-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-import uk.ac.ebi.www.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class WSWUBlastClient\r
-{\r
- AlignmentPanel ap;\r
- AlignmentI al;\r
- CutAndPasteTransfer output = new CutAndPasteTransfer();\r
- int jobsRunning = 0;\r
-\r
- Vector suggestedIds = new Vector();\r
- /**\r
- * Creates a new WSWUBlastClient object.\r
- *\r
- * @param al DOCUMENT ME!\r
- * @param ids DOCUMENT ME!\r
- */\r
- public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)\r
- {\r
- this.ap = ap;\r
- this.al = al;\r
- output.setText(\r
- "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."\r
- + "\nIn order to display these features, try changing the names of your sequences to the ids suggested below."\r
- + "\n\nRunning WSWUBlast at EBI."\r
- + "\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."\r
- +\r
- "\nSOAP-based services provided by the European Bioinformatics Institute."\r
- + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");\r
-\r
- Desktop.addInternalFrame(output,\r
- "BLASTing for unidentified sequences ", 800, 300);\r
-\r
- for (int i = 0; i < ids.size(); i++)\r
- {\r
- Sequence sequence = (Sequence) ids.get(i);\r
- System.out.println(sequence.getName());\r
-\r
- BlastThread thread = new BlastThread(sequence);\r
- thread.start();\r
- jobsRunning++;\r
- }\r
-\r
- ImageTwirler thread = new ImageTwirler();\r
- thread.start();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param id1 DOCUMENT ME!\r
- * @param res DOCUMENT ME!\r
- */\r
- void parseResult(Sequence seq, String res)\r
- {\r
- StringTokenizer st = new StringTokenizer(res, "\n");\r
- String data;\r
- String id2;\r
- int maxFound = 90;\r
- StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");\r
-\r
- while (st.hasMoreTokens())\r
- {\r
- data = st.nextToken();\r
-\r
- if (data.indexOf(">UNIPROT") > -1)\r
- {\r
- int index = data.indexOf(">UNIPROT") + 9;\r
- id2 = data.substring(index, data.indexOf(" ", index));\r
-\r
- boolean identitiesFound = false;\r
- while (!identitiesFound)\r
- {\r
- data = st.nextToken();\r
-\r
- if (data.indexOf("Identities") > -1)\r
- {\r
- identitiesFound = true;\r
-\r
- int value = Integer.parseInt(data.substring(data.indexOf(\r
- "(") + 1,\r
- data.indexOf("%")));\r
-\r
- if (value >= maxFound)\r
- {\r
- maxFound = value;\r
- buffer.append(" " + id2 + " " + value + "%; ");\r
- suggestedIds.addElement(new Object[]\r
- {seq, id2});\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- output.appendText(buffer.toString());\r
- }\r
-\r
- void updateIds()\r
- {\r
- // This must be outside the run() body as java 1.5\r
- // will not return any value from the OptionPane to the expired thread.\r
- int reply = JOptionPane.showConfirmDialog(\r
- Desktop.desktop, "Automatically update suggested ids?",\r
- "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);\r
-\r
- if (reply == JOptionPane.YES_OPTION)\r
- {\r
- Enumeration keys = suggestedIds.elements();\r
- while (keys.hasMoreElements())\r
- {\r
- Object[] object = (Object[]) keys.nextElement();\r
-\r
- Sequence oldseq = (Sequence) object[0];\r
-\r
- oldseq.setName(object[1].toString());\r
-\r
- // Oldseq is actually in the dataset, we must find the\r
- // Visible seq and change its name also.\r
- for (int i = 0; i < al.getHeight(); i++)\r
- {\r
- if (al.getSequenceAt(i).getDatasetSequence() == oldseq)\r
- {\r
- al.getSequenceAt(i).setName(oldseq.getName());\r
- break;\r
- }\r
- }\r
-\r
- DBRefEntry[] entries = oldseq.getDBRef();\r
- if (entries != null)\r
- {\r
- oldseq.addDBRef(new jalview.datamodel.\r
- DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,\r
- "0",\r
- entries[0].getAccessionId()));\r
- }\r
- }\r
- }\r
- ap.repaint();\r
-\r
- }\r
-\r
- class ImageTwirler\r
- extends Thread\r
- {\r
- ImageIcon[] imageIcon;\r
- int imageIndex = 0;\r
-\r
- public ImageTwirler()\r
- {\r
- imageIcon = new ImageIcon[9];\r
-\r
- for (int i = 0; i < 9; i++)\r
- {\r
- java.net.URL url = getClass().getResource("/images/dna" +\r
- (i + 1) + ".gif");\r
-\r
- if (url != null)\r
- {\r
- imageIcon[i] = new ImageIcon(url);\r
- }\r
- }\r
- }\r
-\r
- public void run()\r
- {\r
- while (jobsRunning > 0)\r
- {\r
- try\r
- {\r
- Thread.sleep(100);\r
- imageIndex++;\r
- imageIndex %= 9;\r
- output.setFrameIcon(imageIcon[imageIndex]);\r
- output.setTitle("BLASTing for unidentified sequences - " +\r
- jobsRunning + " jobs running.");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- if (jobsRunning == 0)\r
- {\r
- updateIds();\r
- }\r
- }\r
- }\r
-\r
- class BlastThread\r
- extends Thread\r
- {\r
- Sequence sequence;\r
- String jobid;\r
- boolean jobComplete = false;\r
-\r
- BlastThread(Sequence sequence)\r
- {\r
- System.out.println("blasting for: " + sequence.getName());\r
- this.sequence = sequence;\r
- }\r
-\r
- public void run()\r
- {\r
- StartJob();\r
-\r
- while (!jobComplete)\r
- {\r
- try\r
- {\r
- WSWUBlastService service = new WSWUBlastServiceLocator();\r
- WSWUBlast wublast = service.getWSWUBlast();\r
- WSFile[] results = wublast.getResults(jobid);\r
-\r
- if (results != null)\r
- {\r
- String result = new String(wublast.poll(jobid, "tooloutput"));\r
- parseResult(sequence, result);\r
- jobComplete = true;\r
- jobsRunning--;\r
- }\r
- else\r
- {\r
- Thread.sleep(10000);\r
- System.out.println("WSWuBlastClient: I'm alive " +\r
- sequence.getName() + " " + jobid); // log.debug\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
- }\r
-\r
- void StartJob()\r
- {\r
- InputParams params = new InputParams();\r
-\r
- params.setProgram("blastp");\r
- params.setDatabase("uniprot");\r
- params.setMatrix("pam10");\r
-\r
- params.setNumal(5);\r
- params.setSensitivity("low");\r
- params.setSort("totalscore");\r
- params.setOutformat("txt");\r
- params.setAsync(true);\r
-\r
- try\r
- {\r
- Data inputs[] = new Data[1];\r
- Data input = new Data();\r
- input.setType("sequence");\r
- input.setContent(AlignSeq.extractGaps("-. ",\r
- sequence.getSequenceAsString()));\r
- inputs[0] = input;\r
-\r
- WSWUBlastService service = new WSWUBlastServiceLocator();\r
- WSWUBlast wublast = service.getWSWUBlast();\r
- jobid = wublast.runWUBlast(params, inputs);\r
- }\r
- catch (Exception exp)\r
- {\r
- jobComplete = true;\r
- jobsRunning--;\r
- System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
- exp.printStackTrace();\r
- }\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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.io;
+
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+
+import uk.ac.ebi.www.Data;
+import uk.ac.ebi.www.InputParams;
+import uk.ac.ebi.www.WSFile;
+import uk.ac.ebi.www.WSWUBlast;
+import uk.ac.ebi.www.WSWUBlastService;
+import uk.ac.ebi.www.WSWUBlastServiceLocator;
+
+/**
+ * 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(MessageManager
+ .getString("label.wswublast_client_credits"));
+
+ Desktop.addInternalFrame(output, MessageManager
+ .getString("label.blasting_for_unidentified_sequence"), 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.paintAlignment(true);
+
+ }
+
+ 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(MessageManager.formatMessage(
+ "label.blasting_for_unidentified_sequence_jobs_running",
+ new String[] { Integer.valueOf(jobsRunning).toString() }));
+ } 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.getSequenceAsString()));
+ 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();
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff