago) by lappe
Original Path:	*trunk/iterEvalNbhood.java*
File size:	17922 byte(s)
Log Message:	Buggy version : 2nd to n2th row have same values as the first row - ? temp_nbhood stays the same?
Line	User	Rev	File contents
1	lappe	213	import tools.MySQLConnection;
2
3			import java.sql.SQLException;
4			import java.sql.Statement;
5			import java.sql.ResultSet;
6
7			public class iterEvalNbhood {
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			static int maxRank = 31; // value to replace for non-existence of central redue in the resultvector (rank=0)
16			// 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			static String sideline[], headline[]={"\t\t0","\t\t-","\t\t0","\t\t-"};
25			static String restype="?", ressec="?", newnbhood="";
26
27			static int sumdelta[][], rank[][], total[][];
28			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			printdeltaRank=8;
39
40			public static void main(String[] args) {
41
42			if (args.length<2){
43			System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 9 28");
44			System.exit(1);
45			}
46			graphid = Integer.parseInt( args[0]);
47			resnr = Integer.parseInt( args[1]);
48			int j_num=0, oj_num=0, oj_shell, oj_cnsize, i, j, x, oi, oj, o1, o2, score=0;
49			String sql, oj_res, oj_sec;
50			Statement mstmt, mjst, nstmt;
51			ResultSet mrsst, nrsst;
52
53			try {
54			conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2"); // the UPPERCASE DB!
55			System.out.println("Iterating and Evaluating neighborhood v.0.2. ");
56
57			sql = "select num, res, sstype from single_model_node where graph_id="+graphid+" and num="+resnr+";";
58			mstmt = conn.createStatement();
59			mrsst = mstmt.executeQuery(sql);
60			if (mrsst.next()) {
61			// this is the central node -> get type and secondary structure
62			restype = mrsst.getString( 2).toUpperCase();
63			ressec = mrsst.getString( 3).toUpperCase();
64			} // end if central residue
65			mrsst.close();
66			mstmt.close();
67			System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec);
68
69			// retrieve the original nbhood into orig_shell
70			System.out.println("retrieving original first shell ... ");
71			mstmt = conn.createStatement();
72			mstmt.executeUpdate("drop table if exists orig_shell;");
73			mstmt.close();
74
75			mstmt = conn.createStatement();
76			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+";");
77			mstmt.close();
78
79			System.out.println("adding the original 2nd shell ...");
80			sql = "select j_num from orig_shell where shell=1;";
81			mstmt = conn.createStatement();
82			mrsst = mstmt.executeQuery(sql);
83			i=0;
84			while (mrsst.next()) {
85			i++;
86			oj_num = mrsst.getInt(1);
87			System.out.println(i+":"+oj_num);
88			mjst = conn.createStatement();
89			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+";";
90			// System.out.println(">"+sql);
91			mjst.executeUpdate( sql);
92			mjst.close();
93			} // end while
94			mrsst.close();
95			mstmt.close();
96
97			System.out.println("gathering the original 1st and 2nd shell nbs.");
98			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;";
99			mstmt = conn.createStatement();
100			mrsst = mstmt.executeQuery(sql);
101			o1=0;
102			o2=0;
103			while (mrsst.next()) {
104			if ( mrsst.getInt( 4)==1) { // count 1st shell entry
105			o1++;
106			System.out.print("1#"+o1);
107			rheadline[0]+="\t"+o1;
108			rheadline[1]+="\t"+mrsst.getString(2); // res
109			rheadline[2]+="\t"+mrsst.getInt(1); // resnum
110			rheadline[3]+="\t"+mrsst.getString(3); // SStype
111			} // end if 2st shell
112			if ( mrsst.getInt( 4)==2) { // count 2nd shell entry
113			o2++;
114			System.out.print("2#"+o2);
115			} // end if 2nd shell
116			System.out.println(" :\t"+mrsst.getInt( 1)+"\t"+mrsst.getString( 2)+"\t"+mrsst.getString( 3)+"\t"+mrsst.getInt( 4)+"\t"+mrsst.getInt( 5));
117			} // end while
118			System.out.println("Orig.SIZE 1st shell "+o1);
119			System.out.println("Orig.SIZE 2nd shell "+o2);
120			rsideline = new String[o2+1];
121			rsideline[0]="+0\tRnum:S(cn)";
122			sumdelta = new int[(o1+1)][(o2+1)];
123			newnbs = new String[(o1+1)][(o2+1)];
124			// creating the perturbed version of shell 1 into temp_shell
125			for (j=0; j<=o2; j++) { // <=o2 outer loop through all originally indirect contacts
126
127			for (i=0; i<=o1; i++) { // inner loop through all originally direct contacts
128			System.out.println("---------------------------------------------");
129			System.out.println("Creating perturbed nbhood ("+i+","+j+")\t");
130			// clear first
131			nstmt = conn.createStatement();
132			nstmt.executeUpdate("drop table if exists temp_shell;");
133			nstmt.close();
134			nstmt = conn.createStatement();
135			nstmt.executeUpdate("create table temp_shell select * from orig_shell limit 0;");
136			nstmt.close();
137			oi = 0;
138			oj = 0;
139			mrsst.beforeFirst();
140			newnbhood="";
141			while (mrsst.next()) {
142			oj_num = mrsst.getInt( 1);
143			oj_res = mrsst.getString(2);
144			oj_sec = mrsst.getString(3);
145			oj_shell = mrsst.getInt( 4);
146			oj_cnsize = mrsst.getInt( 5);
147
148			if (oj_shell==1) { // a direct 1st shell neighbour
149			oi++;
150			if (oi!=i) {// if this is NOT the one direct nb 2B dropped
151			// include as 1st shell nbor into temp_shell
152			nstmt = conn.createStatement();
153			sql = "insert into temp_shell values("+resnr+",\'"+restype+"\',"+oj_num+",\'"+oj_res+"\',\'"+oj_sec+"\', 1);";
154			// System.out.println("oi>"+ sql);
155			nstmt.executeUpdate(sql);
156			nstmt.close();
157			newnbhood+=oj_res;
158			} // end if ni!=i
159			} else { // 2nd shell neighbour
160			oj++;
161			if (oj==j) { // this is the 2nd shell nb 2B included
162			// put as new 1st shell nbor
163			nstmt = conn.createStatement();
164			// sql = "insert into temp_shell values("+resnr+",\'"+restype+"\',"+oj_num+",\'"+oj_res+"\',\'"+oj_sec+"\', 1);";
165			// System.out.println("oj>"+ sql);
166			nstmt.executeUpdate(sql);
167			nstmt.close();
168			newnbhood+=oj_res;
169			} // end if
170			if (j==0) { // creating the sideline ruler array for the output
171			rsideline[oj] = "+"+oj+"\t"+oj_res+""+oj_num+":"+oj_sec+"("+oj_cnsize+")";
172			} // end if j==0
173			} // end if 1st/2nd shell
174
175			} // end while through the entire nbhood
176			System.out.println("new direct nbhood "+newnbhood);
177			// Now the "updated" / perturbed version of shell 1 is in temp_shell
178			// we can build 2nd shell accordingly.
179			// System.out.println("building the 2nd shell");
180			sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;";
181			nstmt = conn.createStatement();
182			nrsst = nstmt.executeQuery(sql);
183			x = 0;
184			while (nrsst.next()) {
185			x++;
186			j_num = nrsst.getInt( 1);
187			// System.out.println(x+":"+nrsst.getString( 2)+" "+j_num+" "+nrsst.getString( 3));
188			mjst = conn.createStatement();
189			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+";";
190			// System.out.println(">"+sql);
191			mjst.executeUpdate( sql);
192			mjst.close();
193			} // end while
194			nrsst.close();
195			nstmt.close();
196			// and score this move
197			newnbs[i][j]= newnbhood;
198			System.out.println("Scoring ["+i+"]["+j+"] "+newnbs[i][j]);
199			score = scoreCurrentNbhood();
200			sumdelta[i][j] = score;
201			reportMatrix( printRank );
202			reportMatrix( printdeltaRank );
203			System.out.println("SumDeltaRank Score = \t"+score);
204			// reportMatrix( printNbstring );
205			} // next i
206			System.out.println("\t");
207			} // next j
208			// report total matrix sumdelta
209			reportResults( o1, o2, printRank);
210			reportResults( o1, o2, printNbstring);
211			// Cleanup ...
212			mrsst.close();
213			mstmt.close();
214
215			} catch (SQLException e) {
216			e.printStackTrace();
217			System.err.println("SQLException: " + e.getMessage());
218			System.err.println("SQLState: " + e.getSQLState());
219			} // end try/catch
220			System.out.println("fin.");
221			} // end main
222
223
224
225			public static void reportResults( int o1, int o2, int what2print) {
226			System.out.println("Printing "+what2print);
227			if (what2print==printRank) System.out.println("Overall resulting SumDeltaRank Matrix" );
228			if (what2print==printNbstring) System.out.println("Overall tested new nbhoodStrings" );
229			/*if (what2print==printTotal) System.out.print("total[i][j]" );
230			if (what2print==printEntropy) System.out.print("entropy[i][j]" );
231			if (what2print==printFreq ) System.out.print("freq[i][j]" );
232			if (what2print==printAUC) System.out.print("AUC[i][j]" );
233
234			if (what2print==printMoveset) System.out.print("moveset[i][j]" );
235			if (what2print==printdeltaRank) System.out.print("rank[i][j]-rank[0][0]" );) */
236
237			// print headerline(s)
238			System.out.println(rheadline[0]);
239			System.out.println(rheadline[1]);
240			System.out.println(rheadline[2]);
241			System.out.println(rheadline[3]);
242			for (int j=0; j<=o2; j++) {
243			// print rsideline
244			System.out.print( rsideline[j]+"\t");
245			for ( int i=0; i<=o1; i++) {
246			if (what2print==printRank) System.out.print( sumdelta[i][j] );
247			if (what2print==printNbstring) System.out.print( newnbs[i][j] );
248			System.out.print("\t");
249			} // next i
250			System.out.println("");
251			} // next j
252			} // end of reportResults
253
254
255
256			public static int scoreCurrentNbhood() {
257			int n1=0, n2=0, ni, nj, i, j, j_num, j_shell, j_cnsize, sumdeltarank=0;
258			String sql, j_res, j_sec, nbs, mymove;
259			boolean overx = false;
260			Statement stmt;
261			ResultSet rsst;
262
263			try {
264			headline[0]="\t\t0";
265			headline[1]="\t\t-";
266			headline[2]="\t\t0";
267			headline[3]="\t\t-";
268			// System.out.println("retrieving the entire nbhood (1st and 2nd shell)");
269			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;";
270			stmt = conn.createStatement();
271			rsst = stmt.executeQuery(sql);
272			// counting shell2
273			n2=0;
274			while (rsst.next()) {
275			if ( rsst.getInt( 4)==1) { // count 1st shell entry
276			n1++;
277			System.out.print("1#"+n1);
278			headline[0]+="\t"+n1;
279			headline[1]+="\t"+rsst.getString(2); // res
280			headline[2]+="\t"+rsst.getInt(1); // resnum
281			headline[3]+="\t"+rsst.getString(3); // SStype
282			} // end if 2st shell
283			if ( rsst.getInt( 4)==2) { // count 2nd shell entry
284			n2++;
285			System.out.print("2#"+n2);
286			} // end if 2nd shell
287			System.out.println(" :\t"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5));
288			} // end while
289			size1 = n1;
290			size2 = n2;
291			System.out.println("SIZE 1st shell "+size1);
292			System.out.println("SIZE 2nd shell "+size2);
293
294			// n1 and n2 are known, initialise matrices accordingly.
295			// nbhood, move, rank, entropy, freq, AUC etc. (evtl.+ degree(?))
296			rank = new int[(n1+1)][(n2+1)];
297			total = new int[(n1+1)][(n2+1)];
298			entropy = new double[(n1+1)][(n2+1)];
299			freq = new double[(n1+1)][(n2+1)];
300			AUC = new double[(n1+1)][(n2+1)];
301			nbstring = new String[(n1+1)][(n2+1)];
302			moveset = new String[(n1+1)][(n2+1)];
303			sideline = new String[n2+1];
304
305			for (j=0; j<=n2; j++) { // outer loop through all indirect contacts
306			for (i=0; i<=n1; i++) { // inner loop through all direct contacts
307			mymove = "";
308			overx = false;
309			System.out.print("("+i+","+j+")\t");
310			ni = 0;
311			nj = 0;
312			sideline[0]="+0\tRnum:S";
313			nbs="%";
314			rsst.beforeFirst();
315			while (rsst.next()) {
316			j_num = rsst.getInt(1);
317			j_res = rsst.getString(2);
318			j_sec = rsst.getString(3);
319			j_shell = rsst.getInt(4);
320			j_cnsize = rsst.getInt(5);
321			if (j_num>resnr) { // we are over x
322			if (!overx) {
323			nbs+="x%";
324			overx=true;
325			} // end if over x
326			} // END IF J > X
327			if (j_shell==1) { // a direct 1st shell neighbour
328			ni++;
329			if (ni!=i) {// if this is NOT the one direct nb 2B dropped
330			nbs+=j_res.toUpperCase()+"%"; // it is included
331			} else { // this one IS dropped
332			mymove += "(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")";
333			} // end if ni!=i
334			} else { // 2nd shell neighbour
335			nj++;
336			if (nj==j) { // this is the 2nd shell nb 2B included
337			nbs+=j_res.toUpperCase()+"%";
338			mymove += "(+"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")";
339			} // end if
340			// // only once for building the sidelines
341			if (j==0) {
342			sideline[nj] = "+"+nj+"\t"+j_res+""+j_num+":"+j_sec;
343			} // end if sideline
344			} // end if 1st/2nd shell
345			} // end while through the entire nbhood
346			System.out.print("("+nbs+")\t");
347			getEntropy( nbs, restype);
348			rank[i][j] = lastRank;
349			nbstring[i][j] = nbs;
350			moveset[i][j] = mymove;
351			entropy[i][j] = lastEntropy;
352			freq[i][j] = lastFreq;
353			AUC[i][j] = lastAUC;
354			total[i][j]= lastTotal;
355
356			if (lastRank > 0) {
357			sumdeltarank += (lastRank-(rank[0][0]));
358			} else {
359			sumdeltarank += (maxRank-(rank[0][0]));
360			} // end if lastRank was defined
361			} // close inner loop (i)
362			System.out.println(".");
363			} // next outerloop (j)
364			rsst.close();
365			stmt.close();
366
367			} catch (SQLException e) {
368			e.printStackTrace();
369			System.err.println("SQLException: " + e.getMessage());
370			System.err.println("SQLState: " + e.getSQLState());
371			} // end try/catch
372			// System.out.println("fin.");
373			return sumdeltarank;
374			} // end scoreCurrentNbhood
375
376
377			public static void reportMatrix( int what2print) {
378			System.out.println("Printing "+what2print);
379			if (what2print==printRank) System.out.print("rank[i][j]" );
380			if (what2print==printTotal) System.out.print("total[i][j]" );
381			if (what2print==printEntropy) System.out.print("entropy[i][j]" );
382			if (what2print==printFreq ) System.out.print("freq[i][j]" );
383			if (what2print==printAUC) System.out.print("AUC[i][j]" );
384			if (what2print==printNbstring) System.out.print("nbstring[i][j]" );
385			if (what2print==printMoveset) System.out.print("moveset[i][j]" );
386			if (what2print==printdeltaRank) System.out.print("rank[i][j]-rank[0][0]" );
387			System.out.println("...");
388			// print headerline(s)
389			System.out.println(headline[0]);
390			System.out.println(headline[1]);
391			System.out.println(headline[2]);
392			System.out.println(headline[3]);
393			for (int j=0; j<=size2; j++) {
394			// print sideline
395			System.out.print( sideline[j]+"\t");
396			for ( int i=0; i<=size1; i++) {
397			if (what2print==printRank) System.out.print( rank[i][j] );
398			if (what2print==printTotal) System.out.print( total[i][j] );
399			if (what2print==printEntropy) System.out.print( entropy[i][j] );
400			if (what2print==printFreq ) System.out.print( freq[i][j] );
401			if (what2print==printAUC) System.out.print( AUC[i][j] );
402			if (what2print==printNbstring) System.out.print( nbstring[i][j] );
403			if (what2print==printMoveset) System.out.print( moveset[i][j] );
404			if (what2print==printdeltaRank) System.out.print( rank[i][j]-rank[0][0] );
405			System.out.print("\t");
406			} // next i
407			System.out.println("");
408			} // next j
409			} // end of report
410
411			public static void getEntropy( String nbs, String centRes) {
412			String sql, res;
413			Statement stmt;
414			ResultSet rsst;
415			double p, psum=0.0, logp, plogp, plogpsum=0.0;
416			try {
417			sql = "select count(*) from single_model_node where n like '"+nbs+"';";
418			// System.out.println( sql);
419			stmt = conn.createStatement();
420			rsst = stmt.executeQuery(sql);
421			if (rsst.next()) lastTotal = rsst.getInt( 1);
422			rsst.close();
423			stmt.close();
424
425			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;";
426			stmt = conn.createStatement();
427			rsst = stmt.executeQuery(sql);
428			// System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)");
429			int rank = 0;
430			boolean seenCentRes = false;
431			lastAUC = 0.0;
432			lastRank = 0;
433			lastFreq = 0.0;
434			lastavgk = 0.0;
435			lastdevk = 0.0;
436			while (rsst.next()) {
437			rank ++;
438			res = rsst.getString(1); // 1st column -- res
439			p = rsst.getDouble(3); // 3rd: fraction p
440			// System.out.print(rank+ " : " + res+" : "+num+ " : " + p);
441			logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits
442			// System.out.print(" : " + logp);
443			plogp = -1.0 * p * logp;
444			// System.out.print(" : " + plogp);
445			plogpsum += plogp;
446			psum += p;
447
448			if (res.equals(centRes)) {
449			// System.out.print(" <==" + centRes);
450			seenCentRes = true;
451			lastFreq = p;
452			lastRank = rank;
453			lastavgk = rsst.getDouble(4);
454			lastdevk = rsst.getDouble(5);
455			}
456			if (seenCentRes) lastAUC += p;
457			// System.out.println("");
458			}
459			// System.out.println("Sum :"+lastTotal+" : "+psum+" : "+plogpsum);
460			rsst.close();
461			stmt.close();
462			lastEntropy = plogpsum;
463			if (lastRank==0) lastRank = maxRank;
464			} catch (SQLException e) {
465			e.printStackTrace();
466			System.err.println("SQLException: " + e.getMessage());
467			System.err.println("SQLState: " + e.getSQLState());
468			}
469
470			} // end of getEntropy
471
472			} // end class