--- /dev/null
+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;
+
+
+ //}
+
+}
git://source.jalview.org / jalview.git / blobdiff