Last version

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index dede37e..048f639 100755 (executable)
--- 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 (file)
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 (file)
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;
+                       
+               
+       //}
+
+}