+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
package jalview.ws;\r
\r
-import org.apache.axis.client.*;\r
-import javax.xml.namespace.QName;\r
-import java.util.*;\r
+import ext.vamsas.*;\r
+\r
+import jalview.analysis.AlignSeq;\r
+\r
import jalview.datamodel.*;\r
+\r
import jalview.gui.*;\r
-import javax.swing.*;\r
-import java.util.*;\r
-import java.awt.*;\r
-import jalview.analysis.AlignSeq;\r
-import ext.vamsas.*;\r
+\r
+import org.apache.axis.client.*;\r
+\r
import vamsas.objects.*;\r
\r
-public class MsaWSClient\r
-{\r
- int jobsRunning = 0;\r
- ext.vamsas.MuscleWS server;\r
- WebserviceInfo wsInfo;\r
- /**\r
- * MsaWSClient\r
- *\r
- * @param msa SequenceI[]\r
- */\r
- public MsaWSClient(SequenceI[] msa)\r
- {\r
- wsInfo = new jalview.gui.WebserviceInfo("Muscle Alignment job",\r
- "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.");\r
+import java.awt.*;\r
\r
+import java.util.*;\r
\r
- wsInfo.setProgressText("Job details\n");\r
+import javax.swing.*;\r
\r
+import javax.xml.namespace.QName;\r
\r
- MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default\r
- try {\r
- this.server = (MuscleWS) loc.getMuscleWS(); // JBPNote will be set from properties\r
- }\r
- catch (Exception ex) {\r
- wsInfo.setProgressText("Serious! MuscleWS Service location failed\nfor URL :"\r
- +loc.getMuscleWSAddress()+"\n"+ex.getMessage());\r
- ex.printStackTrace();\r
- }\r
\r
- MsaWSThread musclethread = new MsaWSThread(msa);\r
- wsInfo.setthisService(musclethread);\r
- musclethread.start();\r
- }\r
+public class MsaWSClient extends WSClient {\r
+ /**\r
+ * server is a WSDL2Java generated stub for an archetypal MsaWSI service.\r
+ */\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
- protected class MsaWSThread extends Thread implements WSClientI\r
- {\r
- String ServiceName = "MuscleWS";\r
- public boolean isCancellable()\r
- {\r
- return true;\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
- String OutputHeader;\r
- vamsas.objects.simple.MsaResult result = null;\r
- vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.\r
- SequenceSet();\r
- String jobId;\r
- int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
- MsaWSThread(SequenceI[] msa)\r
- {\r
- OutputHeader = wsInfo.getProgressText();\r
- vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.\r
- Sequence[msa.length];\r
- for (int i = 0; i < msa.length; i++)\r
- {\r
- seqarray[i] = new vamsas.objects.simple.Sequence();\r
- seqarray[i].setId(msa[i].getName());\r
- seqarray[i].setSeq(AlignSeq.extractGaps("-. ", msa[i].getSequence()));\r
- }\r
- this.seqs = new vamsas.objects.simple.SequenceSet();\r
- this.seqs.setSeqs(seqarray);\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
- boolean jobComplete = false;\r
+ private boolean locateWebService() {\r
+ // TODO: MuscleWS transmuted to generic MsaWS client\r
+ MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default\r
\r
- public void cancelJob() {\r
- if (!jobComplete) {\r
- String cancelledMessage="";\r
try {\r
- vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);\r
- if (cancelledJob.getStatus() == 2)\r
- {\r
- // CANCELLED_JOB\r
- cancelledMessage = "Job cancelled.";\r
- jobComplete = true;\r
- jobsRunning--;\r
- result = null;\r
- }\r
- else\r
- if (cancelledJob.getStatus() == 3)\r
- {\r
- // VALID UNSTOPPABLE JOB\r
- cancelledMessage +=\r
- "Server cannot cancel this job. just close the window.\n";\r
- }\r
- if (cancelledJob.getJobId() != null)\r
- cancelledMessage += "[" + cancelledJob.getJobId() + "]";\r
- cancelledMessage +="\n";\r
- } catch (Exception exc) {\r
- cancelledMessage +="\nProblems cancelling the job : Exception received...\n"+exc+"\n";\r
- exc.printStackTrace();\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
- wsInfo.setProgressText(OutputHeader + cancelledMessage+"\n");\r
- }\r
+\r
+ loc.getEngine().setOption("axis", "1");\r
+\r
+ return true;\r
}\r
\r
- public void run()\r
- {\r
-\r
- StartJob();\r
-\r
- while (!jobComplete && (allowedServerExceptions > 0))\r
- {\r
- try\r
- {\r
- result = server.getResult(jobId);\r
-\r
- if( result.isRunning() )\r
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
- else if( result.isQueued() )\r
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
-\r
- if (result.isFinished())\r
- {\r
- parseResult();\r
- jobComplete = true;\r
- jobsRunning--;\r
- }\r
- else\r
- {\r
- wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());\r
- if (! (result.isJobFailed() || result.isServerError()))\r
- {\r
- Thread.sleep(5000);\r
- // System.out.println("I'm alive "+seqid+" "+jobid);\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
+\r
+ this.seqs = new vamsas.objects.simple.SequenceSet();\r
+ this.seqs.setSeqs(seqarray);\r
}\r
- catch (Exception ex)\r
- {\r
- allowedServerExceptions--;\r
- wsInfo.appendProgressText("\n"+ServiceName+" Server exception!\n" + ex.getMessage());\r
- ex.printStackTrace();\r
+\r
+ public boolean isCancellable() {\r
+ return true;\r
}\r
- }\r
\r
- if (! (result!=null && (result.isJobFailed() || result.isServerError())))\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- else\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
+ public void cancelJob() {\r
+ if ((jobId != null) && !jobId.equals("") && !jobComplete) {\r
+ String cancelledMessage = "";\r
\r
- void StartJob()\r
- {\r
- try\r
- {\r
- vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);\r
- if (jobsubmit.getStatus()==1) {\r
- System.out.println(jobId=jobsubmit.getJobId());\r
- } else {\r
- throw new Exception(jobsubmit.getJobId());\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
- catch (Exception e)\r
- {\r
- System.out.println(ServiceName + " Client: Failed to submit the prediction\n" +\r
- e.toString() + "\n");\r
- e.printStackTrace();\r
- }\r
- }\r
\r
- private void addFloatAnnotations(Alignment al, int[] gapmap, Vector values, String Symname, String Visname, float min, float max, int winLength) {\r
+ public void run() {\r
+ StartJob();\r
\r
- Annotation[] annotations = new Annotation[al.getWidth()];\r
- for (int j = 0; j < values.size(); j++)\r
- {\r
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[gapmap[j]] = new Annotation("", value+"",' ',value);\r
- }\r
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations, min, max, winLength));\r
- }\r
- private jalview.datamodel.Sequence[] getVamsasAlignment(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
- for (int i=0, j=seqs.length; i<j;i++)\r
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i].getSeq());\r
- return msa;\r
- }\r
- void parseResult()\r
- {\r
- SequenceI[] seqs=null;\r
- try {\r
- // OutputHeader = output.getText();\r
- if (result.isFailed()) {\r
- OutputHeader +="Job failed.\n";\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
- if (result.getStatus()!=null) {\r
- OutputHeader += "\n"+result.getStatus();\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 (probably a server side problem)\n"\r
+ + "When contacting Server:"+WsURL + "\n" + e.toString() + "\n");\r
+ this.allowedServerExceptions = 0;\r
+ wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
+ wsInfo.appendProgressText("Failed to submit sequences for alignment.\n"\r
+ + "It is most likely that there is a problem with the server.\n"\r
+ + "Just close the window\n");\r
+\r
+ // e.printStackTrace(); // TODO: JBPNote DEBUG\r
+ }\r
}\r
- if (result.getMsa()!=null) {\r
- OutputHeader += "\nAlignment Object Method Notes\n";\r
- String lines[] = result.getMsa().getMethod();\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
+ 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
- wsInfo.setProgressText(OutputHeader);\r
- if (seqs!=null) {\r
- Alignment al;\r
- al = new Alignment(seqs);\r
-\r
- // TODO: JBPNote Should also rename the query sequence sometime...\r
- AlignFrame af = new AlignFrame(al);\r
- Desktop.addInternalFrame(af,\r
- ServiceName + " Alignment",\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\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
- }catch(Exception ex){ex.printStackTrace();}\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
- }\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
git://source.jalview.org / jalview.git / blobdiff