X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FAnnotate3D.java;h=509d4ae91f1487d941fa56fa5100c7abd5803ed9;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=5457c3a575bb46861b569c5b1f8438fadad4a668;hpb=3e7ebcfda0bc54b3b91905e21835142bfd1fe8a0;p=jalview.git
diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
index 5457c3a..509d4ae 100644
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -1,223 +1,281 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
- package jalview.ws.jws1;
+package jalview.ws.jws1;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.InputStreamParser;
+import jalview.util.MessageManager;
-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;
+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 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