/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 <http://www.gnu.org/licenses/>.
+ * 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 jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.io.FileFormat;
import jalview.io.FileParse;
import jalview.io.FormatAdapter;
import jalview.io.InputStreamParser;
+import jalview.util.MessageManager;
import java.io.BufferedReader;
import java.io.FileReader;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLEncoder;
+import java.util.Iterator;
public class Annotate3D
{
public Annotate3D()
{
- System.out.println("Annotate3D");
+ jalview.bin.Console.outPrintln("Annotate3D");
// try {
// Create a URL for the desired page
// String id = "1HR2";
// OutputStream out1 = null;
// out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
// while ((str = in.readLine()) != null) {
- // System.out.println(str);
+ // jalview.bin.Console.outPrintln(str);
// out.write(str);
// }
// in.close();
sb.append(cbuff[i]);
}
}
-
- FileParse fp = new InputStreamParser(
- jalview.ext.paradise.Annotate3D.getRNAMLForPDBFileAsString(sb
- .toString()), source.getDataName());
- AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
- return nal;
+ 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,
+ FileFormat.Rnaml);
+ if (al == null)
+ {
+ al = nal;
+ }
+ else
+ {
+ al.append(nal);
+ }
+ }
+ return al;
} catch (Throwable x)
{
if (x instanceof IOException)
}
else
{
- throw new IOException(
- "Unexpected exception when handling RNAML translation of PDB data",
+ throw new IOException(MessageManager.getString(
+ "exception.unexpected_handling_rnaml_translation_for_pdb"),
x);
}
}
public Annotate3D(String path) throws InterruptedException
{
- System.out.println("Annotate3D");
+ jalview.bin.Console.outPrintln("Annotate3D");
try
{
// //URL url = new
// URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
- // System.out.println("Step1");
+ // jalview.bin.Console.outPrintln("Step1");
// FileReader r = new FileReader(inFile);
// BufferedReader in = new BufferedReader(r);
// StringBuffer content = new StringBuffer();
- // System.out.println("Step2");
+ // jalview.bin.Console.outPrintln("Step2");
// while(in.readLine()!=null){
// content.append(in.readLine());
- // //System.out.println("Step3"+in.readLine());
+ // //jalview.bin.Console.outPrintln("Step3"+in.readLine());
// }
//
// String data = URLEncoder.encode("data", "UTF-8") + "=" +
// FileReader r = new FileReader(path);
// BufferedReader in = new BufferedReader(r);
// StringBuffer content = new StringBuffer();
- // System.out.println("Step1");
+ // jalview.bin.Console.outPrintln("Step1");
// while(in.readLine()!=null){
// content.append(in.readLine());
//
// }
- // System.out.println("Step2");
+ // jalview.bin.Console.outPrintln("Step2");
// String data = URLEncoder.encode("data", "UTF-8") + "=" +
// URLEncoder.encode(content.toString(), "UTF-8");
- // System.out.println("Step2");
+ // jalview.bin.Console.outPrintln("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);
+ // jalview.bin.Console.outPrintln(str);
// //out.write(str);
// }
FileReader r = new FileReader(path);
while ((str = in.readLine()) != null)
{
- // System.out.println(str);
+ // jalview.bin.Console.outPrintln(str);
content = content + str;
}
- System.out.println("pdbfile=" + content.toString());
- System.out.println("capacité=" + content.length());
+ jalview.bin.Console.outPrintln("pdbfile=" + content.toString());
+ jalview.bin.Console.outPrintln("capacité=" + content.length());
String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
- System.out.println("param=" + paramfile);
+ jalview.bin.Console.outPrintln("param=" + paramfile);
URL url = new URL(
"http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
+ content);
- BufferedReader is = new BufferedReader(new InputStreamReader(
- url.openStream()));
+ BufferedReader is = new BufferedReader(
+ new InputStreamReader(url.openStream()));
String str4;
while ((str4 = is.readLine()) != null)
{
- System.out.println(str4);
+ jalview.bin.Console.outPrintln(str4);
// out.write(str);
}
in.close();
// BufferedReader in1 = new BufferedReader(is);
// OutputStream out1 = null;
- // System.out.println("Step3");
+ // jalview.bin.Console.outPrintln("Step3");
// BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1,
// "temp.rnaml"));
//
// return;
- // System.out.println(data.length());
- // System.out.println("step2");
+ // jalview.bin.Console.outPrintln(data.length());
+ // jalview.bin.Console.outPrintln("step2");
// URL url = new
// URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
- // System.out.println("step3");
+ // jalview.bin.Console.outPrintln("step3");
// URLConnection conn = url.openConnection();
// conn.setDoOutput(true);
// OutputStreamWriter writer = new
// //String line;
// while ((line = reader.readLine()) != null) {
// answer.append(line);
- // System.out.println(line);
+ // jalview.bin.Console.outPrintln(line);
// }
// writer.close();
// reader.close();
// out = new BufferedWriter(new FileWriter("temp.rnaml"));
// while ((str = in.readLine()) != null) {
- // System.out.println(str);
+ // jalview.bin.Console.outPrintln(str);
// out.write(str);
- // System.out.println(str);
+ // jalview.bin.Console.outPrintln(str);
// in.close();
// out.close();
// public BufferedWriter getReader()
// {
- // System.out.println("The buffer");
+ // jalview.bin.Console.outPrintln("The buffer");
// return out;
git://source.jalview.org / jalview.git / blobdiff