src/jalview/ws/jws1/Annotate3D.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18  package jalview.ws.jws1;
  19
  20 import java.io.BufferedInputStream;
  21 import java.io.BufferedReader;
  22 import java.io.BufferedWriter;
  23 import java.io.DataInputStream;
  24 import java.io.File;
  25 import java.io.FileOutputStream;
  26 import java.io.FileReader;
  27 import java.io.FileWriter;
  28 import java.io.IOException;
  29 import java.io.InputStream;
  30 import java.io.InputStreamReader;
  31 import java.io.OutputStream;
  32 import java.io.OutputStreamWriter;
  33 import java.io.Reader;
  34 import java.io.StringWriter;
  35 import java.net.HttpURLConnection;
  36 import java.net.MalformedURLException;
  37 import java.net.URL;
  38 import java.net.URLConnection;
  39
  40 import java.net.URLEncoder;
  41
  42
  43
  44 public class Annotate3D {
  45         //protected BufferedReader in;
  46         //protected BufferedWriter out;
  47
  48         public Annotate3D()
  49         {
  50                 System.out.println("Annotate3D");
  51                 //try {
  52                      // Create a URL for the desired page
  53                      //String id = "1HR2";
  54                      //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id);
  55                      //in = new BufferedReader(new InputStreamReader(url.openStream()));
  56                      //String str;
  57                      //OutputStream out1 = null;
  58                      //out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
  59                      //while ((str = in.readLine()) != null) {
  60                      //System.out.println(str);
  61                      //out.write(str);
  62                      //}
  63                      //in.close();
  64                      //out.close();
  65                      //} catch (MalformedURLException e) {
  66                      //} catch (IOException e) {
  67                      //}
  68         }
  69
  70         public Annotate3D(String path) throws InterruptedException{
  71                 System.out.println("Annotate3D");
  72                 try {
  73 //                  //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
  74 //                      System.out.println("Step1");
  75 //                  FileReader r = new FileReader(inFile);
  76 //                  BufferedReader in = new BufferedReader(r);
  77 //                  StringBuffer content = new StringBuffer();
  78 //                  System.out.println("Step2");
  79 //                      while(in.readLine()!=null){
  80 //                              content.append(in.readLine());
  81 //                              //System.out.println("Step3"+in.readLine());
  82 //                      }
  83 //
  84 //                      String data = URLEncoder.encode("data", "UTF-8") + "=" + URLEncoder.encode(content.toString(), "UTF-8");
  85 //                      for (int i=0;i<data.length();i++)
  86 //                      {
  87 //                              System.out.print(data.charAt(i));
  88 //                      }
  89
  90                         //String data = "width=50&height=100";
  91
  92
  93 //                  // Send the request
  94 //                              FileReader r = new FileReader(path);
  95 //                              BufferedReader in = new BufferedReader(r);
  96 //                              StringBuffer content = new StringBuffer();
  97 //                              System.out.println("Step1");
  98 //                              while(in.readLine()!=null){
  99 //                                      content.append(in.readLine());
 100 //
 101 //                              }
 102 //                              System.out.println("Step2");
 103 //                              String data = URLEncoder.encode("data", "UTF-8") + "=" + URLEncoder.encode(content.toString(), "UTF-8");
 104 //                              System.out.println("Step2");
 105 //                              URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
 106 //                              DataInputStream is = new DataInputStream(url.openStream());
 107 //                              String str;
 108 //                              while ((str = is.readLine()) != null) {
 109 //                                   System.out.println(str);
 110 //                                   //out.write(str);
 111 //                                   }
 112                         FileReader r = new FileReader(path);
 113                         BufferedReader in = new BufferedReader(r);
 114                         String content ="";
 115                         String str;
 116
 117                         while((str=in.readLine())!=null){
 118                                 //System.out.println(str);
 119
 120                                 content=content+str;
 121                         }
 122                         System.out.println("pdbfile="+content.toString());
 123                         System.out.println("capacité="+content.length());
 124                         String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
 125                         System.out.println("param="+paramfile);
 126                             URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+content);
 127                             BufferedReader is = new BufferedReader(new InputStreamReader(url.openStream()));
 128                                 String str4;
 129                                 while ((str4 = is.readLine()) != null) {
 130                                      System.out.println(str4);
 131                                      //out.write(str);
 132                                      }
 133                             in.close();
 134                             is.close();
 135
 136 //                          HttpURLConnection connection = (HttpURLConnection)url.openConnection();
 137 //                          connection.setRequestMethod("POST" );
 138 //                          connection.setRequestProperty("data", path );
 139 //                          //connection.setRequestProperty("nomDuChamp2", "valeurDuChamp2" );
 140 //                          BufferedReader input = new BufferedReader(new InputStreamReader(connection.getInputStream()));
 141 //                          //DataInputStream input = new DataInputStream(connection.getInputStream());
 142 //                          String c;
 143 //                          while((c=input.readLine())!=null){
 144 //                           System.out.print(c);
 145 //                          }
 146 //                          input.close();
 147                                 //BufferedReader in1 = new BufferedReader(is);
 148
 149 //                           OutputStream out1 = null;
 150 //                           System.out.println("Step3");
 151 //                           BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
 152 //
 153 //                           in.close();
 154 //                           out.close();
 155
 156
 157                                 //return;
 158
 159                                 //System.out.println(data.length());
 160                                 //System.out.println("step2");
 161                     //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
 162                     //System.out.println("step3");
 163                     //URLConnection conn = url.openConnection();
 164                     //conn.setDoOutput(true);
 165                     //OutputStreamWriter writer = new OutputStreamWriter(conn.getOutputStream());
 166
 167                     //write parameters
 168                     //writer.write(data);
 169                    // writer.flush();
 170
 171                     // Get the response
 172 //                  StringBuffer answer = new StringBuffer();
 173 //                  //BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream()));
 174 //                  //String line;
 175 //                  while ((line = reader.readLine()) != null) {
 176 //                      answer.append(line);
 177 //                      System.out.println(line);
 178 //                  }
 179 //                  writer.close();
 180 //                  reader.close();
 181
 182                     //Output the response
 183
 184
 185                 } catch (MalformedURLException ex) {
 186                     ex.printStackTrace();
 187                 } catch (IOException ex) {
 188                     ex.printStackTrace();
 189                 }
 190         }
 191
 192                         //in = new BufferedReader(new InputStreamReader(url.openStream()));
 193
 194                      //String str;
 195
 196
 197                      //out = new FileOutputStream("temp.rnaml");
 198                      //out = new BufferedWriter(new FileWriter("temp.rnaml"));
 199
 200                      //while ((str = in.readLine()) != null) {
 201                      //System.out.println(str);
 202                      //out.write(str);
 203                      //System.out.println(str);
 204 //                      in.close();
 205
 206
 207                      //out.close();
 208 //                   } catch (MalformedURLException e) {
 209 //                   } catch (IOException e) {
 210 //                   }
 211 //
 212 //      }
 213
 214         //public BufferedWriter getReader()
 215         //{
 216                         //System.out.println("The buffer");
 217
 218                         //return out;
 219
 220
 221         //}
 222
 223 }