formatting
authorjprocter <jprocter@compbio.dundee.ac.uk>
Sat, 17 Nov 2012 21:10:36 +0000 (21:10 +0000)
committerjprocter <jprocter@compbio.dundee.ac.uk>
Sat, 17 Nov 2012 21:10:36 +0000 (21:10 +0000)
src/jalview/ws/jws1/Annotate3D.java

index 5457c3a..9f5ad19 100644 (file)
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
- package jalview.ws.jws1;
+package jalview.ws.jws1;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.InputStreamParser;
 
-import java.io.BufferedInputStream;
 import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.DataInputStream;
-import java.io.File;
-import java.io.FileOutputStream;
 import java.io.FileReader;
-import java.io.FileWriter;
 import java.io.IOException;
-import java.io.InputStream;
 import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
 import java.io.Reader;
-import java.io.StringWriter;
-import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.net.URLConnection;
-
 import java.net.URLEncoder;
 
+public class Annotate3D
+{
+  // protected BufferedReader in;
+  // protected BufferedWriter out;
+
+  public Annotate3D()
+  {
+    System.out.println("Annotate3D");
+    // try {
+    // Create a URL for the desired page
+    // String id = "1HR2";
+    // URL url = new
+    // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id);
+    // in = new BufferedReader(new InputStreamReader(url.openStream()));
+    // String str;
+    // OutputStream out1 = null;
+    // out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
+    // while ((str = in.readLine()) != null) {
+    // System.out.println(str);
+    // out.write(str);
+    // }
+    // in.close();
+    // out.close();
+    // } catch (MalformedURLException e) {
+    // } catch (IOException e) {
+    // }
+  }
+  public Annotate3D(String path) throws InterruptedException
+  {
+    System.out.println("Annotate3D");
+    try
+    {
+      // //URL url = new
+      // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
+      // System.out.println("Step1");
+      // FileReader r = new FileReader(inFile);
+      // BufferedReader in = new BufferedReader(r);
+      // StringBuffer content = new StringBuffer();
+      // System.out.println("Step2");
+      // while(in.readLine()!=null){
+      // content.append(in.readLine());
+      // //System.out.println("Step3"+in.readLine());
+      // }
+      //
+      // String data = URLEncoder.encode("data", "UTF-8") + "=" +
+      // URLEncoder.encode(content.toString(), "UTF-8");
+      // for (int i=0;i<data.length();i++)
+      // {
+      // System.out.print(data.charAt(i));
+      // }
+
+      // String data = "width=50&height=100";
+
+      // // Send the request
+      // FileReader r = new FileReader(path);
+      // BufferedReader in = new BufferedReader(r);
+      // StringBuffer content = new StringBuffer();
+      // System.out.println("Step1");
+      // while(in.readLine()!=null){
+      // content.append(in.readLine());
+      //
+      // }
+      // System.out.println("Step2");
+      // String data = URLEncoder.encode("data", "UTF-8") + "=" +
+      // URLEncoder.encode(content.toString(), "UTF-8");
+      // System.out.println("Step2");
+      // URL url = new
+      // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
+      // DataInputStream is = new DataInputStream(url.openStream());
+      // String str;
+      // while ((str = is.readLine()) != null) {
+      // System.out.println(str);
+      // //out.write(str);
+      // }
+      FileReader r = new FileReader(path);
+      BufferedReader in = new BufferedReader(r);
+      String content = "";
+      String str;
+
+      while ((str = in.readLine()) != null)
+      {
+        // System.out.println(str);
+
+        content = content + str;
+      }
+      System.out.println("pdbfile=" + content.toString());
+      System.out.println("capacité=" + content.length());
+      String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
+      System.out.println("param=" + paramfile);
+      URL url = new URL(
+              "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
+                      + content);
+      BufferedReader is = new BufferedReader(new InputStreamReader(
+              url.openStream()));
+      String str4;
+      while ((str4 = is.readLine()) != null)
+      {
+        System.out.println(str4);
+        // out.write(str);
+      }
+      in.close();
+      is.close();
+
+      // HttpURLConnection connection = (HttpURLConnection)url.openConnection();
+      // connection.setRequestMethod("POST" );
+      // connection.setRequestProperty("data", path );
+      // //connection.setRequestProperty("nomDuChamp2", "valeurDuChamp2" );
+      // BufferedReader input = new BufferedReader(new
+      // InputStreamReader(connection.getInputStream()));
+      // //DataInputStream input = new
+      // DataInputStream(connection.getInputStream());
+      // String c;
+      // while((c=input.readLine())!=null){
+      // System.out.print(c);
+      // }
+      // input.close();
+      // BufferedReader in1 = new BufferedReader(is);
+
+      // OutputStream out1 = null;
+      // System.out.println("Step3");
+      // BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1,
+      // "temp.rnaml"));
+      //
+      // in.close();
+      // out.close();
+
+      // return;
+
+      // System.out.println(data.length());
+      // System.out.println("step2");
+      // URL url = new
+      // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
+      // System.out.println("step3");
+      // URLConnection conn = url.openConnection();
+      // conn.setDoOutput(true);
+      // OutputStreamWriter writer = new
+      // OutputStreamWriter(conn.getOutputStream());
+
+      // write parameters
+      // writer.write(data);
+      // writer.flush();
+
+      // Get the response
+      // StringBuffer answer = new StringBuffer();
+      // //BufferedReader reader = new BufferedReader(new
+      // InputStreamReader(conn.getInputStream()));
+      // //String line;
+      // while ((line = reader.readLine()) != null) {
+      // answer.append(line);
+      // System.out.println(line);
+      // }
+      // writer.close();
+      // reader.close();
+
+      // Output the response
+
+    } catch (MalformedURLException ex)
+    {
+      ex.printStackTrace();
+    } catch (IOException ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  // in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+  // String str;
+
+  // out = new FileOutputStream("temp.rnaml");
+  // out = new BufferedWriter(new FileWriter("temp.rnaml"));
+
+  // while ((str = in.readLine()) != null) {
+  // System.out.println(str);
+  // out.write(str);
+  // System.out.println(str);
+  // in.close();
+
+  // out.close();
+  // } catch (MalformedURLException e) {
+  // } catch (IOException e) {
+  // }
+  //
+  // }
+
+  // public BufferedWriter getReader()
+  // {
+  // System.out.println("The buffer");
 
+  // return out;
 
-public class Annotate3D {
-       //protected BufferedReader in;
-       //protected BufferedWriter out;
-       
-       public Annotate3D()
-       {
-               System.out.println("Annotate3D");
-               //try {
-                    // Create a URL for the desired page
-                    //String id = "1HR2";
-                    //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id);
-                    //in = new BufferedReader(new InputStreamReader(url.openStream()));
-                    //String str;
-                    //OutputStream out1 = null;
-                    //out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
-                    //while ((str = in.readLine()) != null) {
-                    //System.out.println(str);
-                    //out.write(str);
-                    //}
-                    //in.close();
-                    //out.close();
-                    //} catch (MalformedURLException e) {
-                    //} catch (IOException e) {
-                    //}
-       }
-       
-       public Annotate3D(String path) throws InterruptedException{
-               System.out.println("Annotate3D");
-               try {
-//                 //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
-//                     System.out.println("Step1");
-//                 FileReader r = new FileReader(inFile);
-//                 BufferedReader in = new BufferedReader(r);
-//                 StringBuffer content = new StringBuffer();
-//                 System.out.println("Step2");
-//                     while(in.readLine()!=null){
-//                             content.append(in.readLine());
-//                             //System.out.println("Step3"+in.readLine());
-//                     }
-//                     
-//                     String data = URLEncoder.encode("data", "UTF-8") + "=" + URLEncoder.encode(content.toString(), "UTF-8");
-//                     for (int i=0;i<data.length();i++)
-//                     {
-//                             System.out.print(data.charAt(i));
-//                     }
-                       
-                       //String data = "width=50&height=100";
-              
-                   
-//                 // Send the request
-//                             FileReader r = new FileReader(path);
-//                             BufferedReader in = new BufferedReader(r);
-//                             StringBuffer content = new StringBuffer();
-//                             System.out.println("Step1");
-//                             while(in.readLine()!=null){
-//                                     content.append(in.readLine());
-//                                     
-//                             }
-//                             System.out.println("Step2");
-//                             String data = URLEncoder.encode("data", "UTF-8") + "=" + URLEncoder.encode(content.toString(), "UTF-8");
-//                             System.out.println("Step2");
-//                             URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
-//                             DataInputStream is = new DataInputStream(url.openStream());
-//                             String str;
-//                             while ((str = is.readLine()) != null) {
-//                                  System.out.println(str);
-//                                  //out.write(str);
-//                                  }
-                       FileReader r = new FileReader(path);
-                       BufferedReader in = new BufferedReader(r);
-                       String content ="";
-                       String str;
-                       
-                       while((str=in.readLine())!=null){
-                               //System.out.println(str);
-                               
-                               content=content+str;
-                       }
-                       System.out.println("pdbfile="+content.toString());
-                       System.out.println("capacité="+content.length());
-                       String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
-                       System.out.println("param="+paramfile);
-                           URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+content);
-                           BufferedReader is = new BufferedReader(new InputStreamReader(url.openStream()));
-                               String str4;
-                               while ((str4 = is.readLine()) != null) {
-                                    System.out.println(str4);
-                                    //out.write(str);
-                                    }
-                           in.close();
-                           is.close();
-                           
-//                         HttpURLConnection connection = (HttpURLConnection)url.openConnection();
-//                         connection.setRequestMethod("POST" );
-//                         connection.setRequestProperty("data", path );
-//                         //connection.setRequestProperty("nomDuChamp2", "valeurDuChamp2" );
-//                         BufferedReader input = new BufferedReader(new InputStreamReader(connection.getInputStream()));
-//                         //DataInputStream input = new DataInputStream(connection.getInputStream());
-//                         String c;
-//                         while((c=input.readLine())!=null){
-//                          System.out.print(c);
-//                         }
-//                         input.close();
-                               //BufferedReader in1 = new BufferedReader(is);
-                               
-//                          OutputStream out1 = null;
-//                          System.out.println("Step3");
-//                          BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
-//                          
-//                          in.close();
-//                          out.close();
-                               
-                               
-                               //return;
-                               
-                               //System.out.println(data.length());
-                               //System.out.println("step2");
-                   //URL url = new URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
-                   //System.out.println("step3");
-                   //URLConnection conn = url.openConnection();
-                   //conn.setDoOutput(true);
-                   //OutputStreamWriter writer = new OutputStreamWriter(conn.getOutputStream());
-                   
-                   //write parameters
-                   //writer.write(data);
-                  // writer.flush();
-                   
-                   // Get the response
-//                 StringBuffer answer = new StringBuffer();
-//                 //BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream()));
-//                 //String line;
-//                 while ((line = reader.readLine()) != null) {
-//                     answer.append(line);
-//                     System.out.println(line);
-//                 }
-//                 writer.close();
-//                 reader.close();
-                   
-                   //Output the response
-                   
-                   
-               } catch (MalformedURLException ex) {
-                   ex.printStackTrace();
-               } catch (IOException ex) {
-                   ex.printStackTrace();
-               }
-       }
-                       
-                       //in = new BufferedReader(new InputStreamReader(url.openStream()));
-                       
-                    //String str;
-                    
-                    
-                    //out = new FileOutputStream("temp.rnaml");
-                    //out = new BufferedWriter(new FileWriter("temp.rnaml"));
-                    
-                    //while ((str = in.readLine()) != null) {
-                    //System.out.println(str);
-                    //out.write(str);
-                    //System.out.println(str);
-//                     in.close();
-                    
-                    
-                    //out.close();
-//                  } catch (MalformedURLException e) {
-//                  } catch (IOException e) {
-//                  }
-//             
-//     }
-       
-       //public BufferedWriter getReader()
-       //{
-                       //System.out.println("The buffer");
-                       
-                       //return out;
-                       
-               
-       //}
+  // }
 
 }