X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FAnnotate3D.java;h=a30a9a1c161a9a7fc82865facc8670c27c62a991;hb=1af953b3f29ffe11b7bf298ef3fce773012c49e9;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..a30a9a1 100644
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -15,209 +15,252 @@
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
- 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 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 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]);
+ }
+ }
+
+ FileParse fp = new InputStreamParser(
+ jalview.ext.paradise.Annotate3D.getRNAMLForPDBFileAsString(sb
+ .toString()), source.getDataName());
+ AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+ return nal;
+ } catch (Throwable x)
+ {
+ if (x instanceof IOException)
+ {
+ throw ((IOException) x);
+ }
+ else
+ {
+ throw new IOException(
+ "Unexpected exception when handling RNAML translation of PDB data",
+ 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