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