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import tools.MySQLConnection; |
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|
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import java.sql.SQLException; |
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import java.sql.Statement; |
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import java.sql.ResultSet; |
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|
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public class cnex1 { |
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|
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/** |
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* CN2 size x sumdelta |
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* iterating over all steps by exchange of one neighbor at a time by a common neighbor |
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* with subsequent scoring |
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* @author lappe |
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*/ |
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static int maxRank = 21; // value to replace for non-existence of central redue in the resultvector (rank=0) |
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// higher values should penalize non-existence more |
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static int VL=1; // Verbosity Level |
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static String user = "lappe" ; // change user name!! |
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static MySQLConnection conn; |
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static String backgrndDB = "pdb_reps_graph_4_2"; |
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static String targetNodes = "target_node"; |
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static String targetEdges = "target_edge"; |
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static double lastEntropy=0.0, lastFreq, lastAUC, lastavgk, lastdevk, lastCorr; |
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static int lastRank, lastTotal, lastxcn=0; |
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static int graphid=0, resnr=0; |
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static int size1=0, size2=0; // the dimensions of the matrices = |shell1|x|shell2| = nr of direct(1) x indirect(2) nbs |
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static String rsideline[], rheadline[]={" -->\t(-)1st shell\t0"," |\t \t-"," |\t(+) \t0"," V\t2nd shell\t-", " \t \tX"}; |
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static String sideline[], headline[]={"\t\t0","\t\t-","\t\t0","\t\t-","\t\tX"}; |
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static String restype="?", ressec="?", newnbhood=""; |
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static int cn1[], cn2[], matsize[][], oCN1[], oCN2[]; |
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static int sumdelta[][], rank[][], total[][], cnall[][]; |
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static double cnsize[][], correct[][], entropy[][], freq[][], AUC[][]; |
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static String newnbs[][], nbstring[][], moveset[][]; |
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|
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static int printRank=1, |
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printTotal = 2, |
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printEntropy = 3, |
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printFreq = 4, |
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printAUC = 5, |
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printNbstring= 6, |
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printMoveset = 7, |
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printdeltaRank=8, |
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printCNSize =9, |
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printCNSxdelta=10, |
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printMatSize =11, |
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printCNSdMSxdelta=12, |
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printCorrect = 13, |
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printCordMSxdelta=14, |
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printoCN1xoCN2 =15, |
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printCNdelta=16; |
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|
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public static void main(String[] args) { |
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|
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if (args.length<2){ |
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System.err.println("The graph_id and residue-nr. needs to be given .... i.e. 7 110"); |
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System.exit(1); |
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} |
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graphid = Integer.parseInt( args[0]); |
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resnr = Integer.parseInt( args[1]); |
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int j_num=0, oj_num=0, oj_shell, oj_cnsize, i, j, x, oi, oj, o1, o2, ixnum, jxnum, score=0; |
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boolean overx = false; |
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String sql, oj_res, oj_sec; |
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Statement mstmt, mjst, nstmt; |
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ResultSet mrsst, nrsst; |
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|
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try { |
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conn = new MySQLConnection("white",user,"nieve", backgrndDB); // the UPPERCASE DB! |
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System.out.println("Scoring Target neighborhoods v.0.4. "); |
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|
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sql = "select num, res, sstype from "+targetNodes+" where graph_id="+graphid+" and num="+resnr+";"; |
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mstmt = conn.createStatement(); |
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mrsst = mstmt.executeQuery(sql); |
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if (mrsst.next()) { |
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// this is the central node -> get type and secondary structure |
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restype = mrsst.getString( 2).toUpperCase(); |
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ressec = mrsst.getString( 3).toUpperCase(); |
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} // end if central residue |
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mrsst.close(); |
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mstmt.close(); |
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System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec); |
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|
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// retrieve the original nbhood into orig_shell |
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System.out.println("retrieving original first shell ... "); |
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mstmt = conn.createStatement(); |
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mstmt.executeUpdate("drop table if exists orig_shell;"); |
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mstmt.close(); |
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|
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mstmt = conn.createStatement(); |
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mstmt.executeUpdate("create table orig_shell as select i_num, i_res, j_num, j_res, j_sstype, 1 as shell from "+targetEdges+" where graph_id="+graphid+" and i_num="+resnr+";"); |
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mstmt.close(); |
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|
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System.out.println("adding the original 2nd shell ..."); |
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sql = "select j_num from orig_shell where shell=1;"; |
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mstmt = conn.createStatement(); |
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mrsst = mstmt.executeQuery(sql); |
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i=0; |
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while (mrsst.next()) { |
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i++; |
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oj_num = mrsst.getInt(1); |
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System.out.println(i+":"+oj_num); |
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mjst = conn.createStatement(); |
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sql = "insert into orig_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell from "+targetEdges+" where graph_id="+graphid+" and i_num="+oj_num+";"; |
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// System.out.println(">"+sql); |
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mjst.executeUpdate( sql); |
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mjst.close(); |
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} // end while |
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mrsst.close(); |
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mstmt.close(); |
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|
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System.out.println("gathering the original 1st and 2nd shell nbs."); |
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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;"; |
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mstmt = conn.createStatement(); |
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mrsst = mstmt.executeQuery(sql); |
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o1=0; |
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o2=0; |
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while (mrsst.next()) { |
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if ( mrsst.getInt( 4)==1) { // count 1st shell entry |
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o1++; |
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System.out.print("1#"+o1); |
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rheadline[0]+="\t"+o1; |
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rheadline[1]+="\t"+mrsst.getString(2); // res |
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rheadline[2]+="\t"+mrsst.getInt(1); // resnum |
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rheadline[3]+="\t"+mrsst.getString(3); // SStype |
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rheadline[4]+="\t("+(mrsst.getInt(5)-1)+")"; // CN |
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} // end if 2st shell |
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if ( mrsst.getInt( 4)==2) { // count 2nd shell entry |
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o2++; |
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System.out.print("2#"+o2); |
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} // end if 2nd shell |
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System.out.println(" :\t"+mrsst.getInt( 1)+"\t"+mrsst.getString( 2)+"\t"+mrsst.getString( 3)+"\t"+mrsst.getInt( 4)+"\t"+mrsst.getInt( 5)); |
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} // end while |
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System.out.println("Orig.SIZE 1st shell "+o1); |
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System.out.println("Orig.SIZE 2nd shell "+o2); |
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rheadline[4] = rheadline[4].replace("X", ("("+o1)+")"); |
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rsideline = new String[o2+1]; |
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rsideline[0]="+0\tRnum:S(cn)"; |
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sumdelta = new int[(o1+1)][(o2+1)]; |
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newnbs = new String[(o1+1)][(o2+1)]; |
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cnall = new int[(o1+1)][(o2+1)]; |
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matsize = new int[(o1+1)][(o2+1)]; |
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correct = new double[(o1+1)][(o2+1)]; |
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|
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|
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oCN1 = new int[(o1+1)]; |
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oCN2 = new int[(o2+1)]; |
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oCN1[0]=o1; |
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oCN2[0]=o1; |
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mrsst.beforeFirst(); |
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o1=0; |
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o2=0; |
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while (mrsst.next()) { |
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if ( mrsst.getInt( 4)==1) { // 1st shell entry |
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o1++; |
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oCN1[(o1)]=mrsst.getInt(5)-1; // CN |
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} // end if 2st shell |
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if ( mrsst.getInt( 4)==2) { // 2nd shell entry |
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o2++; |
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oCN2[(o2)]=mrsst.getInt(5); |
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} // end if 2nd shell |
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} // end while |
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|
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// creating the perturbed version of shell 1 into temp_shell |
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for (j=0; j<=o2; j++) { // <=o2 outer loop through all originally indirect contacts |
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|
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for (i=0; i<=o1; i++) { // inner loop through all originally direct contacts |
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if (VL>=1) { |
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System.out.println("---------------------------------------------"); |
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System.out.println("Creating perturbed nbhood ("+i+","+j+")\t"); |
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} |
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// clear first |
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nstmt = conn.createStatement(); |
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nstmt.executeUpdate("drop table if exists temp_shell;"); |
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nstmt.close(); |
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nstmt = conn.createStatement(); |
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nstmt.executeUpdate("create table temp_shell select * from orig_shell limit 0;"); |
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nstmt.close(); |
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oi = 0; |
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oj = 0; |
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mrsst.beforeFirst(); |
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newnbhood=""; |
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overx = false; |
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ixnum=0; |
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jxnum=0; |
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while (mrsst.next()) { |
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oj_num = mrsst.getInt( 1); |
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oj_res = mrsst.getString(2); |
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oj_sec = mrsst.getString(3); |
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oj_shell = mrsst.getInt( 4); |
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oj_cnsize = mrsst.getInt( 5); |
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if (oj_num>resnr) { // we are over x |
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if (!overx) { |
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newnbhood+="x"; |
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overx=true; |
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} // end if over x |
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} // END IF J > X |
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if (oj_shell==1) { // a direct 1st shell neighbour |
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oi++; |
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if (oi!=i) {// if this is NOT the one direct nb 2B dropped |
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// include as 1st shell nbor into temp_shell |
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nstmt = conn.createStatement(); |
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sql = "insert into temp_shell values("+resnr+",\'"+restype+"\',"+oj_num+",\'"+oj_res+"\',\'"+oj_sec+"\', 1);"; |
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// System.out.println("oi>"+ sql); |
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nstmt.executeUpdate(sql); |
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nstmt.close(); |
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newnbhood+=oj_res; |
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} else { |
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ixnum=oj_num; |
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} // end if ni!=i |
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} else { // 2nd shell neighbour |
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oj++; |
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if (oj==j) { // this is the 2nd shell nb 2B included |
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// put as new 1st shell nbor |
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nstmt = conn.createStatement(); |
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sql = "insert into temp_shell values("+resnr+",\'"+restype+"\',"+oj_num+",\'"+oj_res+"\',\'"+oj_sec+"\', 1);"; |
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// System.out.println("oj>"+ sql); |
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nstmt.executeUpdate(sql); |
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nstmt.close(); |
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newnbhood+=oj_res; |
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jxnum=oj_num; |
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} // end if |
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if (j==0) { // creating the sideline ruler array for the output |
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rsideline[oj] = "+"+oj+"\t"+oj_res+""+oj_num+":"+oj_sec+"("+oj_cnsize+")"; |
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} // end if j==0 |
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} // end if 1st/2nd shell |
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|
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} // end while through the entire nbhood |
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if (!overx) { // we haven't seen a nb > x yet |
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newnbhood+="x"; // x sits at the end of the nbhoodstring |
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overx=true; |
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} // end if over x |
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// System.out.println("new direct nbhood "+newnbhood); |
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// Now the "updated" / perturbed version of shell 1 is in temp_shell |
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// we can build 2nd shell accordingly. |
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// System.out.println("building the 2nd shell"); |
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sql = "select j_num, j_res, j_sstype from temp_shell where shell=1;"; |
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nstmt = conn.createStatement(); |
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nrsst = nstmt.executeQuery(sql); |
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x = 0; |
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while (nrsst.next()) { |
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x++; |
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j_num = nrsst.getInt( 1); |
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// System.out.println(x+":"+nrsst.getString( 2)+" "+j_num+" "+nrsst.getString( 3)); |
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mjst = conn.createStatement(); |
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sql = "insert into temp_shell select i_num, i_res, j_num, j_res, j_sstype, 2 as shell from "+targetEdges+" where graph_id="+graphid+" and i_num="+j_num+";"; |
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// System.out.println(">"+sql); |
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mjst.executeUpdate( sql); |
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mjst.close(); |
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} // end while |
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nrsst.close(); |
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nstmt.close(); |
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// and score this move |
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lastxcn=0; |
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newnbs[i][j]= newnbhood; |
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if (VL>=1) System.out.print("\n["+i+"]["+j+"]\t-"+ixnum+"/+"+jxnum+"\t"+newnbs[i][j]+"\t "); |
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score = scoreCurrentNbhood( ixnum, jxnum); |
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if (VL>=1) System.out.print( lastRank+"\t "); |
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sumdelta[i][j] = score; |
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cnall[i][j] = lastxcn; |
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matsize[i][j] = (size1*size2)-1; |
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correct[i][j] = lastCorr; |
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if (VL>=1) { |
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//reportMatrix( printNbstring ); |
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reportMatrix( printRank ); |
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reportMatrix( printdeltaRank ); |
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reportMatrix( printCNSize ); |
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reportMatrix( printCNSxdelta); |
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System.out.println("SumDeltaRank Score = \t"+score); |
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System.out.println("corrected Score = \t"+correct[i][j]); |
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System.out.println("Matrix size n1*n2-1= \t("+size1+"*"+size2+")-1 ="+matsize[i][j]); |
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System.out.println("CN1 x CN2 product = \t"+cnall[i][j]); |
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} else { |
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System.out.print("\t"+score+"*"+cnall[i][j]+"\t= "+(score*cnall[i][j])); |
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} |
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|
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} // next i |
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System.out.println("\t"); |
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} // next j |
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// report total matrix sumdelta |
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// if (VL>=1) { |
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System.out.println("GraphID "+graphid+" Central residue is "+restype+":"+resnr+":"+ressec); |
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System.out.println("backgroundDB"+backgrndDB+" \t maxRank : "+maxRank); |
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reportResults( o1, o2, printRank); |
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reportResults( o1, o2, printCNSize); |
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reportResults( o1, o2, printoCN1xoCN2); |
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reportResults( o1, o2, printCNdelta); |
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reportResults( o1, o2, printMatSize); |
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//} |
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reportResults( o1, o2, printCNSxdelta ); |
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reportResults( o1, o2, printCNSdMSxdelta ); |
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reportResults( o1, o2, printCorrect); |
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reportResults( o1, o2, printCordMSxdelta); |
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// Cleanup ... |
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mrsst.close(); |
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mstmt.close(); |
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|
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} catch (SQLException e) { |
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e.printStackTrace(); |
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System.err.println("SQLException: " + e.getMessage()); |
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System.err.println("SQLState: " + e.getSQLState()); |
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} // end try/catch |
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System.out.println("fin."); |
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} // end main |
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|
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|
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|
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public static void reportResults( int o1, int o2, int what2print) { |
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System.out.println("Printing "+what2print); |
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if (what2print==printRank) System.out.println("Overall resulting SumDeltaRank Matrix" ); |
| 309 |
if (what2print==printNbstring) System.out.println("Overall tested new nbhoodStrings" ); |
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if (what2print==printCNSize) System.out.println("Overall cnsize" ); |
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if (what2print==printCNSxdelta) System.out.println("Overall (cnsize*sumDeltaRank)" ); |
| 312 |
if (what2print==printMatSize) System.out.println( "Overall matsize[i][j]" ); |
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if (what2print==printCNSdMSxdelta) System.out.println( "Overall sumdelta[i][j]*cnall[i][j]/matsize[i][j]" ); |
| 314 |
if (what2print==printCorrect) System.out.println( "Overall correct[i][j]" ); |
| 315 |
if (what2print==printCordMSxdelta) System.out.println( "Overall correct[i][j]*cnall[i][j]/matsize[i][j]" ); |
| 316 |
if (what2print==printoCN1xoCN2) System.out.println( "Overall oCN1[i]*oCN2[j]" ); |
| 317 |
if (what2print==printCNdelta) System.out.println( "Overall (oCN1[i]*oCN2[j])-cnall[i][j]" ); |
| 318 |
|
| 319 |
// print headerline(s) |
| 320 |
System.out.println(rheadline[0]); |
| 321 |
System.out.println(rheadline[1]); |
| 322 |
System.out.println(rheadline[2]); |
| 323 |
System.out.println(rheadline[3]); |
| 324 |
System.out.println(rheadline[4]); |
| 325 |
for (int j=0; j<=o2; j++) { |
| 326 |
// print rsideline |
| 327 |
System.out.print( rsideline[j]+"\t"); |
| 328 |
for ( int i=0; i<=o1; i++) { |
| 329 |
if (what2print==printRank) System.out.print( sumdelta[i][j] ); |
| 330 |
if (what2print==printNbstring) System.out.print( newnbs[i][j] ); |
| 331 |
if (what2print==printCNSize) System.out.print( cnall[i][j] ); |
| 332 |
if (what2print==printCNSxdelta) System.out.print( sumdelta[i][j]*cnall[i][j] ); |
| 333 |
if (what2print==printMatSize) System.out.print( matsize[i][j] ); |
| 334 |
if (what2print==printCNSdMSxdelta) System.out.print( sumdelta[i][j]*cnall[i][j]/matsize[i][j] ); |
| 335 |
if (what2print==printCorrect) System.out.print( String.format("%.3f", correct[i][j]) ); |
| 336 |
if (what2print==printCordMSxdelta) System.out.print( String.format("%.3f", correct[i][j]*cnall[i][j]/matsize[i][j]) ); |
| 337 |
if (what2print==printoCN1xoCN2) System.out.print( oCN1[i]*oCN2[j]); |
| 338 |
if (what2print==printCNdelta) System.out.print( (oCN1[i]*oCN2[j])-cnall[i][j]); |
| 339 |
System.out.print("\t"); |
| 340 |
} // next i |
| 341 |
System.out.println(""); |
| 342 |
} // next j |
| 343 |
} // end of reportResults |
| 344 |
|
| 345 |
|
| 346 |
|
| 347 |
public static int scoreCurrentNbhood( int ixnum, int jxnum) { |
| 348 |
int ixcn=0, jxcn=0, n1=0, n2=0, ni, nj, i, j, j_num, j_shell, j_cnsize, sumdeltarank=0; |
| 349 |
String sql, j_res, j_sec, nbs, mymove, precol; |
| 350 |
boolean overx = false; |
| 351 |
lastCorr = 0.0; |
| 352 |
Statement stmt; |
| 353 |
ResultSet rsst; |
| 354 |
|
| 355 |
try { |
| 356 |
headline[0]="\t\t\t0"; |
| 357 |
headline[1]="\t\t\t-"; |
| 358 |
headline[2]="\t\t\t0"; |
| 359 |
headline[3]="\t\t\t-"; |
| 360 |
headline[4]="\t\t\tX"; |
| 361 |
|
| 362 |
// System.out.println("retrieving the entire nbhood (1st and 2nd shell)"); |
| 363 |
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;"; |
| 364 |
stmt = conn.createStatement(); |
| 365 |
rsst = stmt.executeQuery(sql); |
| 366 |
// counting shell2 |
| 367 |
n2=0; |
| 368 |
while (rsst.next()) { |
| 369 |
if ( rsst.getInt( 4)==1) { // count 1st shell entry |
| 370 |
n1++; |
| 371 |
// System.out.print("1#"+n1); |
| 372 |
headline[0]+="\t"+n1; |
| 373 |
headline[1]+="\t"+rsst.getString(2); // res |
| 374 |
headline[2]+="\t"+rsst.getInt(1); // resnum |
| 375 |
headline[3]+="\t"+rsst.getString(3); // SStype |
| 376 |
headline[4]+="\t("+((rsst.getInt(5))-1)+")"; // CNSize |
| 377 |
} // end if 2st shell |
| 378 |
if ( rsst.getInt( 4)==2) { // count 2nd shell entry |
| 379 |
n2++; |
| 380 |
// System.out.print("2#"+n2); |
| 381 |
} // end if 2nd shell |
| 382 |
// System.out.println(" :\t"+rsst.getInt( 1)+"\t"+rsst.getString( 2)+"\t"+rsst.getString( 3)+"\t"+rsst.getInt( 4)+"\t"+rsst.getInt( 5)); |
| 383 |
} // end while |
| 384 |
size1 = n1; |
| 385 |
size2 = n2; |
| 386 |
ixcn = n1; |
| 387 |
jxcn = n1; |
| 388 |
if (VL>=1) { |
| 389 |
System.out.println("|1st shell|="+size1+" \tx\t |2nd shell|="+size2); |
| 390 |
} |
| 391 |
headline[4]=headline[4].replace("X",("("+size1+")")); |
| 392 |
|
| 393 |
// n1 and n2 are known, initialise matrices accordingly. |
| 394 |
// nbhood, move, rank, entropy, freq, AUC etc. (evtl.+ degree(?)) |
| 395 |
rank = new int[(n1+1)][(n2+1)]; |
| 396 |
rank[0][0]=maxRank; |
| 397 |
total = new int[(n1+1)][(n2+1)]; |
| 398 |
entropy = new double[(n1+1)][(n2+1)]; |
| 399 |
freq = new double[(n1+1)][(n2+1)]; |
| 400 |
AUC = new double[(n1+1)][(n2+1)]; |
| 401 |
nbstring = new String[(n1+1)][(n2+1)]; |
| 402 |
moveset = new String[(n1+1)][(n2+1)]; |
| 403 |
sideline = new String[n2+1]; |
| 404 |
cn1 = new int[n1+1]; |
| 405 |
cn2 = new int[n2+1]; |
| 406 |
cnsize = new double[(n1+1)][(n2+1)]; |
| 407 |
|
| 408 |
for (j=0; j<=n2; j++) { // outer loop through all indirect contacts |
| 409 |
for (i=0; i<=n1; i++) { // inner loop through all direct contacts |
| 410 |
mymove = ""; |
| 411 |
overx = false; |
| 412 |
if (VL>=1) { |
| 413 |
System.out.print("("+i+","+j+")\t"); |
| 414 |
} |
| 415 |
ni = 0; |
| 416 |
nj = 0; |
| 417 |
sideline[0]="+0\tRnum:S("+n1+")"; |
| 418 |
cn1[0]=n1; |
| 419 |
cn2[0]=n1; |
| 420 |
nbs="%"; |
| 421 |
rsst.beforeFirst(); |
| 422 |
while (rsst.next()) { |
| 423 |
j_num = rsst.getInt(1); |
| 424 |
j_res = rsst.getString(2); |
| 425 |
j_sec = rsst.getString(3); |
| 426 |
j_shell = rsst.getInt(4); |
| 427 |
j_cnsize = rsst.getInt(5); |
| 428 |
|
| 429 |
// if edge exists between the dropped direct and the new (ind.)nbour then cnsize of dropped+1 |
| 430 |
|
| 431 |
if (j_num>resnr) { // we are over x |
| 432 |
if (!overx) { |
| 433 |
nbs+="x%"; |
| 434 |
overx=true; |
| 435 |
} // end if over x |
| 436 |
} // END IF J > X |
| 437 |
if (j_shell==1) { // a direct 1st shell neighbour |
| 438 |
ni++; |
| 439 |
if (ni!=i) {// if this is NOT the one direct nb 2B dropped |
| 440 |
nbs+=j_res.toUpperCase()+"%"; // it is included |
| 441 |
if ( j_num==jxnum && j==0) { // This is the direct nb dropped |
| 442 |
jxcn=j_cnsize; |
| 443 |
if (VL>=2) System.out.print("(j"+jxnum+":"+jxcn+")"); |
| 444 |
} |
| 445 |
} else { // this one IS dropped |
| 446 |
mymove += "(-"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")"; |
| 447 |
cn1[ni]=j_cnsize; |
| 448 |
} // end if ni!=i |
| 449 |
|
| 450 |
} else { // 2nd shell neighbour |
| 451 |
nj++; |
| 452 |
if (nj==j) { // this is the 2nd shell nb 2B included |
| 453 |
nbs+=j_res.toUpperCase()+"%"; |
| 454 |
mymove += "(+"+j_res+":"+j_num+":"+j_sec+"/"+j_cnsize+")"; |
| 455 |
if ( j_num==ixnum && i==0) { // This is the dropped direct nb, no 2b found in 2ns shell |
| 456 |
ixcn=j_cnsize; |
| 457 |
if (VL>=2) System.out.print("(i"+ixnum+":"+ixcn+")"); |
| 458 |
} |
| 459 |
cn2[nj] = j_cnsize; |
| 460 |
} // end if |
| 461 |
|
| 462 |
// // only once for building the sidelines |
| 463 |
if (j==0) { |
| 464 |
sideline[nj] = "+"+nj+"\t"+j_res+""+j_num+":"+j_sec+"("+j_cnsize+")"; |
| 465 |
// was here: cn2[nj] = j_cnsize; |
| 466 |
} // end if sideline |
| 467 |
} // end if 1st/2nd shell |
| 468 |
|
| 469 |
} // end while through the entire nbhood |
| 470 |
|
| 471 |
if (!overx) { // in case x is the very last we haven't seen it yet |
| 472 |
nbs+="x%"; // add it in the end |
| 473 |
overx=true; |
| 474 |
} // end if over x |
| 475 |
if (VL>=1) { |
| 476 |
System.out.print("("+nbs+")\t"); |
| 477 |
} |
| 478 |
nbstring[i][j] = nbs; |
| 479 |
moveset[i][j] = mymove; |
| 480 |
if (VL>=2) System.out.print(" "+mymove); |
| 481 |
precol = nbstring[i][0]; |
| 482 |
getEntropy( nbs, restype, precol); |
| 483 |
if (lastRank==0) lastRank = maxRank; |
| 484 |
rank[i][j] = lastRank; |
| 485 |
entropy[i][j] = lastEntropy; |
| 486 |
freq[i][j] = lastFreq; |
| 487 |
AUC[i][j] = lastAUC; |
| 488 |
total[i][j]= lastTotal; |
| 489 |
cnsize[i][j]=(double) ((double)cn1[i])/((double)cn2[j]); |
| 490 |
if (VL>=2) System.out.print("= "+cn1[i]+"/"+cn2[j]+"="+String.format("%.3f",cnsize[i][j])+"\t"); |
| 491 |
|
| 492 |
if (lastRank > 0) { |
| 493 |
sumdeltarank += ( (lastRank-rank[0][0]) ); |
| 494 |
lastCorr += ( (lastRank-rank[0][0])*cnsize[i][j] ); |
| 495 |
} else { |
| 496 |
sumdeltarank += ( (maxRank-rank[0][0]) ); |
| 497 |
lastCorr += ( (maxRank-rank[0][0])*cnsize[i][j] ); |
| 498 |
} // end if lastRank was defined |
| 499 |
|
| 500 |
if (VL>=2) System.out.print(""+lastRank+"\t"); |
| 501 |
} // close inner loop (i) |
| 502 |
if (VL>=1) { |
| 503 |
System.out.println("."); |
| 504 |
} else { |
| 505 |
System.out.print("."); |
| 506 |
} |
| 507 |
} // next outerloop (j) |
| 508 |
lastxcn=(ixcn*jxcn); |
| 509 |
if (VL>=1) { |
| 510 |
System.out.println("lastxcn=(ixcn*jxcn)=("+ixcn+"*"+jxcn+")="+lastxcn); |
| 511 |
} |
| 512 |
rsst.close(); |
| 513 |
stmt.close(); |
| 514 |
|
| 515 |
} catch (SQLException e) { |
| 516 |
e.printStackTrace(); |
| 517 |
System.err.println("SQLException: " + e.getMessage()); |
| 518 |
System.err.println("SQLState: " + e.getSQLState()); |
| 519 |
} // end try/catch |
| 520 |
// System.out.println("fin."); |
| 521 |
return sumdeltarank; |
| 522 |
} // end scoreCurrentNbhood |
| 523 |
|
| 524 |
public static boolean edgeExists( int u_num, int v_num) { |
| 525 |
int c=0; |
| 526 |
String sql; |
| 527 |
boolean found = false; |
| 528 |
Statement st; |
| 529 |
ResultSet rs; |
| 530 |
try { |
| 531 |
sql = "select count(*) from temp_shell where i_num="+u_num+" and j_num="+v_num+";"; |
| 532 |
st = conn.createStatement(); |
| 533 |
rs = st.executeQuery(sql); |
| 534 |
if (rs.next()) c = rs.getInt(1); |
| 535 |
found = (c>0); |
| 536 |
rs.close(); |
| 537 |
st.close(); |
| 538 |
} catch (SQLException e) { |
| 539 |
e.printStackTrace(); |
| 540 |
System.err.println("SQLException: " + e.getMessage()); |
| 541 |
System.err.println("SQLState: " + e.getSQLState()); |
| 542 |
} // end try/catch |
| 543 |
return found; |
| 544 |
} // end edgeExists( u_num, v_num) |
| 545 |
|
| 546 |
public static void reportMatrix( int what2print) { |
| 547 |
System.out.println("\nPrinting "+what2print); |
| 548 |
if (what2print==printRank) System.out.print("rank[i][j]" ); |
| 549 |
if (what2print==printTotal) System.out.print("total[i][j]" ); |
| 550 |
if (what2print==printEntropy) System.out.print("entropy[i][j]" ); |
| 551 |
if (what2print==printFreq ) System.out.print("freq[i][j]" ); |
| 552 |
if (what2print==printAUC) System.out.print("AUC[i][j]" ); |
| 553 |
if (what2print==printNbstring) System.out.print("nbstring[i][j]" ); |
| 554 |
if (what2print==printMoveset) System.out.print("moveset[i][j]" ); |
| 555 |
if (what2print==printdeltaRank) System.out.print("rank[i][j]-rank[0][0]" ); |
| 556 |
if (what2print==printCNSize) System.out.print("cnsize[i][j]" ); |
| 557 |
if (what2print==printCNSxdelta) System.out.print("cnsize[i][j]*(rank[i][j]-rank[0][0])" ); |
| 558 |
|
| 559 |
System.out.println("..."); |
| 560 |
// print headerline(s) |
| 561 |
System.out.println(headline[0]); |
| 562 |
System.out.println(headline[1]); |
| 563 |
System.out.println(headline[2]); |
| 564 |
System.out.println(headline[3]); |
| 565 |
System.out.println(headline[4]); |
| 566 |
for (int j=0; j<=size2; j++) { |
| 567 |
// print sideline |
| 568 |
System.out.print( sideline[j]+"\t"); |
| 569 |
for ( int i=0; i<=size1; i++) { |
| 570 |
if (what2print==printRank) System.out.print( rank[i][j] ); |
| 571 |
if (what2print==printTotal) System.out.print( total[i][j] ); |
| 572 |
if (what2print==printEntropy) System.out.print( entropy[i][j] ); |
| 573 |
if (what2print==printFreq ) System.out.print( freq[i][j] ); |
| 574 |
if (what2print==printAUC) System.out.print( AUC[i][j] ); |
| 575 |
if (what2print==printNbstring) System.out.print( nbstring[i][j] ); |
| 576 |
if (what2print==printMoveset) System.out.print( moveset[i][j] ); |
| 577 |
if (what2print==printdeltaRank) System.out.print( rank[i][j]-rank[0][0] ); |
| 578 |
if (what2print==printCNSize) System.out.print( String.format("%.3f",cnsize[i][j]) ); |
| 579 |
if (what2print==printCNSxdelta) System.out.print( String.format("%.3f", (cnsize[i][j]*(rank[i][j]-rank[0][0]))) ); |
| 580 |
System.out.print("\t"); |
| 581 |
} // next i |
| 582 |
System.out.println(""); |
| 583 |
} // next j |
| 584 |
} // end of report |
| 585 |
|
| 586 |
public static void getEntropy( String nbs, String centRes, String predec) { |
| 587 |
String sql, res, this_n, prec_n; |
| 588 |
Statement stmt; |
| 589 |
ResultSet rsst; |
| 590 |
double p, psum=0.0, logp, plogp, plogpsum=0.0; |
| 591 |
int counter=0, c=0, lastc=0; |
| 592 |
try { |
| 593 |
// Hashing first row tables comes first |
| 594 |
if (VL>=2) { |
| 595 |
System.out.println("getEntropy for "); |
| 596 |
System.out.println("nbs : "+nbs); |
| 597 |
System.out.println("centRes: "+centRes); |
| 598 |
System.out.println("predec : "+predec); |
| 599 |
} |
| 600 |
this_n = nbs.replace("%",""); |
| 601 |
prec_n = predec.replace("%",""); |
| 602 |
if (VL>=2) System.out.println("this_n: ["+this_n+"]"); |
| 603 |
if (VL>=2) System.out.println("prec_n: ["+prec_n+"]"); |
| 604 |
if (prec_n.equals(this_n)) { |
| 605 |
if (VL>=2) System.out.println("have to create db for this "+prec_n); |
| 606 |
sql = "create table IF NOT EXISTS nbhashtables."+prec_n+" as select res, n, k from single_model_node where n like '"+nbs+"';"; |
| 607 |
if (VL>=2) System.out.println(" >> "+sql); |
| 608 |
stmt = conn.createStatement(); |
| 609 |
stmt.executeUpdate( sql); |
| 610 |
stmt.close(); |
| 611 |
} else if (VL>=2) System.out.println("using preceding db of "+prec_n); |
| 612 |
|
| 613 |
// now we can safely derive the estimates from the hashtable |
| 614 |
sql = "select count(*) from nbhashtables."+prec_n+" where n like '"+nbs+"';"; |
| 615 |
if (VL>=2) System.out.println( sql); |
| 616 |
stmt = conn.createStatement(); |
| 617 |
rsst = stmt.executeQuery(sql); |
| 618 |
if (rsst.next()) lastTotal = rsst.getInt( 1); |
| 619 |
rsst.close(); |
| 620 |
stmt.close(); |
| 621 |
|
| 622 |
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;"; |
| 623 |
stmt = conn.createStatement(); |
| 624 |
rsst = stmt.executeQuery(sql); |
| 625 |
if (VL>=2) System.out.println("rank : res : total t : fraction p : log2(p) : -p*log2(p)"); |
| 626 |
int rank = 0; |
| 627 |
boolean seenCentRes = false; |
| 628 |
lastAUC = 0.0; |
| 629 |
lastRank = 0; |
| 630 |
lastFreq = 0.0; |
| 631 |
lastavgk = 0.0; |
| 632 |
lastdevk = 0.0; |
| 633 |
while (rsst.next()) { |
| 634 |
counter++; |
| 635 |
res = rsst.getString(1); // 1st column -- res |
| 636 |
c = rsst.getInt( 2); // 2nds column : count/residue |
| 637 |
p = rsst.getDouble(3); // 3rd: fraction p |
| 638 |
if (VL>=2) System.out.print(counter+"/"+rank+ " : " + res+" : "+c+ " : " + p); |
| 639 |
logp = Math.log(p)/Math.log(2.0); // to basis 2 for info in bits |
| 640 |
if (VL>=2) System.out.print(" : " + logp); |
| 641 |
plogp = -1.0 * p * logp; |
| 642 |
if (VL>=2) System.out.print(" : " + plogp); |
| 643 |
plogpsum += plogp; |
| 644 |
psum += p; |
| 645 |
|
| 646 |
if ((c == lastc) && (lastc>0)) { // tie |
| 647 |
if (VL>=2) System.out.print(" <-- TIE!"); |
| 648 |
lastRank = counter; |
| 649 |
} // end if |
| 650 |
|
| 651 |
if (res.equals(centRes)) { |
| 652 |
if (VL>=2) System.out.print(" <== " + centRes); |
| 653 |
seenCentRes = true; |
| 654 |
lastFreq = p; |
| 655 |
lastRank = counter; |
| 656 |
lastavgk = rsst.getDouble(4); |
| 657 |
lastdevk = rsst.getDouble(5); |
| 658 |
lastc = c; |
| 659 |
} |
| 660 |
if (seenCentRes) lastAUC += p; |
| 661 |
|
| 662 |
if (VL>=2) System.out.println(""); |
| 663 |
} |
| 664 |
if (VL>=2) System.out.println("Sum :"+lastTotal+" : "+psum+" : "+plogpsum); |
| 665 |
if (VL>=2) System.out.println("=> rank "+lastRank); |
| 666 |
rsst.close(); |
| 667 |
stmt.close(); |
| 668 |
lastEntropy = plogpsum; |
| 669 |
if (lastRank==0) lastRank = maxRank; |
| 670 |
} catch (SQLException e) { |
| 671 |
e.printStackTrace(); |
| 672 |
System.err.println("SQLException: " + e.getMessage()); |
| 673 |
System.err.println("SQLState: " + e.getSQLState()); |
| 674 |
} |
| 675 |
|
| 676 |
} // end of getEntropy |
| 677 |
|
| 678 |
} // end class |
