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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 rewriteNBHood_parallel { |
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|
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/** |
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* reriting the nbhoodstring such that BB dominated nbs are represented by SSType |
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* |
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* @author lappe |
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*/ |
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|
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static String user = "lappe" ; // change user name!! |
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static MySQLConnection conn; |
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static int k=0, k_sc=0, k_bb=0; |
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static String process, cid, res, sectype, fullnbs; |
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static int graph_id=0, node_id=0, resnr=0; |
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|
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|
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public static void main(String[] args) throws SQLException { |
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String nbhood = "", isql; |
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Statement istmt; |
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|
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System.out.println("rewriteNBHood"); |
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if (args.length!=1){ |
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System.err.println("The processname has to be given .... i.e. tla01"); |
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System.exit(1); |
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} |
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process = args[0]; |
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System.out.println("processID="+process); |
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|
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try { |
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|
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conn = new MySQLConnection("white",user,"nieve","pdb_reps_graph_4_2"); |
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node_id = getNextNode(); |
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while (node_id>0) { |
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System.out.print(graph_id); // graph |
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System.out.print("\t"+node_id); // node |
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System.out.print("\t"+cid); // cid |
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System.out.print("\t"+resnr); // num |
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System.out.print("\t"+res); // res |
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System.out.print("\t"+sectype); // sstype |
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fullnbs = ""; |
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nbhood= getSSNbHoodString( graph_id, node_id, resnr); |
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|
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System.out.println("\t"+nbhood+"\t"+fullnbs); |
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istmt = conn.createStatement(); |
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isql = "update single_model_cofull set k="+k+", k_bb="+k_bb+", k_sc="+k_sc+", n=\'"+nbhood+"\', nf=\'"+fullnbs+"\'" + |
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" where ( graph_id="+graph_id+" and node_id="+node_id+");"; |
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// System.out.println("i>"+isql); |
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istmt.executeUpdate( isql); |
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|
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node_id = getNextNode(); |
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} // end while we have another node |
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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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} |
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|
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System.out.println("fin."); |
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} |
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|
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public static int getNextNode() { |
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String sql; |
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Statement stmt; |
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ResultSet rsst; |
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|
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graph_id=0; |
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node_id =0; |
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try { |
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sql = "update single_model_cofull set n=\'>"+process+"\' where length(n)=0 limit 1;"; |
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stmt = conn.createStatement(); |
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stmt.executeUpdate(sql); |
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sql = "select graph_id, node_id, cid, num, res, sstype from single_model_cofull where n=\'>"+process+"\';"; |
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// System.out.println("node> "+ sql); |
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stmt = conn.createStatement(); |
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rsst = stmt.executeQuery(sql); |
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|
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if (rsst.next()) { |
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// System.out.print(">"); |
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graph_id=rsst.getInt(1); |
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node_id =rsst.getInt(2); |
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cid =rsst.getString(3); |
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resnr =rsst.getInt(4); |
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res =rsst.getString(5); |
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sectype =rsst.getString(6); |
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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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} |
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return node_id; |
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} // end of getnbhoodstring |
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|
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|
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public static String getSSNbHoodString( int gid, int nid, int num ) { |
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int j_num, j_bb, j_sc; |
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boolean overx=false; |
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String sql, nbs="", j_res, j_ss, nextnb; |
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Statement stmt; |
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ResultSet rsst; |
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|
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try { |
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k=0; k_sc=0; k_bb=0; |
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sql = "select j_num, j_res, j_sstype, BB, SC from chain_edge where graph_id="+gid+" and i_node_id="+nid+" order by j_num;"; |
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stmt = conn.createStatement(); |
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rsst = stmt.executeQuery(sql); |
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fullnbs=""; |
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while (rsst.next()) { |
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j_num = rsst.getInt(1); |
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j_res = rsst.getString(2); |
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j_ss = rsst.getString(3); |
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j_bb = rsst.getInt(4); |
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j_sc = rsst.getInt(5); |
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nextnb="?"; |
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if (!overx && j_num>num) { |
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overx=true; |
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nbs+="x"; |
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fullnbs+="x"; |
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} |
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if ( (j_bb>j_sc) ) { // bb dominated -> only symbol for sstype |
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k_bb++; |
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nextnb="o"; // for "other" |
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if (j_ss.equals("H")) nextnb="z"; // Helix |
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if (j_ss.equals("S")) nextnb="b"; // beta strand |
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} else { // sc dominated contact |
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k_sc++; |
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nextnb=j_res; |
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} // end if bb dominated |
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nbs+= nextnb; |
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fullnbs+= j_res; |
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k++; |
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// System.out.print( nextnb); |
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} |
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rsst.close(); |
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stmt.close(); |
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if (!overx) { |
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nbs+="x"; // add if last in string == not seen yet |
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fullnbs+="x"; |
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} |
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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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} |
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return nbs; |
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} // end of getnbhoodstring |
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} |
