src/jalview/ws/jws1/Annotate3D.java

   1 package jalview.ws.jws1;
   2
   3 import java.io.BufferedInputStream;
   4 import java.io.BufferedReader;
   5 import java.io.BufferedWriter;
   6 import java.io.DataInputStream;
   7 import java.io.File;
   8 import java.io.FileOutputStream;
   9 import java.io.FileReader;
  10 import java.io.FileWriter;
  11 import java.io.IOException;
  12 import java.io.InputStream;
  13 import java.io.InputStreamReader;
  14 import java.io.OutputStream;
  15 import java.io.OutputStreamWriter;
  16 import java.io.Reader;
  17 import java.io.StringWriter;
  18 import java.net.HttpURLConnection;
  19 import java.net.MalformedURLException;
  20 import java.net.URL;
  21 import java.net.URLConnection;
  22
  23 import java.net.URLEncoder;
  24
  25
  26
  27 public class Annotate3D {
  28         //protected BufferedReader in;
  29         //protected BufferedWriter out;
  30
  31         public Annotate3D()
  32         {
  33                 System.out.println("Annotate3D");
  34                 //try {
  35                      // Create a URL for the desired page
  36                      //String id = "1HR2";
  37                      //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id);
  38                      //in = new BufferedReader(new InputStreamReader(url.openStream()));
  39                      //String str;
  40                      //OutputStream out1 = null;
  41                      //out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
  42                      //while ((str = in.readLine()) != null) {
  43                      //System.out.println(str);
  44                      //out.write(str);
  45                      //}
  46                      //in.close();
  47                      //out.close();
  48                      //} catch (MalformedURLException e) {
  49                      //} catch (IOException e) {
  50                      //}
  51         }
  52
  53         public Annotate3D(String path) throws InterruptedException{
  54                 System.out.println("Annotate3D");
  55                 try {
  56 //                  //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
  57 //                      System.out.println("Step1");
  58 //                  FileReader r = new FileReader(inFile);
  59 //                  BufferedReader in = new BufferedReader(r);
  60 //                  StringBuffer content = new StringBuffer();
  61 //                  System.out.println("Step2");
  62 //                      while(in.readLine()!=null){
  63 //                              content.append(in.readLine());
  64 //                              //System.out.println("Step3"+in.readLine());
  65 //                      }
  66 //
  67 //                      String data = URLEncoder.encode("data", "UTF-8") + "=" + URLEncoder.encode(content.toString(), "UTF-8");
  68 //                      for (int i=0;i<data.length();i++)
  69 //                      {
  70 //                              System.out.print(data.charAt(i));
  71 //                      }
  72
  73                         //String data = "width=50&height=100";
  74
  75
  76 //                  // Send the request
  77 //                              FileReader r = new FileReader(path);
  78 //                              BufferedReader in = new BufferedReader(r);
  79 //                              StringBuffer content = new StringBuffer();
  80 //                              System.out.println("Step1");
  81 //                              while(in.readLine()!=null){
  82 //                                      content.append(in.readLine());
  83 //
  84 //                              }
  85 //                              System.out.println("Step2");
  86 //                              String data = URLEncoder.encode("data", "UTF-8") + "=" + URLEncoder.encode(content.toString(), "UTF-8");
  87 //                              System.out.println("Step2");
  88 //                              URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
  89 //                              DataInputStream is = new DataInputStream(url.openStream());
  90 //                              String str;
  91 //                              while ((str = is.readLine()) != null) {
  92 //                                   System.out.println(str);
  93 //                                   //out.write(str);
  94 //                                   }
  95                         FileReader r = new FileReader(path);
  96                         BufferedReader in = new BufferedReader(r);
  97                         String content ="";
  98                         String str;
  99
 100                         while((str=in.readLine())!=null){
 101                                 //System.out.println(str);
 102
 103                                 content=content+str;
 104                         }
 105                         System.out.println("pdbfile="+content.toString());
 106                         System.out.println("capacité="+content.length());
 107                         String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
 108                         System.out.println("param="+paramfile);
 109                             URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+content);
 110                             BufferedReader is = new BufferedReader(new InputStreamReader(url.openStream()));
 111                                 String str4;
 112                                 while ((str4 = is.readLine()) != null) {
 113                                      System.out.println(str4);
 114                                      //out.write(str);
 115                                      }
 116                             in.close();
 117                             is.close();
 118
 119 //                          HttpURLConnection connection = (HttpURLConnection)url.openConnection();
 120 //                          connection.setRequestMethod("POST" );
 121 //                          connection.setRequestProperty("data", path );
 122 //                          //connection.setRequestProperty("nomDuChamp2", "valeurDuChamp2" );
 123 //                          BufferedReader input = new BufferedReader(new InputStreamReader(connection.getInputStream()));
 124 //                          //DataInputStream input = new DataInputStream(connection.getInputStream());
 125 //                          String c;
 126 //                          while((c=input.readLine())!=null){
 127 //                           System.out.print(c);
 128 //                          }
 129 //                          input.close();
 130                                 //BufferedReader in1 = new BufferedReader(is);
 131
 132 //                           OutputStream out1 = null;
 133 //                           System.out.println("Step3");
 134 //                           BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
 135 //
 136 //                           in.close();
 137 //                           out.close();
 138
 139
 140                                 //return;
 141
 142                                 //System.out.println(data.length());
 143                                 //System.out.println("step2");
 144                     //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
 145                     //System.out.println("step3");
 146                     //URLConnection conn = url.openConnection();
 147                     //conn.setDoOutput(true);
 148                     //OutputStreamWriter writer = new OutputStreamWriter(conn.getOutputStream());
 149
 150                     //write parameters
 151                     //writer.write(data);
 152                    // writer.flush();
 153
 154                     // Get the response
 155 //                  StringBuffer answer = new StringBuffer();
 156 //                  //BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream()));
 157 //                  //String line;
 158 //                  while ((line = reader.readLine()) != null) {
 159 //                      answer.append(line);
 160 //                      System.out.println(line);
 161 //                  }
 162 //                  writer.close();
 163 //                  reader.close();
 164
 165                     //Output the response
 166
 167
 168                 } catch (MalformedURLException ex) {
 169                     ex.printStackTrace();
 170                 } catch (IOException ex) {
 171                     ex.printStackTrace();
 172                 }
 173         }
 174
 175                         //in = new BufferedReader(new InputStreamReader(url.openStream()));
 176
 177                      //String str;
 178
 179
 180                      //out = new FileOutputStream("temp.rnaml");
 181                      //out = new BufferedWriter(new FileWriter("temp.rnaml"));
 182
 183                      //while ((str = in.readLine()) != null) {
 184                      //System.out.println(str);
 185                      //out.write(str);
 186                      //System.out.println(str);
 187 //                      in.close();
 188
 189
 190                      //out.close();
 191 //                   } catch (MalformedURLException e) {
 192 //                   } catch (IOException e) {
 193 //                   }
 194 //
 195 //      }
 196
 197         //public BufferedWriter getReader()
 198         //{
 199                         //System.out.println("The buffer");
 200
 201                         //return out;
 202
 203
 204         //}
 205
 206 }