From 171ca8730ea146d50b2eb00701d8df986d88f519 Mon Sep 17 00:00:00 2001
From: Anne Menard <menard.annec@gmail.com>
Date: Mon, 16 Jul 2012 11:17:19 +0200
Subject: [PATCH] Last version

---
 src/MCview/PDBfile.java                            |   21 +-
 .../schemes/RNAInteractionColourScheme.java        |   65 ++++++
 src/jalview/ws/jws1/Annotate3D.java                |  206 ++++++++++++++++++++
 3 files changed, 282 insertions(+), 10 deletions(-)
 create mode 100644 src/jalview/schemes/RNAInteractionColourScheme.java
 create mode 100644 src/jalview/ws/jws1/Annotate3D.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index dede37e..048f639 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -182,24 +182,25 @@ public class PDBfile extends jalview.io.AlignFile
         seqs.addElement(chainseq);
        if(isRNA(chainseq)==true)
        {
+    	   String path =inFile.getPath();
     	   System.out.println("this is a PDB format and RNA sequence");
-    	   Annotate3D an3d = new Annotate3D(id);
+    	   Annotate3D an3d = new Annotate3D(path);
     	   System.out.println(id);
     	   //BufferedWriter r = an3d.getReader();
     	   
-    	   BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
+    	  // BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
     	   
-    	   String str;
-    	   while ((str = in.readLine()) != null) {
-  		     System.out.println(str);
-  		     System.out.println("toto");
+    	   //String str;
+    	  // while ((str = in.readLine()) != null) {
+  		    // System.out.println(str);
+  		    // System.out.println("toto");
 
-  		     }
-    	   String type = "File";
-    	   RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
+  		    // }
+    	   //String type = "File";
+    	   //RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
     	   System.out.println("Create rnamfile object");
     	   //rnaml.parse("temp");
-    	   this.annotations =rnaml.getAnnot();
+    	   //this.annotations =rnaml.getAnnot();
     	   
        }
         
diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
new file mode 100644
index 0000000..3197caf
--- /dev/null
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -0,0 +1,65 @@
+package jalview.schemes;
+
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+
+public class RNAInteractionColourScheme extends ResidueColourScheme{
+	 public RNAInteractionColourScheme()
+	  {
+	    super(ResidueProperties.nucleotide, 0);
+	  }
+
+	  /**
+	   * DOCUMENT ME!
+	   * 
+	   * @param n
+	   *          DOCUMENT ME!
+	   * 
+	   * @return DOCUMENT ME!
+	   */
+	  @Override
+	  public Color findColour(char c)
+	  {
+	    // System.out.println("called"); log.debug
+	    return colors[ResidueProperties.nucleotideIndex[c]];
+	  }
+
+	  /**
+	   * DOCUMENT ME!
+	   * 
+	   * @param n
+	   *          DOCUMENT ME!
+	   * @param j
+	   *          DOCUMENT ME!
+	   * 
+	   * @return DOCUMENT ME!
+	   */
+	  @Override
+	  public Color findColour(char c, int j, SequenceI seq)
+	  {
+	    Color currentColour;
+	    if ((threshold == 0) || aboveThreshold(c, j))
+	    {
+	      try
+	      {
+	        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+	      } catch (Exception ex)
+	      {
+	        return Color.white;
+	      }
+	    }
+	    else
+	    {
+	      return Color.white;
+	    }
+
+	    if (conservationColouring)
+	    {
+	      currentColour = applyConservation(currentColour, j);
+	    }
+
+	    return currentColour;
+	  }
+	}
diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
new file mode 100644
index 0000000..505e15f
--- /dev/null
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -0,0 +1,206 @@
+package jalview.ws.jws1;
+
+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;
+			
+		
+	//}
+
+}
-- 
1.7.10.2