src/jalview/ws/jws1/Annotate3D.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.ws.jws1;
  22
  23 import jalview.datamodel.AlignmentI;
  24 import jalview.io.FileFormat;
  25 import jalview.io.FileParse;
  26 import jalview.io.FormatAdapter;
  27 import jalview.io.InputStreamParser;
  28 import jalview.util.MessageManager;
  29
  30 import java.io.BufferedReader;
  31 import java.io.FileReader;
  32 import java.io.IOException;
  33 import java.io.InputStreamReader;
  34 import java.io.Reader;
  35 import java.net.MalformedURLException;
  36 import java.net.URL;
  37 import java.net.URLEncoder;
  38 import java.util.Iterator;
  39
  40 public class Annotate3D
  41 {
  42   // protected BufferedReader in;
  43   // protected BufferedWriter out;
  44
  45   public Annotate3D()
  46   {
  47     System.out.println("Annotate3D");
  48     // try {
  49     // Create a URL for the desired page
  50     // String id = "1HR2";
  51     // URL url = new
  52     // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id);
  53     // in = new BufferedReader(new InputStreamReader(url.openStream()));
  54     // String str;
  55     // OutputStream out1 = null;
  56     // out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
  57     // while ((str = in.readLine()) != null) {
  58     // System.out.println(str);
  59     // out.write(str);
  60     // }
  61     // in.close();
  62     // out.close();
  63     // } catch (MalformedURLException e) {
  64     // } catch (IOException e) {
  65     // }
  66   }
  67
  68   public AlignmentI getRNAMLFor(final FileParse source) throws IOException
  69   {
  70     try
  71     {
  72       StringBuffer sb = new StringBuffer();
  73
  74       Reader fpr = source.getReader();
  75       int p = 0;
  76       char[] cbuff = new char[2048];
  77       while ((p = fpr.read(cbuff)) > 0)
  78       {
  79         for (int i = 0; i < p; i++)
  80         {
  81           sb.append(cbuff[i]);
  82         }
  83       }
  84       Iterator<Reader> r = jalview.ext.paradise.Annotate3D
  85               .getRNAMLForPDBFileAsString(sb.toString());
  86       AlignmentI al = null;
  87       while (r.hasNext())
  88       {
  89         FileParse fp = new InputStreamParser(r.next(), source.getDataName());
  90         AlignmentI nal = new FormatAdapter().readFromFile(fp,
  91                 FileFormat.Rnaml);
  92         if (al == null)
  93         {
  94           al = nal;
  95         }
  96         else
  97         {
  98           al.append(nal);
  99         }
 100       }
 101       return al;
 102     } catch (Throwable x)
 103     {
 104       if (x instanceof IOException)
 105       {
 106         throw ((IOException) x);
 107       }
 108       else
 109       {
 110         throw new IOException(
 111                 MessageManager
 112                         .getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
 113                 x);
 114       }
 115     }
 116   }
 117
 118   public Annotate3D(String path) throws InterruptedException
 119   {
 120     System.out.println("Annotate3D");
 121     try
 122     {
 123       // //URL url = new
 124       // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
 125       // System.out.println("Step1");
 126       // FileReader r = new FileReader(inFile);
 127       // BufferedReader in = new BufferedReader(r);
 128       // StringBuffer content = new StringBuffer();
 129       // System.out.println("Step2");
 130       // while(in.readLine()!=null){
 131       // content.append(in.readLine());
 132       // //System.out.println("Step3"+in.readLine());
 133       // }
 134       //
 135       // String data = URLEncoder.encode("data", "UTF-8") + "=" +
 136       // URLEncoder.encode(content.toString(), "UTF-8");
 137       // for (int i=0;i<data.length();i++)
 138       // {
 139       // System.out.print(data.charAt(i));
 140       // }
 141
 142       // String data = "width=50&height=100";
 143
 144       // // Send the request
 145       // FileReader r = new FileReader(path);
 146       // BufferedReader in = new BufferedReader(r);
 147       // StringBuffer content = new StringBuffer();
 148       // System.out.println("Step1");
 149       // while(in.readLine()!=null){
 150       // content.append(in.readLine());
 151       //
 152       // }
 153       // System.out.println("Step2");
 154       // String data = URLEncoder.encode("data", "UTF-8") + "=" +
 155       // URLEncoder.encode(content.toString(), "UTF-8");
 156       // System.out.println("Step2");
 157       // URL url = new
 158       // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
 159       // DataInputStream is = new DataInputStream(url.openStream());
 160       // String str;
 161       // while ((str = is.readLine()) != null) {
 162       // System.out.println(str);
 163       // //out.write(str);
 164       // }
 165       FileReader r = new FileReader(path);
 166       BufferedReader in = new BufferedReader(r);
 167       String content = "";
 168       String str;
 169
 170       while ((str = in.readLine()) != null)
 171       {
 172         // System.out.println(str);
 173
 174         content = content + str;
 175       }
 176       System.out.println("pdbfile=" + content.toString());
 177       System.out.println("capacité=" + content.length());
 178       String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
 179       System.out.println("param=" + paramfile);
 180       URL url = new URL(
 181               "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
 182                       + content);
 183       BufferedReader is = new BufferedReader(new InputStreamReader(
 184               url.openStream()));
 185       String str4;
 186       while ((str4 = is.readLine()) != null)
 187       {
 188         System.out.println(str4);
 189         // out.write(str);
 190       }
 191       in.close();
 192       is.close();
 193
 194       // HttpURLConnection connection = (HttpURLConnection)url.openConnection();
 195       // connection.setRequestMethod("POST" );
 196       // connection.setRequestProperty("data", path );
 197       // //connection.setRequestProperty("nomDuChamp2", "valeurDuChamp2" );
 198       // BufferedReader input = new BufferedReader(new
 199       // InputStreamReader(connection.getInputStream()));
 200       // //DataInputStream input = new
 201       // DataInputStream(connection.getInputStream());
 202       // String c;
 203       // while((c=input.readLine())!=null){
 204       // System.out.print(c);
 205       // }
 206       // input.close();
 207       // BufferedReader in1 = new BufferedReader(is);
 208
 209       // OutputStream out1 = null;
 210       // System.out.println("Step3");
 211       // BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1,
 212       // "temp.rnaml"));
 213       //
 214       // in.close();
 215       // out.close();
 216
 217       // return;
 218
 219       // System.out.println(data.length());
 220       // System.out.println("step2");
 221       // URL url = new
 222       // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
 223       // System.out.println("step3");
 224       // URLConnection conn = url.openConnection();
 225       // conn.setDoOutput(true);
 226       // OutputStreamWriter writer = new
 227       // OutputStreamWriter(conn.getOutputStream());
 228
 229       // write parameters
 230       // writer.write(data);
 231       // writer.flush();
 232
 233       // Get the response
 234       // StringBuffer answer = new StringBuffer();
 235       // //BufferedReader reader = new BufferedReader(new
 236       // InputStreamReader(conn.getInputStream()));
 237       // //String line;
 238       // while ((line = reader.readLine()) != null) {
 239       // answer.append(line);
 240       // System.out.println(line);
 241       // }
 242       // writer.close();
 243       // reader.close();
 244
 245       // Output the response
 246
 247     } catch (MalformedURLException ex)
 248     {
 249       ex.printStackTrace();
 250     } catch (IOException ex)
 251     {
 252       ex.printStackTrace();
 253     }
 254   }
 255
 256   // in = new BufferedReader(new InputStreamReader(url.openStream()));
 257
 258   // String str;
 259
 260   // out = new FileOutputStream("temp.rnaml");
 261   // out = new BufferedWriter(new FileWriter("temp.rnaml"));
 262
 263   // while ((str = in.readLine()) != null) {
 264   // System.out.println(str);
 265   // out.write(str);
 266   // System.out.println(str);
 267   // in.close();
 268
 269   // out.close();
 270   // } catch (MalformedURLException e) {
 271   // } catch (IOException e) {
 272   // }
 273   //
 274   // }
 275
 276   // public BufferedWriter getReader()
 277   // {
 278   // System.out.println("The buffer");
 279
 280   // return out;
 281
 282   // }
 283
 284 }