X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FWSWUBlastClient.java;h=d526a3135a43edcae5849ac4dfc04d10fbac9112;hb=ed581b841fe9361bfe80bb006df190a29df264fb;hp=ad291db0258ffb4bf835b6f3c799e9319dfd01d7;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java index ad291db..d526a31 100755 --- a/src/jalview/io/WSWUBlastClient.java +++ b/src/jalview/io/WSWUBlastClient.java @@ -1,31 +1,48 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; -import java.util.*; - -import javax.swing.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.gui.*; -import uk.ac.ebi.www.*; +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.gui.JvOptionPane; +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 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! @@ -49,24 +66,19 @@ public class WSWUBlastClient * Creates a new WSWUBlastClient object. * * @param al - * DOCUMENT ME! + * DOCUMENT ME! * @param ids - * DOCUMENT ME! + * 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));"); + output.setText( + MessageManager.getString("label.wswublast_client_credits")); - Desktop.addInternalFrame(output, - "BLASTing for unidentified sequences ", 800, 300); + Desktop.addInternalFrame(output, MessageManager.getString( + "label.blasting_for_unidentified_sequence"), 800, 300); for (int i = 0; i < ids.size(); i++) { @@ -86,9 +98,9 @@ public class WSWUBlastClient * DOCUMENT ME! * * @param id1 - * DOCUMENT ME! + * DOCUMENT ME! * @param res - * DOCUMENT ME! + * DOCUMENT ME! */ void parseResult(Sequence seq, String res) { @@ -116,15 +128,14 @@ public class WSWUBlastClient { identitiesFound = true; - int value = Integer.parseInt(data.substring( - data.indexOf("(") + 1, data.indexOf("%"))); + 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 }); + suggestedIds.addElement(new Object[] { seq, id2 }); } } } @@ -138,11 +149,11 @@ public class WSWUBlastClient { // 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, + int reply = JvOptionPane.showConfirmDialog(Desktop.desktop, "Automatically update suggested ids?", - "Auto replace sequence ids", JOptionPane.YES_NO_OPTION); + "Auto replace sequence ids", JvOptionPane.YES_NO_OPTION); - if (reply == JOptionPane.YES_OPTION) + if (reply == JvOptionPane.YES_OPTION) { Enumeration keys = suggestedIds.elements(); while (keys.hasMoreElements()) @@ -164,16 +175,16 @@ public class WSWUBlastClient } } - DBRefEntry[] entries = oldseq.getDBRef(); + DBRefEntry[] entries = oldseq.getDBRefs(); if (entries != null) { oldseq.addDBRef(new jalview.datamodel.DBRefEntry( - jalview.datamodel.DBRefSource.UNIPROT, "0", entries[0] - .getAccessionId())); + jalview.datamodel.DBRefSource.UNIPROT, "0", + entries[0].getAccessionId())); } } } - ap.paintAlignment(true); + ap.paintAlignment(true, false); } @@ -189,8 +200,8 @@ public class WSWUBlastClient for (int i = 0; i < 9; i++) { - java.net.URL url = getClass().getResource( - "/images/dna" + (i + 1) + ".gif"); + java.net.URL url = getClass() + .getResource("/images/dna" + (i + 1) + ".gif"); if (url != null) { @@ -199,6 +210,7 @@ public class WSWUBlastClient } } + @Override public void run() { while (jobsRunning > 0) @@ -209,8 +221,10 @@ public class WSWUBlastClient imageIndex++; imageIndex %= 9; output.setFrameIcon(imageIcon[imageIndex]); - output.setTitle("BLASTing for unidentified sequences - " - + jobsRunning + " jobs running."); + output.setTitle(MessageManager.formatMessage( + "label.blasting_for_unidentified_sequence_jobs_running", + new String[] + { Integer.valueOf(jobsRunning).toString() })); } catch (Exception ex) { } @@ -237,6 +251,7 @@ public class WSWUBlastClient this.sequence = sequence; } + @Override public void run() { StartJob(); @@ -287,8 +302,8 @@ public class WSWUBlastClient Data inputs[] = new Data[1]; Data input = new Data(); input.setType("sequence"); - input.setContent(AlignSeq.extractGaps("-. ", sequence - .getSequenceAsString())); + input.setContent(AlignSeq.extractGaps("-. ", + sequence.getSequenceAsString())); inputs[0] = input; WSWUBlastService service = new WSWUBlastServiceLocator();