X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FWSWUBlastClient.java;h=abfd1b2c8c80b94442d214d4d38034fdd687fda6;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=c221d074c6e5b9a65379129c3837ec1f2b29dffa;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java index c221d07..abfd1b2 100755 --- a/src/jalview/io/WSWUBlastClient.java +++ b/src/jalview/io/WSWUBlastClient.java @@ -1,255 +1,319 @@ -/* -* 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.util.*; - -import javax.swing.*; - -import javax.xml.namespace.QName; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class WSWUBlastClient -{ - CutAndPasteTransfer output = new CutAndPasteTransfer(); - int jobsRunning = 0; - - /** - * Creates a new WSWUBlastClient object. - * - * @param al DOCUMENT ME! - * @param ids DOCUMENT ME! - */ - 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(); - } - - /** - * DOCUMENT ME! - * - * @param id1 DOCUMENT ME! - * @param res DOCUMENT ME! - */ - 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("") == -1) - { - data = st.nextToken(); - - if (data.indexOf("") > -1) - { - int value = Integer.parseInt(data.substring(data.indexOf( - "") + 10, - data.indexOf(""))); - - 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 (Version 2.9.0b2) + * 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 . + * 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(); + } + } + } +}