branches/aglappe-jung/iterateUpperNbs.java

import tools.MySQLConnection;

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

public class iterateUpperNbs {

        /**
         *  
         * exchange of one neighbor at a time by a common neighbor 
         * @author lappe
         */
        static int maxRank = 31; // value to replace for non-existence of central redue in the resultvector (rank=0) 
        // higher values should penalize non-existence more
        static String user = "lappe"    ; // change user name!!
        static MySQLConnection conn;
        static double lastEntropy=0.0, lastFreq, lastAUC, lastavgk, lastdevk; 
        static double  orgEntropy=0.0, orgFreq, orgAUC, orgavgk, orgdevk; 
        static int lastRank, lastTotal;  
        static int orgRank, orgTotal;
        
        public static void main(String[] args) throws SQLException {
                
            if (args.length<2){
                        System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 9 28");
                        System.exit(1);
                }               
                int graphid = Integer.parseInt( args[0]);
                int resnr = Integer.parseInt( args[1]); 
                int n1=0, n2=0, ni=0, nj=0, j_num=0, j_shell, j_cnsize, i, j, sumdelta, j_num12=0, j_num21=0; 
                conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2"); // the UPPERCASE DB!  
                String sql, j_res, j_sec, restype="?", ressec="?", nbs, mymove; 
                Statement stmt, jst;  
                ResultSet rsst;
                
                try {
                        System.out.println("getting direct neighborhood ... "); 
                        stmt = conn.createStatement();
                        stmt.executeUpdate("drop table if exists temp_shell;"); 
                        stmt.close(); 
        
                        stmt = conn.createStatement();
                        stmt.executeUpdate("create table temp_shell as select i_num, i_res, j_num, j_res, j_sstype, 1 as shell from single_model_edge where graph_id="+graphid+" and i_num="+resnr+";");
                        stmt.close(); 
        
                        System.out.println("building the 2nd shell");  
                        sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        while (rsst.next()) {
                                n1++; 
                                j_num = rsst.getInt(1);
                                System.out.println(n1+":"+j_num); 
                                jst = conn.createStatement();
                                sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell from single_model_edge where graph_id="+graphid+" and i_num="+j_num+";";
                                // System.out.println(">"+sql); 
                                jst.executeUpdate( sql); 
                                jst.close(); 
                        } // end while 
                        rsst.close(); 
                        stmt.close(); 
                        
                        // remove from here for unperturbed version 
                        System.out.println("retrieving the entire 1st and 2nd shell");  
                        sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell group by j_num;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        // counting shell2
                        n2=0; 
                        while (rsst.next()) {
                                if ( rsst.getInt( 4)==2) { // count 2nd shell entry 
                                        n2++;
                                        if ( rsst.getInt( 1)==resnr) { // this is the central node -> get type and secondary structure 
                                                restype =  rsst.getString( 2).toUpperCase(); 
                                                ressec  =  rsst.getString( 3).toUpperCase();
                                        } // end if central residue 
                                } // end if 2nds shell 
                                System.out.println(n2+":"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)); 
                        } // end while 
                        System.out.println("SIZE 1st shell "+n1); 
                        System.out.println("SIZE 2nd shell "+n2);
                        System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec); 
                        rsst.close(); 
                        stmt.close(); 
                        
                        // create matrices accordingly 
                        
                        // percolate the environment  
                        System.out.println("removing a contact from shell1 -> shell2");  
                        sql = "select j_num, j_res, j_sstype, shell from temp_shell where i_num="+resnr+" and shell = 1 order by rand() limit 1;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        if (rsst.next()) {
                                j_num12 = rsst.getInt( 1); 
                                System.out.println(rsst.getInt( 4)+" -> 2 : ("+rsst.getString( 2)+":"+j_num12+":"+rsst.getString( 3)+")");
                        }
                        rsst.close();
                        stmt.close(); 
                        stmt = conn.createStatement();
                        stmt.executeUpdate("delete from temp_shell where j_num="+j_num12+";"); 
                        stmt.close(); 
                        
                        
                // and move an indirect nbor from shell2 -> shell 1; 
                        System.out.println("adding a contact from shell2 -> shell1");  
                        sql = "select j_num, j_res, j_sstype, shell from temp_shell where i_num!="+resnr+" and j_num!="+resnr+" and i_num!="+j_num12+" and j_num!="+j_num12+" and shell = 2 order by rand() limit 1;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        if (rsst.next()) {
                                j_num21 = rsst.getInt( 1); 
                                System.out.println(rsst.getInt( 4)+" -> 1 : ("+rsst.getString( 2)+":"+j_num21+":"+rsst.getString( 3)+")");
                        }
                        rsst.close();
                        stmt.close(); 
                        stmt = conn.createStatement();
                        stmt.executeUpdate("update temp_shell set i_num="+resnr+", i_res='"+restype+"', j_sstype='"+ressec+"', shell=1 where j_num="+j_num21+";");
                        stmt.close(); 
                        stmt = conn.createStatement();
                        stmt.executeUpdate("delete from temp_shell where shell>1;");
                        stmt.close(); 
                        n1 = 0; 
                        System.out.println("re-building the 2nd shell");  
                        sql = "select distinct j_num from temp_shell where shell=1 order by j_num;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        while (rsst.next()) {
                                n1++; 
                                j_num = rsst.getInt(1);
                                System.out.println(n1+":"+j_num); 
                                jst = conn.createStatement();
                                sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell from single_model_edge where graph_id="+graphid+" and i_num="+j_num+";";
                                // System.out.println(">"+sql); 
                                jst.executeUpdate( sql); 
                                jst.close(); 
                        } // end while 
                        rsst.close(); 
                        stmt.close(); 
                        // end of remove for unperturbed version 
                        
                        System.out.println("retrieving the entire 1st and 2nd shell");  
                        sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell group by j_num order by j_num;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        // counting shell2
                        n2=0; 
                        while (rsst.next()) {
                                if ( rsst.getInt( 4)==2) { // count 2nd shell entry 
                                        n2++;
                                        if ( rsst.getInt( 1)==resnr) { // this is the central node -> get type and secondary structure 
                                                restype =  rsst.getString( 2).toUpperCase(); 
                                                ressec  =  rsst.getString( 3).toUpperCase();
                                        } // end if central residue 
                                } // end if 2nds shell 
                                System.out.println(n2+":"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)); 
                        } // end while 
                        System.out.println("SIZE 1st shell "+n1); 
                        System.out.println("SIZE 2nd shell "+n2);
                        System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec); 
                         
                        
                        for (j=0; j<=n2; j++) { // outer loop through all indirect contacts
                                // System.out.print(i+" - "); 
                                sumdelta=0; 
                                for (i=0; i<=n1; i++) { // inner loop through all direct contacts
                                        mymove = "("+i+","+j+")";
                                        ni = 0; 
                                        nj = 0; 
                                        nbs="%";
                                        rsst.beforeFirst();
                                        while (rsst.next()) {
                                                j_num = rsst.getInt( 1); 
                                                j_res = rsst.getString(2);
                                                j_sec = rsst.getString(3);
                                                j_shell = rsst.getInt( 4);
                                                j_cnsize = rsst.getInt( 5);
                                          
                                                if (j_shell==1) { // a direct 1st shell neighbour 
                                                        ni++;
                                                        if (ni!=i) {// if this is NOT the one direct nb 2B dropped 
                                                                nbs+=j_res.toUpperCase()+"%";                                                           
                                                        } else { // this one IS dropped 
                                                                mymove += "(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")"; 
                                                        } // end if ni!=i 
                                                } else { // 2nd shell neighbour 
                                                        nj++; 
                                                        if (j_num==resnr) { // the central residue is part if the 2nd shell
                                                                if (nj!=j) { // drop x if marked for inclusion 
                                                                        nbs+="x%"; 
                                                                } else {
                                                                        mymove += " no x ..."; 
                                                                }
                                                        } else { // this is not x 
                                                                if (nj==j) { // this is the 2nd shell nb 2B included
                                                                        nbs+=j_res.toUpperCase()+"%";
                                                                        mymove += "(+"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")"; 
                                                                } // end if 
                                                        } // end if this is central residue x 
                                                } // end if 1st/2nd shell
                                        } // end while through the entire nbhood 
                                        
                                        getEntropy( nbs, restype); 
                                        if (i==0 && j==0) { // original nbhoodstring without any insertions/deletions 
                                                orgEntropy = lastEntropy;
                                                orgFreq = lastFreq;
                                                orgAUC  = lastAUC;
                                                orgavgk = lastavgk;
                                                orgdevk = lastdevk; 
                                                orgRank = lastRank;
                                                orgTotal= lastTotal; 
                                        } // end if 0/0 for defining org*
                                        if (lastRank > 0) { 
                                                sumdelta += (lastRank-orgRank);
                                        } else {
                                                sumdelta += (maxRank-orgRank);
                                        }
                                        
                                        // System.out.println(" t="+orgTotal+" \tentropy = "+String.format("%.5f", orgEntropy)+" \trank#"+String.format("%2d",orgRank)+" \tp("+restype+") = "+String.format("%.5f",orgFreq)+" \t\tAUC = "+String.format("%.5f",orgAUC)+" \t\tavg(k)="+String.format("%.2f",orgavgk)+"\tstddev="+String.format("%.2f",orgdevk));
                                        //if ((lastRank>0 && lastRank<orgRank) || (i==0 && j==0)) {
                                                System.out.print(mymove+"\t"+nbs);
                                                printValues();  
                                        //}
                                                                
                                        
                                        // System.out.println(".");
                                } // close inner loop (i)
                                System.out.println( "Summ "+j+":"+sumdelta);
                        } // next outerloop (j)
                        rsst.close(); 
                        stmt.close(); 
                        
                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                } // end try/catch 
                System.out.println("fin."); 
        }       // end main 
        
        public static void printValues() {
                System.out.print( "\t"+lastTotal+"("+(lastTotal-orgTotal)+")"); 
                System.out.print( "\t"+String.format("%.5f", lastEntropy) +" ("+String.format("%.5f", lastEntropy-orgEntropy)+")");
                System.out.print( "\t#"+String.format("%2d",lastRank) +" ("+String.format("%2d",(lastRank-orgRank))+")");
                System.out.print( "\t"+String.format("%.5f", lastFreq) +" ("+String.format("%.5f", (lastFreq-orgFreq))+")");
                System.out.print( "\t"+String.format("%.5f", lastAUC) +" ("+String.format("%.5f", (lastAUC-orgAUC))+")");
                System.out.print( "\t"+String.format("%.2f", lastavgk) +" ("+String.format("%.2f", (lastavgk-orgavgk))+")");
                System.out.print( "\t"+String.format("%.2f", lastdevk) +" ("+String.format("%.2f", (lastdevk-orgdevk))+")");
                System.out.println("");
        }
        
        public static void getEntropy( String nbs, String centRes) {
                String sql, res; 
                Statement stmt;  
                ResultSet rsst;
                double p, psum=0.0, logp, plogp, plogpsum=0.0; 
                try {
                        sql = "select count(*) from single_model_node where n like '"+nbs+"';";
                        // System.out.println( sql); 
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        if (rsst.next()) lastTotal = rsst.getInt( 1); 
                        rsst.close(); 
                        stmt.close(); 
                        
                        sql = "select res, count(*) as t, count(*)/"+lastTotal+" as p, avg( k), stddev( k) from single_model_node where n like '"+nbs+"' group by res order by p DESC;";
                        stmt = conn.createStatement();
                        rsst = stmt.executeQuery(sql);
                        // System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)");
                        int rank = 0; 
                        boolean seenCentRes = false;  
                        lastAUC = 0.0; 
                        lastRank = 0; 
                        lastFreq = 0.0;
                        lastavgk = 0.0;
                        lastdevk = 0.0;
                        while (rsst.next()) {   
                                rank ++;
                                res = rsst.getString(1); // 1st column -- res
                                p = rsst.getDouble(3); // 3rd: fraction p 
                                // System.out.print(rank+ " : " + res+"   : "+num+ " : " + p);
                                logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits 
                                // System.out.print(" : " + logp); 
                                plogp = -1.0 * p * logp;  
                                // System.out.print(" : " + plogp);
                                plogpsum += plogp;  
                                psum += p; 
                                
                                if (res.equals(centRes)) { 
                                        // System.out.print(" <==" + centRes);
                                        seenCentRes = true;
                                        lastFreq = p;
                                        lastRank = rank; 
                                        lastavgk = rsst.getDouble(4);
                                        lastdevk = rsst.getDouble(5);
                                }
                                if (seenCentRes) lastAUC += p; 
                                // System.out.println("");
                        }
                        // System.out.println("Sum :"+lastTotal+"       : "+psum+"       : "+plogpsum);
                        rsst.close(); 
                        stmt.close(); 
                        lastEntropy = plogpsum; 
                        if (lastRank==0) lastRank = maxRank;  
                } catch (SQLException e) {
                        e.printStackTrace();
                        System.err.println("SQLException: " + e.getMessage());
                        System.err.println("SQLState:     " + e.getSQLState());
                }
                
        } // end of getEntropy 

} // end class 
Revision:	419
Committed:	Thu Nov 22 14:09:18 2007 UTC (16 years, 10 months ago) by duarte
File size:	12342 byte(s)
Log Message:	Re-branching for JUNG2 development
Line	File contents
1	import tools.MySQLConnection;
2
3	import java.sql.SQLException;
4	import java.sql.Statement;
5	import java.sql.ResultSet;
6
7	public class iterateUpperNbs {
8
9	/**
10	*
11	* exchange of one neighbor at a time by a common neighbor
12	* @author lappe
13	*/
14	static int maxRank = 31; // value to replace for non-existence of central redue in the resultvector (rank=0)
15	// higher values should penalize non-existence more
16	static String user = "lappe" ; // change user name!!
17	static MySQLConnection conn;
18	static double lastEntropy=0.0, lastFreq, lastAUC, lastavgk, lastdevk;
19	static double orgEntropy=0.0, orgFreq, orgAUC, orgavgk, orgdevk;
20	static int lastRank, lastTotal;
21	static int orgRank, orgTotal;
22
23	public static void main(String[] args) throws SQLException {
24
25	if (args.length<2){
26	System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 9 28");
27	System.exit(1);
28	}
29	int graphid = Integer.parseInt( args[0]);
30	int resnr = Integer.parseInt( args[1]);
31	int n1=0, n2=0, ni=0, nj=0, j_num=0, j_shell, j_cnsize, i, j, sumdelta, j_num12=0, j_num21=0;
32	conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2"); // the UPPERCASE DB!
33	String sql, j_res, j_sec, restype="?", ressec="?", nbs, mymove;
34	Statement stmt, jst;
35	ResultSet rsst;
36
37	try {
38	System.out.println("getting direct neighborhood ... ");
39	stmt = conn.createStatement();
40	stmt.executeUpdate("drop table if exists temp_shell;");
41	stmt.close();
42
43	stmt = conn.createStatement();
44	stmt.executeUpdate("create table temp_shell as select i_num, i_res, j_num, j_res, j_sstype, 1 as shell from single_model_edge where graph_id="+graphid+" and i_num="+resnr+";");
45	stmt.close();
46
47	System.out.println("building the 2nd shell");
48	sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;";
49	stmt = conn.createStatement();
50	rsst = stmt.executeQuery(sql);
51	while (rsst.next()) {
52	n1++;
53	j_num = rsst.getInt(1);
54	System.out.println(n1+":"+j_num);
55	jst = conn.createStatement();
56	sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell from single_model_edge where graph_id="+graphid+" and i_num="+j_num+";";
57	// System.out.println(">"+sql);
58	jst.executeUpdate( sql);
59	jst.close();
60	} // end while
61	rsst.close();
62	stmt.close();
63
64	// remove from here for unperturbed version
65	System.out.println("retrieving the entire 1st and 2nd shell");
66	sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell group by j_num;";
67	stmt = conn.createStatement();
68	rsst = stmt.executeQuery(sql);
69	// counting shell2
70	n2=0;
71	while (rsst.next()) {
72	if ( rsst.getInt( 4)==2) { // count 2nd shell entry
73	n2++;
74	if ( rsst.getInt( 1)==resnr) { // this is the central node -> get type and secondary structure
75	restype = rsst.getString( 2).toUpperCase();
76	ressec = rsst.getString( 3).toUpperCase();
77	} // end if central residue
78	} // end if 2nds shell
79	System.out.println(n2+":"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5));
80	} // end while
81	System.out.println("SIZE 1st shell "+n1);
82	System.out.println("SIZE 2nd shell "+n2);
83	System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec);
84	rsst.close();
85	stmt.close();
86
87	// create matrices accordingly
88
89	// percolate the environment
90	System.out.println("removing a contact from shell1 -> shell2");
91	sql = "select j_num, j_res, j_sstype, shell from temp_shell where i_num="+resnr+" and shell = 1 order by rand() limit 1;";
92	stmt = conn.createStatement();
93	rsst = stmt.executeQuery(sql);
94	if (rsst.next()) {
95	j_num12 = rsst.getInt( 1);
96	System.out.println(rsst.getInt( 4)+" -> 2 : ("+rsst.getString( 2)+":"+j_num12+":"+rsst.getString( 3)+")");
97	}
98	rsst.close();
99	stmt.close();
100	stmt = conn.createStatement();
101	stmt.executeUpdate("delete from temp_shell where j_num="+j_num12+";");
102	stmt.close();
103
104
105	// and move an indirect nbor from shell2 -> shell 1;
106	System.out.println("adding a contact from shell2 -> shell1");
107	sql = "select j_num, j_res, j_sstype, shell from temp_shell where i_num!="+resnr+" and j_num!="+resnr+" and i_num!="+j_num12+" and j_num!="+j_num12+" and shell = 2 order by rand() limit 1;";
108	stmt = conn.createStatement();
109	rsst = stmt.executeQuery(sql);
110	if (rsst.next()) {
111	j_num21 = rsst.getInt( 1);
112	System.out.println(rsst.getInt( 4)+" -> 1 : ("+rsst.getString( 2)+":"+j_num21+":"+rsst.getString( 3)+")");
113	}
114	rsst.close();
115	stmt.close();
116	stmt = conn.createStatement();
117	stmt.executeUpdate("update temp_shell set i_num="+resnr+", i_res='"+restype+"', j_sstype='"+ressec+"', shell=1 where j_num="+j_num21+";");
118	stmt.close();
119	stmt = conn.createStatement();
120	stmt.executeUpdate("delete from temp_shell where shell>1;");
121	stmt.close();
122	n1 = 0;
123	System.out.println("re-building the 2nd shell");
124	sql = "select distinct j_num from temp_shell where shell=1 order by j_num;";
125	stmt = conn.createStatement();
126	rsst = stmt.executeQuery(sql);
127	while (rsst.next()) {
128	n1++;
129	j_num = rsst.getInt(1);
130	System.out.println(n1+":"+j_num);
131	jst = conn.createStatement();
132	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+";";
133	// System.out.println(">"+sql);
134	jst.executeUpdate( sql);
135	jst.close();
136	} // end while
137	rsst.close();
138	stmt.close();
139	// end of remove for unperturbed version
140
141	System.out.println("retrieving the entire 1st and 2nd shell");
142	sql = "select j_num, j_res, j_sstype, min(shell) as shell, count(*) as cn from temp_shell group by j_num order by j_num;";
143	stmt = conn.createStatement();
144	rsst = stmt.executeQuery(sql);
145	// counting shell2
146	n2=0;
147	while (rsst.next()) {
148	if ( rsst.getInt( 4)==2) { // count 2nd shell entry
149	n2++;
150	if ( rsst.getInt( 1)==resnr) { // this is the central node -> get type and secondary structure
151	restype = rsst.getString( 2).toUpperCase();
152	ressec = rsst.getString( 3).toUpperCase();
153	} // end if central residue
154	} // end if 2nds shell
155	System.out.println(n2+":"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5));
156	} // end while
157	System.out.println("SIZE 1st shell "+n1);
158	System.out.println("SIZE 2nd shell "+n2);
159	System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec);
160
161
162	for (j=0; j<=n2; j++) { // outer loop through all indirect contacts
163	// System.out.print(i+" - ");
164	sumdelta=0;
165	for (i=0; i<=n1; i++) { // inner loop through all direct contacts
166	mymove = "("+i+","+j+")";
167	ni = 0;
168	nj = 0;
169	nbs="%";
170	rsst.beforeFirst();
171	while (rsst.next()) {
172	j_num = rsst.getInt( 1);
173	j_res = rsst.getString(2);
174	j_sec = rsst.getString(3);
175	j_shell = rsst.getInt( 4);
176	j_cnsize = rsst.getInt( 5);
177
178	if (j_shell==1) { // a direct 1st shell neighbour
179	ni++;
180	if (ni!=i) {// if this is NOT the one direct nb 2B dropped
181	nbs+=j_res.toUpperCase()+"%";
182	} else { // this one IS dropped
183	mymove += "(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")";
184	} // end if ni!=i
185	} else { // 2nd shell neighbour
186	nj++;
187	if (j_num==resnr) { // the central residue is part if the 2nd shell
188	if (nj!=j) { // drop x if marked for inclusion
189	nbs+="x%";
190	} else {
191	mymove += " no x ...";
192	}
193	} else { // this is not x
194	if (nj==j) { // this is the 2nd shell nb 2B included
195	nbs+=j_res.toUpperCase()+"%";
196	mymove += "(+"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")";
197	} // end if
198	} // end if this is central residue x
199	} // end if 1st/2nd shell
200	} // end while through the entire nbhood
201
202	getEntropy( nbs, restype);
203	if (i==0 && j==0) { // original nbhoodstring without any insertions/deletions
204	orgEntropy = lastEntropy;
205	orgFreq = lastFreq;
206	orgAUC = lastAUC;
207	orgavgk = lastavgk;
208	orgdevk = lastdevk;
209	orgRank = lastRank;
210	orgTotal= lastTotal;
211	} // end if 0/0 for defining org*
212	if (lastRank > 0) {
213	sumdelta += (lastRank-orgRank);
214	} else {
215	sumdelta += (maxRank-orgRank);
216	}
217
218	// System.out.println(" t="+orgTotal+" \tentropy = "+String.format("%.5f", orgEntropy)+" \trank#"+String.format("%2d",orgRank)+" \tp("+restype+") = "+String.format("%.5f",orgFreq)+" \t\tAUC = "+String.format("%.5f",orgAUC)+" \t\tavg(k)="+String.format("%.2f",orgavgk)+"\tstddev="+String.format("%.2f",orgdevk));
219	//if ((lastRank>0 && lastRank<orgRank) \|\| (i==0 && j==0)) {
220	System.out.print(mymove+"\t"+nbs);
221	printValues();
222	//}
223
224
225	// System.out.println(".");
226	} // close inner loop (i)
227	System.out.println( "Summ "+j+":"+sumdelta);
228	} // next outerloop (j)
229	rsst.close();
230	stmt.close();
231
232	} catch (SQLException e) {
233	e.printStackTrace();
234	System.err.println("SQLException: " + e.getMessage());
235	System.err.println("SQLState: " + e.getSQLState());
236	} // end try/catch
237	System.out.println("fin.");
238	} // end main
239
240	public static void printValues() {
241	System.out.print( "\t"+lastTotal+"("+(lastTotal-orgTotal)+")");
242	System.out.print( "\t"+String.format("%.5f", lastEntropy) +" ("+String.format("%.5f", lastEntropy-orgEntropy)+")");
243	System.out.print( "\t#"+String.format("%2d",lastRank) +" ("+String.format("%2d",(lastRank-orgRank))+")");
244	System.out.print( "\t"+String.format("%.5f", lastFreq) +" ("+String.format("%.5f", (lastFreq-orgFreq))+")");
245	System.out.print( "\t"+String.format("%.5f", lastAUC) +" ("+String.format("%.5f", (lastAUC-orgAUC))+")");
246	System.out.print( "\t"+String.format("%.2f", lastavgk) +" ("+String.format("%.2f", (lastavgk-orgavgk))+")");
247	System.out.print( "\t"+String.format("%.2f", lastdevk) +" ("+String.format("%.2f", (lastdevk-orgdevk))+")");
248	System.out.println("");
249	}
250
251	public static void getEntropy( String nbs, String centRes) {
252	String sql, res;
253	Statement stmt;
254	ResultSet rsst;
255	double p, psum=0.0, logp, plogp, plogpsum=0.0;
256	try {
257	sql = "select count(*) from single_model_node where n like '"+nbs+"';";
258	// System.out.println( sql);
259	stmt = conn.createStatement();
260	rsst = stmt.executeQuery(sql);
261	if (rsst.next()) lastTotal = rsst.getInt( 1);
262	rsst.close();
263	stmt.close();
264
265	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;";
266	stmt = conn.createStatement();
267	rsst = stmt.executeQuery(sql);
268	// System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)");
269	int rank = 0;
270	boolean seenCentRes = false;
271	lastAUC = 0.0;
272	lastRank = 0;
273	lastFreq = 0.0;
274	lastavgk = 0.0;
275	lastdevk = 0.0;
276	while (rsst.next()) {
277	rank ++;
278	res = rsst.getString(1); // 1st column -- res
279	p = rsst.getDouble(3); // 3rd: fraction p
280	// System.out.print(rank+ " : " + res+" : "+num+ " : " + p);
281	logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits
282	// System.out.print(" : " + logp);
283	plogp = -1.0 * p * logp;
284	// System.out.print(" : " + plogp);
285	plogpsum += plogp;
286	psum += p;
287
288	if (res.equals(centRes)) {
289	// System.out.print(" <==" + centRes);
290	seenCentRes = true;
291	lastFreq = p;
292	lastRank = rank;
293	lastavgk = rsst.getDouble(4);
294	lastdevk = rsst.getDouble(5);
295	}
296	if (seenCentRes) lastAUC += p;
297	// System.out.println("");
298	}
299	// System.out.println("Sum :"+lastTotal+" : "+psum+" : "+plogpsum);
300	rsst.close();
301	stmt.close();
302	lastEntropy = plogpsum;
303	if (lastRank==0) lastRank = maxRank;
304	} catch (SQLException e) {
305	e.printStackTrace();
306	System.err.println("SQLException: " + e.getMessage());
307	System.err.println("SQLState: " + e.getSQLState());
308	}
309
310	} // end of getEntropy
311
312	} // end class