/*
-* 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
-*/\r
-package jalview.ws;\r
-\r
-import ext.vamsas.*;\r
-\r
-import jalview.analysis.AlignSeq;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.gui.*;\r
-\r
-import org.apache.axis.client.*;\r
-\r
-import vamsas.objects.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-import javax.xml.namespace.QName;\r
-\r
-\r
-public class MsaWSClient extends WSClient {\r
- /**
- * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
- */\r
- ext.vamsas.MuscleWS server;\r
-\r
- public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa,\r
- boolean submitGaps, boolean preserveOrder) {\r
- if (setWebService(MsaWSName) == false) {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The Multiple Sequence Alignment Service named " + MsaWSName +\r
- " is unknown", "Internal Jalview Error",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
-\r
- wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle,\r
- WebServiceReference);\r
-\r
- if (!locateWebService()) {\r
- return;\r
- }\r
-\r
- wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") +\r
- " of " + altitle + "\nJob details\n");\r
-\r
- MsaWSThread musclethread = new MsaWSThread(WebServiceName +\r
- " alignment of " + altitle, msa, submitGaps, preserveOrder);\r
- wsInfo.setthisService(musclethread);\r
- musclethread.start();\r
- }\r
-\r
- // JBPNote Nasty object-global state setting methods shouldn't be allowed\r
- private boolean setWebService(String MsaWSName) {\r
- if (MsaWServices.info.containsKey(MsaWSName)) {\r
- WebServiceName = MsaWSName;\r
-\r
- String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);\r
- WsURL = wsinfo[0];\r
- WebServiceJobTitle = wsinfo[1];\r
- WebServiceReference = wsinfo[2];\r
-\r
- return true;\r
- } else {\r
- return false;\r
- }\r
- }\r
-\r
- private boolean locateWebService() {\r
- // TODO: MuscleWS transmuted to generic MsaWS client\r
- MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default\r
-\r
- try {\r
- this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));\r
- ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout\r
- } catch (Exception ex) {\r
- wsInfo.setProgressText("Serious! " + WebServiceName +\r
- " Service location failed\nfor URL :" + WsURL + "\n" +\r
- ex.getMessage());\r
- wsInfo.setStatus(wsInfo.ERROR);\r
- ex.printStackTrace();\r
-\r
- return false;\r
- }\r
-\r
- loc.getEngine().setOption("axis", "1");\r
-\r
- return true;\r
- }\r
-\r
- protected class MsaWSThread extends Thread implements WSClientI {\r
- String ServiceName = WebServiceName;\r
- String OutputHeader;\r
- vamsas.objects.simple.MsaResult result = null;\r
- vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
- Hashtable SeqNames = null;\r
- boolean submitGaps = false; // and always store and recover sequence order\r
- boolean preserveOrder = true; // and always store and recover sequence order\r
- String jobId;\r
- String alTitle; // name which will be used to form new alignment window.\r
- int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
- boolean jobComplete = false;\r
-\r
- MsaWSThread(String title, SequenceI[] msa, boolean subgaps,\r
- boolean presorder) {\r
- alTitle = title;\r
- submitGaps = subgaps;\r
- preserveOrder = presorder;\r
-\r
- OutputHeader = wsInfo.getProgressText();\r
- SeqNames = new Hashtable();\r
-\r
- vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.Sequence[msa.length];\r
-\r
- for (int i = 0; i < msa.length; i++) {\r
- String newname = jalview.analysis.SeqsetUtils.unique_name(i);\r
-\r
- // uniquify as we go\r
- // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation\r
- SeqNames.put(newname,\r
- jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));\r
- seqarray[i] = new vamsas.objects.simple.Sequence();\r
- seqarray[i].setId(newname);\r
- seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()\r
- : AlignSeq.extractGaps(\r
- jalview.util.Comparison.GapChars, msa[i].getSequence()));\r
- }\r
-\r
- this.seqs = new vamsas.objects.simple.SequenceSet();\r
- this.seqs.setSeqs(seqarray);\r
- }\r
-\r
- public boolean isCancellable() {\r
- return true;\r
- }\r
-\r
- public void cancelJob() {\r
- if ((jobId != null) && !jobId.equals("") && !jobComplete) {\r
- String cancelledMessage = "";\r
-\r
- try {\r
- vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);\r
-\r
- if (cancelledJob.getStatus() == 2) {\r
- // CANCELLED_JOB\r
- cancelledMessage = "Job cancelled.";\r
- wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);\r
- jobComplete = true;\r
- jobsRunning--;\r
- result = null;\r
- } else if (cancelledJob.getStatus() == 3) {\r
- // VALID UNSTOPPABLE JOB\r
- cancelledMessage += "Server cannot cancel this job. just close the window.\n";\r
- }\r
-\r
- if (cancelledJob.getJobId() != null) {\r
- cancelledMessage += ("[" + cancelledJob.getJobId() +\r
- "]");\r
- }\r
-\r
- cancelledMessage += "\n";\r
- } catch (Exception exc) {\r
- cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" +\r
- exc + "\n");\r
- exc.printStackTrace();\r
- }\r
-\r
- wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");\r
- } else {\r
- if (!jobComplete) {\r
- wsInfo.setProgressText(OutputHeader +\r
- "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");\r
- }\r
- }\r
- }\r
-\r
- public void run() {\r
- StartJob();\r
-\r
- while (!jobComplete && (allowedServerExceptions > 0)) {\r
- try {\r
- if ((result = server.getResult(jobId)) == null) {\r
- throw (new Exception(\r
- "Timed out when communicating with server\nTry again later.\n"));\r
- }\r
-\r
- if (result.isRunning()) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
- } else if (result.isQueued()) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
- }\r
-\r
- if (result.isFinished()) {\r
- parseResult();\r
- jobComplete = true;\r
- jobsRunning--;\r
- } else {\r
- if (result.getStatus() != null) {\r
- wsInfo.setProgressText(OutputHeader + "\n" +\r
- result.getStatus());\r
- }\r
-\r
- if (!(result.isJobFailed() || result.isServerError())) {\r
- Thread.sleep(5000);\r
-\r
- // System.out.println("I'm alive "+seqid+" "+jobid);\r
- } else {\r
- break;\r
- }\r
- }\r
- } catch (Exception ex) {\r
- allowedServerExceptions--;\r
- wsInfo.appendProgressText("\n" + ServiceName +\r
- " Server exception!\n" + ex.getMessage());\r
- System.err.println(ServiceName + " Server exception: " +\r
- ex.getMessage());\r
-\r
- // ex.printStackTrace(); JBPNote Debug\r
- try {\r
- if (allowedServerExceptions > 0) {\r
- Thread.sleep(5000);\r
- }\r
- } catch (InterruptedException ex1) {\r
- }\r
- }\r
- }\r
-\r
- if (allowedServerExceptions == 0) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- } else {\r
- if (!((result != null) &&\r
- (result.isJobFailed() || result.isServerError()))) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- } else {\r
- if (result.isFailed()) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
-\r
- if (result.isServerError()) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- }\r
- }\r
- }\r
- }\r
-\r
- void StartJob() {\r
- try {\r
- vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);\r
-\r
- if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) {\r
- jobId = jobsubmit.getJobId();\r
- System.out.println(WsURL + " Job Id '" + jobId + "'");\r
- } else {\r
- if (jobsubmit == null) {\r
- throw new Exception("Server at " + WsURL +\r
- " returned null object, it probably cannot be contacted. Try again later ?");\r
- }\r
-\r
- throw new Exception(jobsubmit.getJobId());\r
- }\r
- } catch (Exception e) {\r
- // TODO: JBPNote catch timeout or other fault types explicitly\r
- // For unexpected errors\r
- System.err.println(WebServiceName +\r
- " Client: Failed to submit the sequences for alignment.\n" +\r
- WsURL + " : " + e.toString() + "\n");\r
- this.allowedServerExceptions = 0;\r
- wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo.appendProgressText("Server problems! " + e.toString() +\r
- "\nFailed to submit sequences for alignment. Just close the window\n");\r
-\r
- // e.printStackTrace(); // TODO: JBPNote DEBUG\r
- }\r
- }\r
-\r
- private void addFloatAnnotations(Alignment al, int[] gapmap,\r
- Vector values, String Symname, String Visname, float min,\r
- float max, int winLength) {\r
- Annotation[] annotations = new Annotation[al.getWidth()];\r
-\r
- for (int j = 0; j < values.size(); j++) {\r
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
- value);\r
- }\r
-\r
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
- annotations, min, max, winLength));\r
- }\r
-\r
- private jalview.datamodel.Sequence[] getVamsasAlignment(\r
- vamsas.objects.simple.Alignment valign) {\r
- vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();\r
- jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];\r
-\r
- for (int i = 0, j = seqs.length; i < j; i++)\r
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),\r
- seqs[i].getSeq());\r
-\r
- return msa;\r
- }\r
-\r
- void parseResult() {\r
- SequenceI[] seqs = null;\r
-\r
- try {\r
- // OutputHeader = output.getText();\r
- if (result.isFailed()) {\r
- OutputHeader += "Job failed.\n";\r
- }\r
-\r
- if (result.getStatus() != null) {\r
- OutputHeader += ("\n" + result.getStatus());\r
- }\r
-\r
- if (result.getMsa() != null) {\r
- OutputHeader += "\nAlignment Object Method Notes\n";\r
-\r
- String[] lines = result.getMsa().getMethod();\r
-\r
- for (int line = 0; line < lines.length; line++)\r
- OutputHeader += (lines[line] + "\n");\r
-\r
- // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
- seqs = getVamsasAlignment(result.getMsa());\r
- }\r
-\r
- wsInfo.setProgressText(OutputHeader);\r
-\r
- if (seqs != null) {\r
- AlignmentOrder msaorder = new AlignmentOrder(seqs);\r
-\r
- if (preserveOrder) {\r
- jalview.analysis.AlignmentSorter.recoverOrder(seqs);\r
- }\r
-\r
- jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);\r
-\r
- Alignment al = new Alignment(seqs);\r
-\r
- // TODO: JBPNote Should also rename the query sequence sometime...\r
- AlignFrame af = new AlignFrame(al);\r
- af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
- msaorder);\r
-\r
- Desktop.addInternalFrame(af, alTitle,\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- }\r
- } catch (Exception ex) {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-}\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.ws;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.*;
+
+import ext.vamsas.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class MsaWSClient extends WS1Client
+{
+ /**
+ * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+ */
+ ext.vamsas.MuscleWS server;
+
+ AlignFrame alignFrame;
+
+ /**
+ * Creates a new MsaWSClient object that uses a service given by an externally
+ * retrieved ServiceHandle
+ *
+ * @param sh
+ * service handle of type AbstractName(MsaWS)
+ * @param altitle
+ * DOCUMENT ME!
+ * @param msa
+ * DOCUMENT ME!
+ * @param submitGaps
+ * DOCUMENT ME!
+ * @param preserveOrder
+ * DOCUMENT ME!
+ */
+
+ public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
+ jalview.datamodel.AlignmentView msa, boolean submitGaps,
+ boolean preserveOrder, Alignment seqdataset,
+ AlignFrame _alignFrame)
+ {
+ super();
+ alignFrame = _alignFrame;
+ if (!sh.getAbstractName().equals("MsaWS"))
+ {
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ "The Service called \n"
+ + sh.getName()
+ + "\nis not a \nMultiple Sequence Alignment Service !",
+ "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ if ((wsInfo = setWebService(sh)) == null)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "The Multiple Sequence Alignment Service named "
+ + sh.getName() + " is unknown",
+ "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+ startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
+
+ }
+
+ public MsaWSClient()
+ {
+ super();
+ // add a class reference to the list
+ }
+
+ private void startMsaWSClient(String altitle, AlignmentView msa,
+ boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+ {
+ if (!locateWebService())
+ {
+ return;
+ }
+
+ wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ + " of " + altitle + "\nJob details\n");
+ String jobtitle = WebServiceName.toLowerCase();
+ if (jobtitle.endsWith("alignment"))
+ {
+ if (submitGaps
+ && (!jobtitle.endsWith("realignment") || jobtitle
+ .indexOf("profile") == -1))
+ {
+ int pos = jobtitle.indexOf("alignment");
+ jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
+ + altitle;
+ }
+ else
+ {
+ jobtitle = WebServiceName + " of " + altitle;
+ }
+ }
+ else
+ {
+ jobtitle = WebServiceName + (submitGaps ? " re" : " ")
+ + "alignment of " + altitle;
+ }
+
+ MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo,
+ alignFrame, WebServiceName, jobtitle, msa, submitGaps,
+ preserveOrder, seqdataset);
+ wsInfo.setthisService(msathread);
+ msathread.start();
+ }
+
+ /**
+ * Initializes the server field with a valid service implementation.
+ *
+ * @return true if service was located.
+ */
+ private boolean locateWebService()
+ {
+ // TODO: MuscleWS transmuted to generic MsaWS client
+ MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
+
+ try
+ {
+ this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+ ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute
+ // timeout
+ } catch (Exception ex)
+ {
+ wsInfo.setProgressText("Serious! " + WebServiceName
+ + " Service location failed\nfor URL :" + WsURL + "\n"
+ + ex.getMessage());
+ wsInfo.setStatus(WebserviceInfo.ERROR);
+ ex.printStackTrace();
+
+ return false;
+ }
+
+ loc.getEngine().setOption("axis", "1");
+
+ return true;
+ }
+
+ protected String getServiceActionKey()
+ {
+ return "MsaWS";
+ }
+
+ protected String getServiceActionDescription()
+ {
+ return "Multiple Sequence Alignment";
+ }
+
+ /**
+ * look at ourselves and work out if we are a service that can take a profile
+ * and align to it
+ *
+ * @return true if we can send gapped sequences to the alignment service
+ */
+ private boolean canSubmitGaps()
+ {
+ // TODO: query service or extract service handle props to check if we can
+ // realign
+ return (WebServiceName.indexOf("lustal") > -1); // cheat!
+ }
+
+ public void attachWSMenuEntry(JMenu msawsmenu,
+ final ServiceHandle serviceHandle, final AlignFrame alignFrame)
+ {
+ setWebService(serviceHandle, true); // headless
+ JMenuItem method = new JMenuItem(WebServiceName);
+ method.setToolTipText(WsURL);
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ new jalview.ws.MsaWSClient(serviceHandle, alignFrame.getTitle(),
+ msa, false, true, alignFrame.getViewport().getAlignment()
+ .getDataset(), alignFrame);
+
+ }
+
+ });
+ msawsmenu.add(method);
+ if (canSubmitGaps())
+ {
+ // We know that ClustalWS can accept partial alignments for refinement.
+ final JMenuItem methodR = new JMenuItem(serviceHandle.getName()
+ + " Realign");
+ methodR.setToolTipText(WsURL);
+ methodR.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ new jalview.ws.MsaWSClient(serviceHandle, alignFrame.getTitle(),
+ msa, true, true, alignFrame.getViewport().getAlignment()
+ .getDataset(), alignFrame);
+
+ }
+
+ });
+ msawsmenu.add(methodR);
+
+ }
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff