| 1 |
lappe |
221 |
import tools.MySQLConnection; |
| 2 |
|
|
|
| 3 |
|
|
import java.sql.SQLException; |
| 4 |
|
|
import java.sql.Statement; |
| 5 |
|
|
import java.sql.ResultSet; |
| 6 |
|
|
|
| 7 |
|
|
public class cnHashIterNbhood { |
| 8 |
|
|
|
| 9 |
|
|
/** |
| 10 |
|
|
* CN2 size x sumdelta |
| 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 = 21; // 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 |
lappe |
266 |
static String backgrndDB = "pdb_reps_graph_4_2"; |
| 20 |
lappe |
221 |
static double lastEntropy=0.0, lastFreq, lastAUC, lastavgk, lastdevk; |
| 21 |
|
|
static int lastRank, lastTotal, lastxcn=0; |
| 22 |
|
|
static int graphid=0, resnr=0; |
| 23 |
|
|
static int size1=0, size2=0; // the dimensions of the matrices = |shell1|x|shell2| = nr of direct(1) x indirect(2) nbs |
| 24 |
lappe |
225 |
static String rsideline[], rheadline[]={" -->\t(-)1st shell\t0"," |\t \t-"," |\t(+) \t0"," V\t2nd shell\t-", " \t \tX"}; |
| 25 |
lappe |
221 |
static String sideline[], headline[]={"\t\t0","\t\t-","\t\t0","\t\t-","\t\tX"}; |
| 26 |
|
|
static String restype="?", ressec="?", newnbhood=""; |
| 27 |
|
|
static int cn1[], cn2[]; |
| 28 |
|
|
static int sumdelta[][], rank[][], total[][], cnsize[][], cnall[][]; |
| 29 |
|
|
static double entropy[][], freq[][], AUC[][]; |
| 30 |
|
|
static String newnbs[][], nbstring[][], moveset[][]; |
| 31 |
|
|
|
| 32 |
|
|
static int printRank=1, |
| 33 |
|
|
printTotal = 2, |
| 34 |
|
|
printEntropy = 3, |
| 35 |
|
|
printFreq = 4, |
| 36 |
|
|
printAUC = 5, |
| 37 |
|
|
printNbstring= 6, |
| 38 |
|
|
printMoveset = 7, |
| 39 |
|
|
printdeltaRank=8, |
| 40 |
|
|
printCNSize =9, |
| 41 |
|
|
printCNSxdelta=10; |
| 42 |
|
|
|
| 43 |
|
|
public static void main(String[] args) { |
| 44 |
|
|
|
| 45 |
|
|
if (args.length<2){ |
| 46 |
|
|
System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 7 110"); |
| 47 |
|
|
System.exit(1); |
| 48 |
|
|
} |
| 49 |
|
|
graphid = Integer.parseInt( args[0]); |
| 50 |
|
|
resnr = Integer.parseInt( args[1]); |
| 51 |
|
|
int j_num=0, oj_num=0, oj_shell, oj_cnsize, i, j, x, oi, oj, o1, o2, ixnum, jxnum, score=0; |
| 52 |
|
|
boolean overx = false; |
| 53 |
|
|
String sql, oj_res, oj_sec; |
| 54 |
|
|
Statement mstmt, mjst, nstmt; |
| 55 |
|
|
ResultSet mrsst, nrsst; |
| 56 |
|
|
|
| 57 |
|
|
try { |
| 58 |
|
|
conn = new MySQLConnection("white",user,"nieve", backgrndDB); // the UPPERCASE DB! |
| 59 |
|
|
System.out.println("CN Size Hashed Iterating / Evaluating neighborhood v.0.3. "); |
| 60 |
|
|
|
| 61 |
|
|
sql = "select num, res, sstype from single_model_node where graph_id="+graphid+" and num="+resnr+";"; |
| 62 |
|
|
mstmt = conn.createStatement(); |
| 63 |
|
|
mrsst = mstmt.executeQuery(sql); |
| 64 |
|
|
if (mrsst.next()) { |
| 65 |
|
|
// this is the central node -> get type and secondary structure |
| 66 |
|
|
restype = mrsst.getString( 2).toUpperCase(); |
| 67 |
|
|
ressec = mrsst.getString( 3).toUpperCase(); |
| 68 |
|
|
} // end if central residue |
| 69 |
|
|
mrsst.close(); |
| 70 |
|
|
mstmt.close(); |
| 71 |
|
|
System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec); |
| 72 |
|
|
|
| 73 |
|
|
// retrieve the original nbhood into orig_shell |
| 74 |
|
|
System.out.println("retrieving original first shell ... "); |
| 75 |
|
|
mstmt = conn.createStatement(); |
| 76 |
|
|
mstmt.executeUpdate("drop table if exists orig_shell;"); |
| 77 |
|
|
mstmt.close(); |
| 78 |
|
|
|
| 79 |
|
|
mstmt = conn.createStatement(); |
| 80 |
|
|
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+";"); |
| 81 |
|
|
mstmt.close(); |
| 82 |
|
|
|
| 83 |
|
|
System.out.println("adding the original 2nd shell ..."); |
| 84 |
|
|
sql = "select j_num from orig_shell where shell=1;"; |
| 85 |
|
|
mstmt = conn.createStatement(); |
| 86 |
|
|
mrsst = mstmt.executeQuery(sql); |
| 87 |
|
|
i=0; |
| 88 |
|
|
while (mrsst.next()) { |
| 89 |
|
|
i++; |
| 90 |
|
|
oj_num = mrsst.getInt(1); |
| 91 |
|
|
System.out.println(i+":"+oj_num); |
| 92 |
|
|
mjst = conn.createStatement(); |
| 93 |
|
|
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+";"; |
| 94 |
|
|
// System.out.println(">"+sql); |
| 95 |
|
|
mjst.executeUpdate( sql); |
| 96 |
|
|
mjst.close(); |
| 97 |
|
|
} // end while |
| 98 |
|
|
mrsst.close(); |
| 99 |
|
|
mstmt.close(); |
| 100 |
|
|
|
| 101 |
|
|
System.out.println("gathering the original 1st and 2nd shell nbs."); |
| 102 |
|
|
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;"; |
| 103 |
|
|
mstmt = conn.createStatement(); |
| 104 |
|
|
mrsst = mstmt.executeQuery(sql); |
| 105 |
|
|
o1=0; |
| 106 |
|
|
o2=0; |
| 107 |
|
|
while (mrsst.next()) { |
| 108 |
|
|
if ( mrsst.getInt( 4)==1) { // count 1st shell entry |
| 109 |
|
|
o1++; |
| 110 |
|
|
System.out.print("1#"+o1); |
| 111 |
|
|
rheadline[0]+="\t"+o1; |
| 112 |
|
|
rheadline[1]+="\t"+mrsst.getString(2); // res |
| 113 |
|
|
rheadline[2]+="\t"+mrsst.getInt(1); // resnum |
| 114 |
|
|
rheadline[3]+="\t"+mrsst.getString(3); // SStype |
| 115 |
lappe |
225 |
rheadline[4]+="\t("+mrsst.getInt(5)+")"; // CN |
| 116 |
lappe |
221 |
} // end if 2st shell |
| 117 |
|
|
if ( mrsst.getInt( 4)==2) { // count 2nd shell entry |
| 118 |
|
|
o2++; |
| 119 |
|
|
System.out.print("2#"+o2); |
| 120 |
|
|
} // end if 2nd shell |
| 121 |
|
|
System.out.println(" :\t"+mrsst.getInt( 1)+"\t"+mrsst.getString( 2)+"\t"+mrsst.getString( 3)+"\t"+mrsst.getInt( 4)+"\t"+mrsst.getInt( 5)); |
| 122 |
|
|
} // end while |
| 123 |
|
|
System.out.println("Orig.SIZE 1st shell "+o1); |
| 124 |
|
|
System.out.println("Orig.SIZE 2nd shell "+o2); |
| 125 |
lappe |
225 |
rheadline[4] = rheadline[4].replace("X", ("("+o1)+")"); |
| 126 |
lappe |
221 |
rsideline = new String[o2+1]; |
| 127 |
|
|
rsideline[0]="+0\tRnum:S(cn)"; |
| 128 |
|
|
sumdelta = new int[(o1+1)][(o2+1)]; |
| 129 |
|
|
newnbs = new String[(o1+1)][(o2+1)]; |
| 130 |
|
|
cnall = new int[(o1+1)][(o2+1)]; |
| 131 |
|
|
// creating the perturbed version of shell 1 into temp_shell |
| 132 |
|
|
for (j=0; j<=o2; j++) { // <=o2 outer loop through all originally indirect contacts |
| 133 |
|
|
|
| 134 |
|
|
for (i=0; i<=o1; i++) { // inner loop through all originally direct contacts |
| 135 |
|
|
System.out.println("---------------------------------------------"); |
| 136 |
|
|
System.out.println("Creating perturbed nbhood ("+i+","+j+")\t"); |
| 137 |
|
|
// clear first |
| 138 |
|
|
nstmt = conn.createStatement(); |
| 139 |
|
|
nstmt.executeUpdate("drop table if exists temp_shell;"); |
| 140 |
|
|
nstmt.close(); |
| 141 |
|
|
nstmt = conn.createStatement(); |
| 142 |
|
|
nstmt.executeUpdate("create table temp_shell select * from orig_shell limit 0;"); |
| 143 |
|
|
nstmt.close(); |
| 144 |
|
|
oi = 0; |
| 145 |
|
|
oj = 0; |
| 146 |
|
|
mrsst.beforeFirst(); |
| 147 |
|
|
newnbhood=""; |
| 148 |
|
|
overx = false; |
| 149 |
|
|
ixnum=0; |
| 150 |
|
|
jxnum=0; |
| 151 |
|
|
while (mrsst.next()) { |
| 152 |
|
|
oj_num = mrsst.getInt( 1); |
| 153 |
|
|
oj_res = mrsst.getString(2); |
| 154 |
|
|
oj_sec = mrsst.getString(3); |
| 155 |
|
|
oj_shell = mrsst.getInt( 4); |
| 156 |
|
|
oj_cnsize = mrsst.getInt( 5); |
| 157 |
|
|
if (oj_num>resnr) { // we are over x |
| 158 |
|
|
if (!overx) { |
| 159 |
|
|
newnbhood+="x"; |
| 160 |
|
|
overx=true; |
| 161 |
|
|
} // end if over x |
| 162 |
|
|
} // END IF J > X |
| 163 |
|
|
if (oj_shell==1) { // a direct 1st shell neighbour |
| 164 |
|
|
oi++; |
| 165 |
|
|
if (oi!=i) {// if this is NOT the one direct nb 2B dropped |
| 166 |
|
|
// include as 1st shell nbor into temp_shell |
| 167 |
|
|
nstmt = conn.createStatement(); |
| 168 |
|
|
sql = "insert into temp_shell values("+resnr+",\'"+restype+"\',"+oj_num+",\'"+oj_res+"\',\'"+oj_sec+"\', 1);"; |
| 169 |
|
|
// System.out.println("oi>"+ sql); |
| 170 |
|
|
nstmt.executeUpdate(sql); |
| 171 |
|
|
nstmt.close(); |
| 172 |
|
|
newnbhood+=oj_res; |
| 173 |
|
|
} else { |
| 174 |
|
|
ixnum=oj_num; |
| 175 |
|
|
} // end if ni!=i |
| 176 |
|
|
} else { // 2nd shell neighbour |
| 177 |
|
|
oj++; |
| 178 |
|
|
if (oj==j) { // this is the 2nd shell nb 2B included |
| 179 |
|
|
// put as new 1st shell nbor |
| 180 |
|
|
nstmt = conn.createStatement(); |
| 181 |
|
|
sql = "insert into temp_shell values("+resnr+",\'"+restype+"\',"+oj_num+",\'"+oj_res+"\',\'"+oj_sec+"\', 1);"; |
| 182 |
|
|
// System.out.println("oj>"+ sql); |
| 183 |
|
|
nstmt.executeUpdate(sql); |
| 184 |
|
|
nstmt.close(); |
| 185 |
|
|
newnbhood+=oj_res; |
| 186 |
|
|
jxnum=oj_num; |
| 187 |
|
|
} // end if |
| 188 |
|
|
if (j==0) { // creating the sideline ruler array for the output |
| 189 |
|
|
rsideline[oj] = "+"+oj+"\t"+oj_res+""+oj_num+":"+oj_sec+"("+oj_cnsize+")"; |
| 190 |
|
|
} // end if j==0 |
| 191 |
|
|
} // end if 1st/2nd shell |
| 192 |
|
|
|
| 193 |
|
|
} // end while through the entire nbhood |
| 194 |
|
|
if (!overx) { // we haven't seen a nb > x yet |
| 195 |
|
|
newnbhood+="x"; // x sits at the end of the nbhoodstring |
| 196 |
|
|
overx=true; |
| 197 |
|
|
} // end if over x |
| 198 |
|
|
// System.out.println("new direct nbhood "+newnbhood); |
| 199 |
|
|
// Now the "updated" / perturbed version of shell 1 is in temp_shell |
| 200 |
|
|
// we can build 2nd shell accordingly. |
| 201 |
|
|
// System.out.println("building the 2nd shell"); |
| 202 |
|
|
sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;"; |
| 203 |
|
|
nstmt = conn.createStatement(); |
| 204 |
|
|
nrsst = nstmt.executeQuery(sql); |
| 205 |
|
|
x = 0; |
| 206 |
|
|
while (nrsst.next()) { |
| 207 |
|
|
x++; |
| 208 |
|
|
j_num = nrsst.getInt( 1); |
| 209 |
|
|
// System.out.println(x+":"+nrsst.getString( 2)+" "+j_num+" "+nrsst.getString( 3)); |
| 210 |
|
|
mjst = conn.createStatement(); |
| 211 |
|
|
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+";"; |
| 212 |
|
|
// System.out.println(">"+sql); |
| 213 |
|
|
mjst.executeUpdate( sql); |
| 214 |
|
|
mjst.close(); |
| 215 |
|
|
} // end while |
| 216 |
|
|
nrsst.close(); |
| 217 |
|
|
nstmt.close(); |
| 218 |
|
|
// and score this move |
| 219 |
|
|
lastxcn=0; |
| 220 |
|
|
newnbs[i][j]= newnbhood; |
| 221 |
|
|
System.out.println("Scoring ["+i+"]["+j+"] (-"+ixnum+"/+"+jxnum+")\t"+newnbs[i][j]); |
| 222 |
|
|
score = scoreCurrentNbhood( ixnum, jxnum); |
| 223 |
|
|
sumdelta[i][j] = score; |
| 224 |
|
|
cnall[i][j] = lastxcn; |
| 225 |
|
|
reportMatrix( printCNSize ); |
| 226 |
|
|
reportMatrix( printdeltaRank ); |
| 227 |
|
|
System.out.println("SumDeltaRank Score = \t"+score); |
| 228 |
|
|
System.out.println("CN1 x CN2 product = \t"+cnall[i][j]); |
| 229 |
|
|
// reportMatrix( printNbstring ); |
| 230 |
|
|
} // next i |
| 231 |
|
|
System.out.println("\t"); |
| 232 |
|
|
} // next j |
| 233 |
|
|
// report total matrix sumdelta |
| 234 |
|
|
System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec); |
| 235 |
|
|
System.out.println("backgroundDB"+backgrndDB+" \t maxRank : "+maxRank); |
| 236 |
|
|
reportResults( o1, o2, printRank); |
| 237 |
|
|
reportResults( o1, o2, printCNSize); |
| 238 |
|
|
reportResults( o1, o2, printCNSxdelta ); |
| 239 |
|
|
// Cleanup ... |
| 240 |
|
|
mrsst.close(); |
| 241 |
|
|
mstmt.close(); |
| 242 |
|
|
|
| 243 |
|
|
} catch (SQLException e) { |
| 244 |
|
|
e.printStackTrace(); |
| 245 |
|
|
System.err.println("SQLException: " + e.getMessage()); |
| 246 |
|
|
System.err.println("SQLState: " + e.getSQLState()); |
| 247 |
|
|
} // end try/catch |
| 248 |
|
|
System.out.println("fin."); |
| 249 |
|
|
} // end main |
| 250 |
|
|
|
| 251 |
|
|
|
| 252 |
|
|
|
| 253 |
|
|
public static void reportResults( int o1, int o2, int what2print) { |
| 254 |
|
|
System.out.println("Printing "+what2print); |
| 255 |
|
|
if (what2print==printRank) System.out.println("Overall resulting SumDeltaRank Matrix" ); |
| 256 |
|
|
if (what2print==printNbstring) System.out.println("Overall tested new nbhoodStrings" ); |
| 257 |
|
|
if (what2print==printCNSize) System.out.println("Overall cnsize" ); |
| 258 |
lappe |
225 |
if (what2print==printCNSxdelta) System.out.println("Overall (cnsize*sumDeltaRank)" ); |
| 259 |
lappe |
221 |
/*if (what2print==printTotal) System.out.print("total[i][j]" ); |
| 260 |
|
|
if (what2print==printEntropy) System.out.print("entropy[i][j]" ); |
| 261 |
|
|
if (what2print==printFreq ) System.out.print("freq[i][j]" ); |
| 262 |
|
|
if (what2print==printAUC) System.out.print("AUC[i][j]" ); |
| 263 |
|
|
|
| 264 |
|
|
if (what2print==printMoveset) System.out.print("moveset[i][j]" ); |
| 265 |
|
|
if (what2print==printdeltaRank) System.out.print("rank[i][j]-rank[0][0]" );) */ |
| 266 |
|
|
|
| 267 |
|
|
// print headerline(s) |
| 268 |
|
|
System.out.println(rheadline[0]); |
| 269 |
|
|
System.out.println(rheadline[1]); |
| 270 |
|
|
System.out.println(rheadline[2]); |
| 271 |
|
|
System.out.println(rheadline[3]); |
| 272 |
lappe |
225 |
System.out.println(rheadline[4]); |
| 273 |
lappe |
221 |
for (int j=0; j<=o2; j++) { |
| 274 |
|
|
// print rsideline |
| 275 |
|
|
System.out.print( rsideline[j]+"\t"); |
| 276 |
|
|
for ( int i=0; i<=o1; i++) { |
| 277 |
|
|
if (what2print==printRank) System.out.print( sumdelta[i][j] ); |
| 278 |
|
|
if (what2print==printNbstring) System.out.print( newnbs[i][j] ); |
| 279 |
|
|
if (what2print==printCNSize) System.out.print( cnall[i][j] ); |
| 280 |
|
|
if (what2print==printCNSxdelta) System.out.print( sumdelta[i][j]*cnall[i][j] ); |
| 281 |
|
|
System.out.print("\t"); |
| 282 |
|
|
} // next i |
| 283 |
|
|
System.out.println(""); |
| 284 |
|
|
} // next j |
| 285 |
|
|
} // end of reportResults |
| 286 |
|
|
|
| 287 |
|
|
|
| 288 |
|
|
|
| 289 |
|
|
public static int scoreCurrentNbhood( int ixnum, int jxnum) { |
| 290 |
|
|
int ixcn=0, jxcn=0, n1=0, n2=0, ni, nj, i, j, j_num, j_shell, j_cnsize, sumdeltarank=0; |
| 291 |
|
|
String sql, j_res, j_sec, nbs, mymove, precol; |
| 292 |
|
|
boolean overx = false; |
| 293 |
|
|
Statement stmt; |
| 294 |
|
|
ResultSet rsst; |
| 295 |
|
|
|
| 296 |
|
|
try { |
| 297 |
|
|
headline[0]="\t\t\t0"; |
| 298 |
|
|
headline[1]="\t\t\t-"; |
| 299 |
|
|
headline[2]="\t\t\t0"; |
| 300 |
|
|
headline[3]="\t\t\t-"; |
| 301 |
|
|
headline[4]="\t\t\tX"; |
| 302 |
|
|
|
| 303 |
|
|
// System.out.println("retrieving the entire nbhood (1st and 2nd shell)"); |
| 304 |
|
|
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;"; |
| 305 |
|
|
stmt = conn.createStatement(); |
| 306 |
|
|
rsst = stmt.executeQuery(sql); |
| 307 |
|
|
// counting shell2 |
| 308 |
|
|
n2=0; |
| 309 |
|
|
while (rsst.next()) { |
| 310 |
|
|
if ( rsst.getInt( 4)==1) { // count 1st shell entry |
| 311 |
|
|
n1++; |
| 312 |
|
|
// System.out.print("1#"+n1); |
| 313 |
|
|
headline[0]+="\t"+n1; |
| 314 |
|
|
headline[1]+="\t"+rsst.getString(2); // res |
| 315 |
|
|
headline[2]+="\t"+rsst.getInt(1); // resnum |
| 316 |
|
|
headline[3]+="\t"+rsst.getString(3); // SStype |
| 317 |
lappe |
225 |
headline[4]+="\t("+rsst.getInt(5)+")"; // CNSize |
| 318 |
lappe |
221 |
} // end if 2st shell |
| 319 |
|
|
if ( rsst.getInt( 4)==2) { // count 2nd shell entry |
| 320 |
|
|
n2++; |
| 321 |
|
|
// System.out.print("2#"+n2); |
| 322 |
|
|
} // end if 2nd shell |
| 323 |
|
|
// System.out.println(" :\t"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)); |
| 324 |
|
|
} // end while |
| 325 |
|
|
size1 = n1; |
| 326 |
|
|
size2 = n2; |
| 327 |
|
|
ixcn = n1; |
| 328 |
|
|
jxcn = n1; |
| 329 |
|
|
System.out.println("|1st shell|="+size1+" \tx\t |2nd shell|="+size2); |
| 330 |
lappe |
225 |
headline[4]=headline[4].replace("X",("("+size1+")")); |
| 331 |
lappe |
221 |
|
| 332 |
|
|
// n1 and n2 are known, initialise matrices accordingly. |
| 333 |
|
|
// nbhood, move, rank, entropy, freq, AUC etc. (evtl.+ degree(?)) |
| 334 |
|
|
rank = new int[(n1+1)][(n2+1)]; |
| 335 |
|
|
rank[0][0]=maxRank; |
| 336 |
|
|
total = new int[(n1+1)][(n2+1)]; |
| 337 |
|
|
entropy = new double[(n1+1)][(n2+1)]; |
| 338 |
|
|
freq = new double[(n1+1)][(n2+1)]; |
| 339 |
|
|
AUC = new double[(n1+1)][(n2+1)]; |
| 340 |
|
|
nbstring = new String[(n1+1)][(n2+1)]; |
| 341 |
|
|
moveset = new String[(n1+1)][(n2+1)]; |
| 342 |
|
|
sideline = new String[n2+1]; |
| 343 |
|
|
cn1 = new int[n1+1]; |
| 344 |
|
|
cn2 = new int[n2+1]; |
| 345 |
|
|
cnsize = new int[(n1+1)][(n2+1)]; |
| 346 |
|
|
|
| 347 |
|
|
for (j=0; j<=n2; j++) { // outer loop through all indirect contacts |
| 348 |
|
|
for (i=0; i<=n1; i++) { // inner loop through all direct contacts |
| 349 |
|
|
mymove = ""; |
| 350 |
|
|
overx = false; |
| 351 |
|
|
System.out.print("("+i+","+j+")\t"); |
| 352 |
|
|
ni = 0; |
| 353 |
|
|
nj = 0; |
| 354 |
|
|
sideline[0]="+0\tRnum:S("+n1+")"; |
| 355 |
|
|
cn1[0]=n1; |
| 356 |
|
|
cn2[0]=n1; |
| 357 |
|
|
nbs="%"; |
| 358 |
|
|
rsst.beforeFirst(); |
| 359 |
|
|
while (rsst.next()) { |
| 360 |
|
|
j_num = rsst.getInt(1); |
| 361 |
|
|
j_res = rsst.getString(2); |
| 362 |
|
|
j_sec = rsst.getString(3); |
| 363 |
|
|
j_shell = rsst.getInt(4); |
| 364 |
|
|
j_cnsize = rsst.getInt(5); |
| 365 |
|
|
if (j_num>resnr) { // we are over x |
| 366 |
|
|
if (!overx) { |
| 367 |
|
|
nbs+="x%"; |
| 368 |
|
|
overx=true; |
| 369 |
|
|
} // end if over x |
| 370 |
|
|
} // END IF J > X |
| 371 |
|
|
if (j_shell==1) { // a direct 1st shell neighbour |
| 372 |
|
|
ni++; |
| 373 |
|
|
if (ni!=i) {// if this is NOT the one direct nb 2B dropped |
| 374 |
|
|
nbs+=j_res.toUpperCase()+"%"; // it is included |
| 375 |
|
|
if ( j_num==jxnum && j==0) { // This is the direct nb dropped |
| 376 |
|
|
jxcn=j_cnsize; |
| 377 |
|
|
System.out.print("(j"+jxnum+":"+jxcn+")"); |
| 378 |
|
|
} |
| 379 |
|
|
} else { // this one IS dropped |
| 380 |
|
|
mymove += "(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")"; |
| 381 |
|
|
cn1[ni]=j_cnsize; |
| 382 |
|
|
} // end if ni!=i |
| 383 |
|
|
|
| 384 |
|
|
} else { // 2nd shell neighbour |
| 385 |
|
|
nj++; |
| 386 |
|
|
if (nj==j) { // this is the 2nd shell nb 2B included |
| 387 |
|
|
nbs+=j_res.toUpperCase()+"%"; |
| 388 |
|
|
mymove += "(+"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")"; |
| 389 |
|
|
if ( j_num==ixnum && i==0) { // This is the dropped direct nb, no 2b found in 2ns shell |
| 390 |
|
|
ixcn=j_cnsize; |
| 391 |
|
|
System.out.print("(i"+ixnum+":"+ixcn+")"); |
| 392 |
|
|
} |
| 393 |
|
|
} // end if |
| 394 |
|
|
|
| 395 |
|
|
// // only once for building the sidelines |
| 396 |
|
|
if (j==0) { |
| 397 |
|
|
sideline[nj] = "+"+nj+"\t"+j_res+""+j_num+":"+j_sec+"("+j_cnsize+")"; |
| 398 |
|
|
cn2[nj] = j_cnsize; |
| 399 |
|
|
} // end if sideline |
| 400 |
|
|
} // end if 1st/2nd shell |
| 401 |
|
|
|
| 402 |
|
|
} // end while through the entire nbhood |
| 403 |
|
|
if (!overx) { // in case x is the very last we haven't seen it yet |
| 404 |
|
|
nbs+="x%"; // add it in the end |
| 405 |
|
|
overx=true; |
| 406 |
|
|
} // end if over x |
| 407 |
|
|
System.out.print("("+nbs+")\t"); |
| 408 |
|
|
nbstring[i][j] = nbs; |
| 409 |
|
|
moveset[i][j] = mymove; |
| 410 |
|
|
precol = nbstring[i][0]; |
| 411 |
|
|
getEntropy( nbs, restype, precol); |
| 412 |
|
|
if (lastRank==0) lastRank = maxRank; |
| 413 |
|
|
rank[i][j] = lastRank; |
| 414 |
|
|
entropy[i][j] = lastEntropy; |
| 415 |
|
|
freq[i][j] = lastFreq; |
| 416 |
|
|
AUC[i][j] = lastAUC; |
| 417 |
|
|
total[i][j]= lastTotal; |
| 418 |
|
|
cnsize[i][j]=cn1[i]*cn2[j]; |
| 419 |
|
|
System.out.print(""+cnsize[i][j]+"\t"); |
| 420 |
|
|
if (lastRank > 0) { |
| 421 |
|
|
sumdeltarank += ( (lastRank-rank[0][0]) ); |
| 422 |
|
|
// sumdeltarank += ( (lastRank-rank[0][0]) * (cnsize[i][j]) ); |
| 423 |
|
|
} else { |
| 424 |
|
|
sumdeltarank += ( (maxRank-rank[0][0]) ); |
| 425 |
|
|
// sumdeltarank += ( (maxRank-rank[0][0]) * (cnsize[i][j]) ); |
| 426 |
|
|
} // end if lastRank was defined |
| 427 |
|
|
} // close inner loop (i) |
| 428 |
|
|
System.out.println("."); |
| 429 |
|
|
} // next outerloop (j) |
| 430 |
|
|
lastxcn=(ixcn*jxcn); |
| 431 |
|
|
System.out.println("lastxcn=(ixcn*jxcn)=("+ixcn+"*"+jxcn+")="+lastxcn); |
| 432 |
|
|
rsst.close(); |
| 433 |
|
|
stmt.close(); |
| 434 |
|
|
|
| 435 |
|
|
} catch (SQLException e) { |
| 436 |
|
|
e.printStackTrace(); |
| 437 |
|
|
System.err.println("SQLException: " + e.getMessage()); |
| 438 |
|
|
System.err.println("SQLState: " + e.getSQLState()); |
| 439 |
|
|
} // end try/catch |
| 440 |
|
|
// System.out.println("fin."); |
| 441 |
|
|
return sumdeltarank; |
| 442 |
|
|
} // end scoreCurrentNbhood |
| 443 |
|
|
|
| 444 |
|
|
|
| 445 |
|
|
public static void reportMatrix( int what2print) { |
| 446 |
|
|
System.out.println("\nPrinting "+what2print); |
| 447 |
|
|
if (what2print==printRank) System.out.print("rank[i][j]" ); |
| 448 |
|
|
if (what2print==printTotal) System.out.print("total[i][j]" ); |
| 449 |
|
|
if (what2print==printEntropy) System.out.print("entropy[i][j]" ); |
| 450 |
|
|
if (what2print==printFreq ) System.out.print("freq[i][j]" ); |
| 451 |
|
|
if (what2print==printAUC) System.out.print("AUC[i][j]" ); |
| 452 |
|
|
if (what2print==printNbstring) System.out.print("nbstring[i][j]" ); |
| 453 |
|
|
if (what2print==printMoveset) System.out.print("moveset[i][j]" ); |
| 454 |
|
|
if (what2print==printdeltaRank) System.out.print("rank[i][j]-rank[0][0]" ); |
| 455 |
|
|
if (what2print==printCNSize) System.out.print("cnsize[i][j]" ); |
| 456 |
|
|
if (what2print==printCNSxdelta) System.out.print("cnsize[i][j]*(rank[i][j]-rank[0][0])" ); |
| 457 |
|
|
|
| 458 |
|
|
System.out.println("..."); |
| 459 |
|
|
// print headerline(s) |
| 460 |
|
|
System.out.println(headline[0]); |
| 461 |
|
|
System.out.println(headline[1]); |
| 462 |
|
|
System.out.println(headline[2]); |
| 463 |
|
|
System.out.println(headline[3]); |
| 464 |
|
|
System.out.println(headline[4]); |
| 465 |
|
|
for (int j=0; j<=size2; j++) { |
| 466 |
|
|
// print sideline |
| 467 |
|
|
System.out.print( sideline[j]+"\t"); |
| 468 |
|
|
for ( int i=0; i<=size1; i++) { |
| 469 |
|
|
if (what2print==printRank) System.out.print( rank[i][j] ); |
| 470 |
|
|
if (what2print==printTotal) System.out.print( total[i][j] ); |
| 471 |
|
|
if (what2print==printEntropy) System.out.print( entropy[i][j] ); |
| 472 |
|
|
if (what2print==printFreq ) System.out.print( freq[i][j] ); |
| 473 |
|
|
if (what2print==printAUC) System.out.print( AUC[i][j] ); |
| 474 |
|
|
if (what2print==printNbstring) System.out.print( nbstring[i][j] ); |
| 475 |
|
|
if (what2print==printMoveset) System.out.print( moveset[i][j] ); |
| 476 |
|
|
if (what2print==printdeltaRank) System.out.print( rank[i][j]-rank[0][0] ); |
| 477 |
|
|
if (what2print==printCNSize) System.out.print( cnsize[i][j] ); |
| 478 |
|
|
if (what2print==printCNSxdelta) System.out.print( cnsize[i][j]*(rank[i][j]-rank[0][0]) ); |
| 479 |
|
|
System.out.print("\t"); |
| 480 |
|
|
} // next i |
| 481 |
|
|
System.out.println(""); |
| 482 |
|
|
} // next j |
| 483 |
|
|
} // end of report |
| 484 |
|
|
|
| 485 |
|
|
public static void getEntropy( String nbs, String centRes, String predec) { |
| 486 |
|
|
String sql, res, this_n, prec_n; |
| 487 |
|
|
Statement stmt; |
| 488 |
|
|
ResultSet rsst; |
| 489 |
|
|
double p, psum=0.0, logp, plogp, plogpsum=0.0; |
| 490 |
|
|
try { |
| 491 |
|
|
// Hashing first row tables comes first |
| 492 |
|
|
// System.out.println("nbs : "+nbs); |
| 493 |
|
|
// System.out.println("predec: "+predec); |
| 494 |
|
|
this_n = nbs.replace("%",""); |
| 495 |
|
|
prec_n = predec.replace("%",""); |
| 496 |
|
|
// System.out.println("this_n: ["+this_n+"]"); |
| 497 |
|
|
// System.out.println("prec_n: ["+prec_n+"]"); |
| 498 |
|
|
if (prec_n.equals(this_n)) { |
| 499 |
|
|
// System.out.println("have to create db for this "+prec_n); |
| 500 |
|
|
sql = "create table IF NOT EXISTS nbhashtables."+prec_n+" as select res, n, k from single_model_node where n like '"+nbs+"';"; |
| 501 |
|
|
// System.out.println(" >> "+sql); |
| 502 |
|
|
stmt = conn.createStatement(); |
| 503 |
|
|
stmt.executeUpdate( sql); |
| 504 |
|
|
stmt.close(); |
| 505 |
|
|
} // else System.out.println("using preceding db of "+prec_n); |
| 506 |
|
|
|
| 507 |
|
|
// now we can safely derive the estimates from the hashtable |
| 508 |
|
|
sql = "select count(*) from nbhashtables."+prec_n+" where n like '"+nbs+"';"; |
| 509 |
|
|
// System.out.println( sql); |
| 510 |
|
|
stmt = conn.createStatement(); |
| 511 |
|
|
rsst = stmt.executeQuery(sql); |
| 512 |
|
|
if (rsst.next()) lastTotal = rsst.getInt( 1); |
| 513 |
|
|
rsst.close(); |
| 514 |
|
|
stmt.close(); |
| 515 |
|
|
|
| 516 |
|
|
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;"; |
| 517 |
|
|
stmt = conn.createStatement(); |
| 518 |
|
|
rsst = stmt.executeQuery(sql); |
| 519 |
|
|
// System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)"); |
| 520 |
|
|
int rank = 0; |
| 521 |
|
|
boolean seenCentRes = false; |
| 522 |
|
|
lastAUC = 0.0; |
| 523 |
|
|
lastRank = 0; |
| 524 |
|
|
lastFreq = 0.0; |
| 525 |
|
|
lastavgk = 0.0; |
| 526 |
|
|
lastdevk = 0.0; |
| 527 |
|
|
while (rsst.next()) { |
| 528 |
|
|
rank ++; |
| 529 |
|
|
res = rsst.getString(1); // 1st column -- res |
| 530 |
|
|
p = rsst.getDouble(3); // 3rd: fraction p |
| 531 |
|
|
// System.out.print(rank+ " : " + res+" : "+num+ " : " + p); |
| 532 |
|
|
logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits |
| 533 |
|
|
// System.out.print(" : " + logp); |
| 534 |
|
|
plogp = -1.0 * p * logp; |
| 535 |
|
|
// System.out.print(" : " + plogp); |
| 536 |
|
|
plogpsum += plogp; |
| 537 |
|
|
psum += p; |
| 538 |
|
|
|
| 539 |
|
|
if (res.equals(centRes)) { |
| 540 |
|
|
// System.out.print(" <==" + centRes); |
| 541 |
|
|
seenCentRes = true; |
| 542 |
|
|
lastFreq = p; |
| 543 |
|
|
lastRank = rank; |
| 544 |
|
|
lastavgk = rsst.getDouble(4); |
| 545 |
|
|
lastdevk = rsst.getDouble(5); |
| 546 |
|
|
} |
| 547 |
|
|
if (seenCentRes) lastAUC += p; |
| 548 |
|
|
// System.out.println(""); |
| 549 |
|
|
} |
| 550 |
|
|
// System.out.println("Sum :"+lastTotal+" : "+psum+" : "+plogpsum); |
| 551 |
|
|
rsst.close(); |
| 552 |
|
|
stmt.close(); |
| 553 |
|
|
lastEntropy = plogpsum; |
| 554 |
|
|
if (lastRank==0) lastRank = maxRank; |
| 555 |
|
|
} catch (SQLException e) { |
| 556 |
|
|
e.printStackTrace(); |
| 557 |
|
|
System.err.println("SQLException: " + e.getMessage()); |
| 558 |
|
|
System.err.println("SQLState: " + e.getSQLState()); |
| 559 |
|
|
} |
| 560 |
|
|
|
| 561 |
|
|
} // end of getEntropy |
| 562 |
|
|
|
| 563 |
|
|
} // end class |
