X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FWSWUBlastClient.java;h=d7cd478df04dcf1e40a1df57a37e45108507f0a0;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=0906d12fa49c8f16c401eacd374cce89a73c956f;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java index 0906d12..d7cd478 100755 --- a/src/jalview/io/WSWUBlastClient.java +++ b/src/jalview/io/WSWUBlastClient.java @@ -1,306 +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.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; - } - } - - Vector entries = oldseq.getDBRef(); - if (entries != null) - { - DBRefEntry entry = (DBRefEntry) entries.elementAt(0); - oldseq.addDBRef(new jalview.datamodel. - DBRefEntry("UNIPROT", - "0", - entry.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(); - } - } - } -} +/* +* 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(); + } + } + } +}