X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FWSWUBlastClient.java;h=d7cd478df04dcf1e40a1df57a37e45108507f0a0;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=29a0900aa4ed54d1b0d1590a0c668326a3cc1211;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 29a0900..d7cd478 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -1,205 +1,305 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.io;
-
-import jalview.datamodel.*;
-
-import jalview.gui.*;
-
-import org.apache.axis.client.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-import javax.swing.*;
-
-import javax.xml.namespace.QName;
-
-
-public class WSWUBlastClient {
-    CutAndPasteTransfer output = new CutAndPasteTransfer();
-    int jobsRunning = 0;
-
-    public WSWUBlastClient(AlignmentI al, ArrayList ids) {
-        output.setText(
-            "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +
-            "\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");
-        Desktop.addInternalFrame(output,
-            "BLASTing for unidentified sequences ", 800, 300);
-
-        for (int i = 0; i < ids.size(); i++) {
-            SequenceI sequence = al.findName(ids.get(i).toString());
-            StringBuffer nonGapped = new StringBuffer();
-
-            for (int n = 0; n < sequence.getSequence().length(); n++) {
-                if (!jalview.util.Comparison.isGap(sequence.getCharAt(n))) {
-                    nonGapped.append(sequence.getCharAt(n));
-                }
-            }
-
-            BlastThread thread = new BlastThread(ids.get(i).toString(),
-                    nonGapped.toString());
-            thread.start();
-            jobsRunning++;
-        }
-
-        ImageTwirler thread = new ImageTwirler();
-        thread.start();
-    }
-
-    void parseResult(String id1, String res) {
-        StringTokenizer st = new StringTokenizer(res, "\n");
-        String data;
-        String id2;
-        int maxFound = 90;
-        StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");
-
-        while (st.hasMoreTokens()) {
-            data = st.nextToken();
-
-            if (data.indexOf("database=\"uniprot\" id=") > -1) {
-                int index = data.indexOf("database=\"uniprot\" id=") + 23;
-                id2 = data.substring(index, data.indexOf("\"", index));
-
-                while (data.indexOf("</alignment>") == -1) {
-                    data = st.nextToken();
-
-                    if (data.indexOf("<identity>") > -1) {
-                        int value = Integer.parseInt(data.substring(data.indexOf(
-                                        "<identity>") + 10,
-                                    data.indexOf("</identity>")));
-
-                        if (value >= maxFound) {
-                            maxFound = value;
-                            buffer.append(" " + id2 + " " + value + "%; ");
-                        }
-                    }
-                }
-            }
-        }
-
-        output.setText(output.getText() + buffer.toString());
-    }
-
-    class ImageTwirler extends Thread {
-        ImageIcon[] imageIcon;
-        int imageIndex = 0;
-
-        public ImageTwirler() {
-            imageIcon = new ImageIcon[9];
-
-            for (int i = 0; i < 9; i++) {
-                java.net.URL url = getClass().getResource("/images/dna" +
-                        (i + 1) + ".gif");
-
-                if (url != null) {
-                    imageIcon[i] = new ImageIcon(url);
-                }
-            }
-        }
-
-        public void run() {
-            while (jobsRunning > 0) {
-                try {
-                    Thread.sleep(100);
-                    imageIndex++;
-                    imageIndex %= 9;
-                    output.setFrameIcon(imageIcon[imageIndex]);
-                    output.setTitle("BLASTing for unidentified sequences - " +
-                        jobsRunning + " jobs running.");
-                } catch (Exception ex) {
-                }
-            }
-        }
-    }
-
-    class BlastThread extends Thread {
-        String sequence;
-        String seqid;
-        String jobid;
-        boolean jobComplete = false;
-
-        BlastThread(String id, String sequence) {
-            this.sequence = sequence;
-            seqid = id;
-        }
-
-        public void run() {
-            StartJob();
-
-            while (!jobComplete) {
-                try {
-                    Call call = (Call) new Service().createCall();
-                    call.setTargetEndpointAddress(new java.net.URL(
-                            "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
-                    call.setOperationName(new QName("WSWUBlast", "polljob"));
-
-                    String result = (String) call.invoke(new Object[] {
-                                jobid, "xml"
-                            });
-
-                    if ((result.indexOf("JOB PENDING") == -1) &&
-                            (result.indexOf("JOB RUNNING") == -1)) {
-                        parseResult(seqid, result);
-                        jobComplete = true;
-                        jobsRunning--;
-                    }
-
-                    Thread.sleep(5000);
-
-                    // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug
-                } catch (Exception ex) {
-                }
-            }
-        }
-
-        void StartJob() {
-            HashMap params = new HashMap();
-            params.put("database", "uniprot");
-            params.put("sensitivity", "low");
-            params.put("sort", "totalscore");
-            params.put("matrix", "pam10");
-            params.put("program", "blastp");
-            params.put("alignments", "5");
-            params.put("outformat", "xml");
-            params.put("searchtype", "1");
-
-            byte[] seqbytes = sequence.getBytes();
-
-            try {
-                Call call = (Call) new Service().createCall();
-                call.setTargetEndpointAddress(new java.net.URL(
-                        "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
-                call.setOperationName(new QName("WSWUBlast", "doWUBlast"));
-
-                String result = (String) call.invoke(new Object[] {
-                            params, seqbytes
-                        });
-                jobid = result;
-                System.out.println(
-                    "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +
-                    jobid + "'");
-            } catch (Exception exp) {
-                System.err.println("WSWUBlastClient error:\n" + exp.toString());
-                exp.printStackTrace();
-            }
-        }
-    }
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program 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 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+package jalview.io;
+
+import jalview.datamodel.*;
+
+import jalview.gui.*;
+
+import org.apache.axis.client.*;
+
+import java.util.*;
+
+import javax.swing.*;
+
+import javax.xml.namespace.QName;
+import jalview.analysis.AlignSeq;
+
+import uk.ac.ebi.www.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class WSWUBlastClient
+{
+    AlignmentPanel ap;
+    AlignmentI al;
+    CutAndPasteTransfer output = new CutAndPasteTransfer();
+    int jobsRunning = 0;
+
+    Vector suggestedIds = new Vector();
+    /**
+     * Creates a new WSWUBlastClient object.
+     *
+     * @param al DOCUMENT ME!
+     * @param ids DOCUMENT ME!
+     */
+    public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
+    {
+        this.ap = ap;
+        this.al = al;
+        output.setText(
+            "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
+            +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
+            +"\n\nRunning WSWUBlast at EBI."
+            +"\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
+            +"\nSOAP-based services provided by the European Bioinformatics Institute."
+            +"\nNucleic Acids Res. 33(1):W25-W28 (2005));");
+
+        Desktop.addInternalFrame(output,
+            "BLASTing for unidentified sequences ", 800, 300);
+
+        for (int i = 0; i < ids.size(); i++)
+        {
+            Sequence sequence = (Sequence)ids.get(i);
+            System.out.println(sequence.getName());
+
+            BlastThread thread = new BlastThread(sequence);
+            thread.start();
+            jobsRunning++;
+        }
+
+        ImageTwirler thread = new ImageTwirler();
+        thread.start();
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id1 DOCUMENT ME!
+     * @param res DOCUMENT ME!
+     */
+    void parseResult(Sequence seq, String res)
+    {
+        StringTokenizer st = new StringTokenizer(res, "\n");
+        String data;
+        String id2;
+        int maxFound = 90;
+        StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
+
+        while (st.hasMoreTokens())
+        {
+            data = st.nextToken();
+
+            if (data.indexOf(">UNIPROT") > -1)
+            {
+                int index = data.indexOf(">UNIPROT") + 9;
+                id2 = data.substring(index, data.indexOf(" ", index));
+
+                boolean identitiesFound = false;
+                while (!identitiesFound)
+                {
+                    data = st.nextToken();
+
+                    if (data.indexOf("Identities") > -1)
+                    {
+                       identitiesFound = true;
+
+                       int value = Integer.parseInt(data.substring(data.indexOf(
+                           "(") + 1,
+                                                                   data.indexOf("%")));
+
+                        if (value >= maxFound)
+                        {
+                            maxFound = value;
+                            buffer.append(" " + id2 + " " + value + "%; ");
+                            suggestedIds.addElement( new Object[]{seq, id2});
+                        }
+                    }
+                }
+            }
+        }
+
+        output.appendText(buffer.toString());
+    }
+
+    void updateIds()
+    {
+        // This must be outside the run() body as java 1.5
+     // will not return any value from the OptionPane to the expired thread.
+      int reply = JOptionPane.showConfirmDialog(
+          Desktop.desktop, "Automatically update suggested ids?",
+          "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
+
+      if (reply == JOptionPane.YES_OPTION)
+      {
+        Enumeration keys = suggestedIds.elements();
+        while(keys.hasMoreElements())
+        {
+          Object [] object = (Object[])keys.nextElement();
+
+          Sequence oldseq = (Sequence)object[0];
+
+          oldseq.setName( object[1].toString() );
+
+          // Oldseq is actually in the dataset, we must find the
+          // Visible seq and change its name also.
+          for (int i = 0; i < al.getHeight(); i++)
+          {
+            if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
+            {
+              al.getSequenceAt(i).setName(oldseq.getName());
+              break;
+            }
+          }
+
+          DBRefEntry [] entries = oldseq.getDBRef();
+          if (entries != null)
+          {
+            oldseq.addDBRef(new jalview.datamodel.
+                                                 DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,
+                "0",
+                entries[0].getAccessionId()));
+          }
+        }
+      }
+      ap.repaint();
+
+    }
+
+    class ImageTwirler extends Thread
+    {
+        ImageIcon[] imageIcon;
+        int imageIndex = 0;
+
+        public ImageTwirler()
+        {
+            imageIcon = new ImageIcon[9];
+
+            for (int i = 0; i < 9; i++)
+            {
+                java.net.URL url = getClass().getResource("/images/dna" +
+                        (i + 1) + ".gif");
+
+                if (url != null)
+                {
+                    imageIcon[i] = new ImageIcon(url);
+                }
+            }
+        }
+
+        public void run()
+        {
+            while (jobsRunning > 0)
+            {
+                try
+                {
+                    Thread.sleep(100);
+                    imageIndex++;
+                    imageIndex %= 9;
+                    output.setFrameIcon(imageIcon[imageIndex]);
+                    output.setTitle("BLASTing for unidentified sequences - " +
+                        jobsRunning + " jobs running.");
+                }
+                catch (Exception ex)
+                {
+                }
+            }
+
+            if (jobsRunning == 0)
+            {
+              updateIds();
+            }
+        }
+    }
+
+    class BlastThread extends Thread
+    {
+        Sequence sequence;
+        String jobid;
+        boolean jobComplete = false;
+
+        BlastThread(Sequence sequence)
+        {
+          System.out.println("blasting for: "+sequence.getName());
+          this.sequence = sequence;
+        }
+
+        public void run()
+        {
+            StartJob();
+
+            while (!jobComplete)
+            {
+                try
+                {
+                  WSWUBlastService service =  new WSWUBlastServiceLocator();
+                  WSWUBlast wublast = service.getWSWUBlast();
+                  WSFile[] results = wublast.getResults(jobid);
+
+                  if(results!=null)
+                  {
+                      String result = new String(wublast.poll(jobid, "tooloutput"));
+                      parseResult(sequence, result);
+                      jobComplete = true;
+                      jobsRunning--;
+                  }
+                  else
+                  {
+                    Thread.sleep(10000);
+                    System.out.println("WSWuBlastClient: I'm alive " +
+                                       sequence.getName() + " " + jobid); // log.debug
+                  }
+                }
+                catch (Exception ex)
+                {
+                }
+            }
+        }
+
+        void StartJob()
+        {
+          InputParams params = new InputParams();
+
+          params.setProgram("blastp");
+          params.setDatabase("uniprot");
+          params.setMatrix("pam10");
+
+          params.setNumal(5);
+          params.setSensitivity("low");
+          params.setSort("totalscore");
+          params.setOutformat("txt");
+          params.setAsync(true);
+
+            try
+            {
+              Data inputs[] = new Data[1];
+              Data input= new Data();
+              input.setType("sequence");
+              input.setContent(AlignSeq.extractGaps("-. ",sequence.getSequence()));
+              inputs[0]=input;
+
+              WSWUBlastService service = new WSWUBlastServiceLocator();
+              WSWUBlast wublast = service.getWSWUBlast();
+              jobid = wublast.runWUBlast(params, inputs);
+            }
+            catch (Exception exp)
+            {
+              jobComplete = true;
+              jobsRunning--;
+              System.err.println("WSWUBlastClient error:\n" + exp.toString());
+              exp.printStackTrace();
+            }
+        }
+    }
+}