2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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21 import ext.vamsas.*;
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23 import jalview.analysis.AlignSeq;
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25 import jalview.datamodel.*;
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27 import jalview.gui.*;
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29 import org.apache.axis.client.*;
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31 import vamsas.objects.*;
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37 import javax.swing.*;
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39 import javax.xml.namespace.QName;
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42 public class MsaWSClient extends WSClient {
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44 * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
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46 ext.vamsas.MuscleWS server;
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48 public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa,
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49 boolean submitGaps, boolean preserveOrder) {
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50 if (setWebService(MsaWSName) == false) {
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51 JOptionPane.showMessageDialog(Desktop.desktop,
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52 "The Multiple Sequence Alignment Service named " + MsaWSName +
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53 " is unknown", "Internal Jalview Error",
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54 JOptionPane.WARNING_MESSAGE);
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59 wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle,
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60 WebServiceReference);
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62 if (!locateWebService()) {
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66 wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") +
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67 " of " + altitle + "\nJob details\n");
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69 MsaWSThread musclethread = new MsaWSThread(WebServiceName +
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70 " alignment of " + altitle, msa, submitGaps, preserveOrder);
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71 wsInfo.setthisService(musclethread);
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72 musclethread.start();
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75 // JBPNote Nasty object-global state setting methods shouldn't be allowed
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76 private boolean setWebService(String MsaWSName) {
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77 if (MsaWServices.info.containsKey(MsaWSName)) {
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78 WebServiceName = MsaWSName;
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80 String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
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82 WebServiceJobTitle = wsinfo[1];
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83 WebServiceReference = wsinfo[2];
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91 private boolean locateWebService() {
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92 // TODO: MuscleWS transmuted to generic MsaWS client
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93 MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
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96 this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
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97 ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout
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98 } catch (Exception ex) {
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99 wsInfo.setProgressText("Serious! " + WebServiceName +
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100 " Service location failed\nfor URL :" + WsURL + "\n" +
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102 wsInfo.setStatus(wsInfo.ERROR);
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103 ex.printStackTrace();
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108 loc.getEngine().setOption("axis", "1");
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113 protected class MsaWSThread extends Thread implements WSClientI {
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114 String ServiceName = WebServiceName;
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115 String OutputHeader;
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116 vamsas.objects.simple.MsaResult result = null;
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117 vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
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118 Hashtable SeqNames = null;
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119 boolean submitGaps = false; // and always store and recover sequence order
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120 boolean preserveOrder = true; // and always store and recover sequence order
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122 String alTitle; // name which will be used to form new alignment window.
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123 int allowedServerExceptions = 3; // thread dies if too many exceptions.
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124 boolean jobComplete = false;
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126 MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
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127 boolean presorder) {
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129 submitGaps = subgaps;
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130 preserveOrder = presorder;
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132 OutputHeader = wsInfo.getProgressText();
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133 SeqNames = new Hashtable();
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135 vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.Sequence[msa.length];
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137 for (int i = 0; i < msa.length; i++) {
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138 String newname = jalview.analysis.SeqsetUtils.unique_name(i);
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140 // uniquify as we go
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141 // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
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142 SeqNames.put(newname,
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143 jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
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144 seqarray[i] = new vamsas.objects.simple.Sequence();
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145 seqarray[i].setId(newname);
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146 seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()
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147 : AlignSeq.extractGaps(
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148 jalview.util.Comparison.GapChars, msa[i].getSequence()));
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151 this.seqs = new vamsas.objects.simple.SequenceSet();
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152 this.seqs.setSeqs(seqarray);
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155 public boolean isCancellable() {
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159 public void cancelJob() {
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160 if ((jobId != null) && !jobId.equals("") && !jobComplete) {
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161 String cancelledMessage = "";
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164 vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
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166 if (cancelledJob.getStatus() == 2) {
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168 cancelledMessage = "Job cancelled.";
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169 wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
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170 jobComplete = true;
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173 } else if (cancelledJob.getStatus() == 3) {
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174 // VALID UNSTOPPABLE JOB
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175 cancelledMessage += "Server cannot cancel this job. just close the window.\n";
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178 if (cancelledJob.getJobId() != null) {
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179 cancelledMessage += ("[" + cancelledJob.getJobId() +
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183 cancelledMessage += "\n";
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184 } catch (Exception exc) {
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185 cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" +
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187 exc.printStackTrace();
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190 wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");
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192 if (!jobComplete) {
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193 wsInfo.setProgressText(OutputHeader +
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194 "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
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199 public void run() {
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202 while (!jobComplete && (allowedServerExceptions > 0)) {
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204 if ((result = server.getResult(jobId)) == null) {
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205 throw (new Exception(
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206 "Timed out when communicating with server\nTry again later.\n"));
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209 if (result.isRunning()) {
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210 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
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211 } else if (result.isQueued()) {
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212 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
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215 if (result.isFinished()) {
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217 jobComplete = true;
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220 if (result.getStatus() != null) {
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221 wsInfo.setProgressText(OutputHeader + "\n" +
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222 result.getStatus());
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225 if (!(result.isJobFailed() || result.isServerError())) {
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226 Thread.sleep(5000);
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228 // System.out.println("I'm alive "+seqid+" "+jobid);
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233 } catch (Exception ex) {
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234 allowedServerExceptions--;
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235 wsInfo.appendProgressText("\n" + ServiceName +
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236 " Server exception!\n" + ex.getMessage());
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237 System.err.println(ServiceName + " Server exception: " +
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240 // ex.printStackTrace(); JBPNote Debug
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242 if (allowedServerExceptions > 0) {
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243 Thread.sleep(5000);
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245 } catch (InterruptedException ex1) {
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250 if (allowedServerExceptions == 0) {
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251 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
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253 if (!((result != null) &&
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254 (result.isJobFailed() || result.isServerError()))) {
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255 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
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257 if (result.isFailed()) {
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258 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
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261 if (result.isServerError()) {
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262 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
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270 vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
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272 if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) {
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273 jobId = jobsubmit.getJobId();
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274 System.out.println(WsURL + " Job Id '" + jobId + "'");
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276 if (jobsubmit == null) {
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277 throw new Exception("Server at " + WsURL +
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278 " returned null object, it probably cannot be contacted. Try again later ?");
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281 throw new Exception(jobsubmit.getJobId());
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283 } catch (Exception e) {
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284 // TODO: JBPNote catch timeout or other fault types explicitly
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285 // For unexpected errors
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286 System.err.println(WebServiceName +
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287 "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
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288 + "When contacting Server:"+WsURL + "\n" + e.toString() + "\n");
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289 this.allowedServerExceptions = 0;
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290 wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
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291 wsInfo.appendProgressText("Failed to submit sequences for alignment.\n"
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292 + "It is most likely that there is a problem with the server.\n"
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293 + "Just close the window\n");
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295 // e.printStackTrace(); // TODO: JBPNote DEBUG
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299 private void addFloatAnnotations(Alignment al, int[] gapmap,
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300 Vector values, String Symname, String Visname, float min,
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301 float max, int winLength) {
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302 Annotation[] annotations = new Annotation[al.getWidth()];
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304 for (int j = 0; j < values.size(); j++) {
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305 float value = Float.parseFloat(values.get(j).toString());
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306 annotations[gapmap[j]] = new Annotation("", value + "", ' ',
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310 al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
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311 annotations, min, max, winLength));
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314 private jalview.datamodel.Sequence[] getVamsasAlignment(
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315 vamsas.objects.simple.Alignment valign) {
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316 vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
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317 jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
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319 for (int i = 0, j = seqs.length; i < j; i++)
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320 msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
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326 void parseResult() {
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327 SequenceI[] seqs = null;
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330 // OutputHeader = output.getText();
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331 if (result.isFailed()) {
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332 OutputHeader += "Job failed.\n";
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335 if (result.getStatus() != null) {
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336 OutputHeader += ("\n" + result.getStatus());
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339 if (result.getMsa() != null) {
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340 OutputHeader += "\nAlignment Object Method Notes\n";
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342 String[] lines = result.getMsa().getMethod();
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344 for (int line = 0; line < lines.length; line++)
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345 OutputHeader += (lines[line] + "\n");
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347 // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
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348 seqs = getVamsasAlignment(result.getMsa());
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351 wsInfo.setProgressText(OutputHeader);
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353 if (seqs != null) {
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354 AlignmentOrder msaorder = new AlignmentOrder(seqs);
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356 if (preserveOrder) {
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357 jalview.analysis.AlignmentSorter.recoverOrder(seqs);
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360 jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
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362 Alignment al = new Alignment(seqs);
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364 // TODO: JBPNote Should also rename the query sequence sometime...
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365 AlignFrame af = new AlignFrame(al);
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366 af.addSortByOrderMenuItem(ServiceName + " Ordering",
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369 Desktop.addInternalFrame(af, alTitle,
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370 AlignFrame.NEW_WINDOW_WIDTH,
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371 AlignFrame.NEW_WINDOW_HEIGHT);
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373 } catch (Exception ex) {
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374 ex.printStackTrace();
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