X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FAnnotate3D.java;h=f3516b70c29b18c658844da34c77757389d789d5;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=505e15f946967be11404b99461868ac8b04dc451;hpb=171ca8730ea146d50b2eb00701d8df986d88f519;p=jalview.git

diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
index 505e15f..f3516b7 100644
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -1,206 +1,282 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.jws1;
 
-import java.io.BufferedInputStream;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.InputStreamParser;
+import jalview.util.MessageManager;
+
 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;
+import java.util.Iterator;
+
+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 AlignmentI getRNAMLFor(final FileParse source) throws IOException
+  {
+    try
+    {
+      StringBuffer sb = new StringBuffer();
+
+      Reader fpr = source.getReader();
+      int p = 0;
+      char[] cbuff = new char[2048];
+      while ((p = fpr.read(cbuff)) > 0)
+      {
+        for (int i = 0; i < p; i++)
+        {
+          sb.append(cbuff[i]);
+        }
+      }
+      Iterator<Reader> r = jalview.ext.paradise.Annotate3D
+              .getRNAMLForPDBFileAsString(sb.toString());
+      AlignmentI al = null;
+      while (r.hasNext())
+      {
+        FileParse fp = new InputStreamParser(r.next(), source.getDataName());
+        AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+        if (al == null)
+        {
+          al = nal;
+        }
+        else
+        {
+          al.append(nal);
+        }
+      }
+      return al;
+    } catch (Throwable x)
+    {
+      if (x instanceof IOException)
+      {
+        throw ((IOException) x);
+      }
+      else
+      {
+        throw new IOException(
+                MessageManager
+                        .getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
+                x);
+      }
+    }
+  }
+
+  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;
-			
-		
-	//}
+  // }
 
 }