Package uk.ac.bbsrc.tgac.miso.core.data.impl.pacbio

Examples of uk.ac.bbsrc.tgac.miso.core.data.impl.pacbio.PacBioRun

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  }

  public JSONObject changePacBioContainer(HttpSession session, JSONObject json) {
    int numContainers = json.getInt("numContainers");
    StringBuilder b = new StringBuilder();
    PacBioRun run = (PacBioRun) session.getAttribute("run_" + json.getString("run_cId"));
    run.getSequencerPartitionContainers().clear();

    for (int i = 0; i < numContainers; i++) {
      b.append("<h2>Container " + (i + 1) + "</h2>");
      b.append("<table class='in'>");
      b.append("<tr><td>ID:</td><td><button onclick='Run.container.lookupContainer(this, " + i + ");' type='button' class='right-button ui-state-default ui-corner-all'>Lookup</button><div style='overflow:hidden'><input type='text' id='sequencerPartitionContainers[" + i + "].identificationBarcode' name='sequencerPartitionContainers[" + i + "].identificationBarcode'/></div></td></tr>");
      b.append("<tr><td>Location:</td><td><input type='text' id='sequencerPartitionContainers[" + i + "].locationBarcode' name='sequencerPartitionContainers[" + i + "].locationBarcode'/></td></tr>");
      b.append("<tr><td>Paired:</td><td><input type='checkbox' id='sequencerPartitionContainers[" + i + "].paired' name='sequencerPartitionContainers[" + i + "].paired'/></td></tr>");
      b.append("</table>");
      b.append("<div id='partitionErrorDiv'> </div>");
      b.append("<div id='partitionDiv'>");

      b.append("<input id='chamber1' name='container" + i + "Select' onchange='Run.ui.changePacBioChamber(this, " + i + ");' type='radio' value='1'/>1 ");
      b.append("<input id='chamber2' name='container" + i + "Select' onchange='Run.ui.changePacBioChamber(this, " + i + ");' type='radio' value='2'/>2 ");
      b.append("<input id='chamber3' name='container" + i + "Select' onchange='Run.ui.changePacBioChamber(this, " + i + ");' type='radio' value='3'/>3 ");
      b.append("<input id='chamber4' name='container" + i + "Select' onchange='Run.ui.changePacBioChamber(this, " + i + ");' type='radio' value='4'/>4 ");
      b.append("<input id='chamber5' name='container" + i + "Select' onchange='Run.ui.changePacBioChamber(this, " + i + ");' type='radio' value='5'/>5 ");
      b.append("<input id='chamber6' name='container" + i + "Select' onchange='Run.ui.changePacBioChamber(this, " + i + ");' type='radio' value='6'/>6 ");
      b.append("<input id='chamber7' name='container" + i + "Select' onchange='Run.ui.changePacBioChamber(this, " + i + ");' type='radio' value='7'/>7 ");
      b.append("<input id='chamber8' name='container" + i + "Select' onchange='Run.ui.changePacBioChamber(this, " + i + ");' type='radio' value='8'/>8<br/>");

      b.append("<div id='containerdiv" + i + "'> </div>");
      b.append("</div>");
      SequencerPartitionContainer<SequencerPoolPartition> f = dataObjectFactory.getSequencerPartitionContainer();
      run.addSequencerPartitionContainer(f);
    }
    return JSONUtils.SimpleJSONResponse(b.toString());
  }
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  public JSONObject changePacBioChamber(HttpSession session, JSONObject json) {
    int numChambers = json.getInt("numChambers");
    int container = json.getInt("container");

    PacBioRun run = (PacBioRun) session.getAttribute("run_" + json.getString("run_cId"));
    SequencerPartitionContainer<SequencerPoolPartition> f = run.getSequencerPartitionContainers().get(container);
    f.setPartitionLimit(numChambers);
    f.initEmptyPartitions();

    StringBuilder b = new StringBuilder();
    b.append("<table class='in'>");
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            }

            if (attemptRunPopulation) {
              if (r == null) {
                log.info("\\_ Saving new run and status: " + is.getRunName());
                r = new PacBioRun(status);
                r.setAlias(run.getString("runName"));
                r.setDescription(m.group(2));
                r.setPairedEnd(false);

                if (run.has("fullPath")) {
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      throw new SecurityException();
    }
  }

  public Run getPacBioRun() {
    return new PacBioRun();
  }
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  public Run getPacBioRun() {
    return new PacBioRun();
  }

  public Run getPacBioRun(User user) {
    return new PacBioRun(user);
  }
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    return new PacBioRun(user);
  }

  public Run getPacBioRun(Experiment experiment, User user) {
    if (experiment.userCanWrite(user)) {
      return new PacBioRun(user);

    }
    else {
      throw new SecurityException();
    }
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Related Classes of uk.ac.bbsrc.tgac.miso.core.data.impl.pacbio.PacBioRun

  • com.eaglegenomics.simlims.core.SecurityProfile
  • uk.ac.bbsrc.tgac.miso.core.factory.TgacDataObjectFactory
  • uk.ac.bbsrc.tgac.miso.notification.consumer.service.mechanism.PacBioNotificationMessageConsumerMechanism
  • uk.ac.bbsrc.tgac.miso.spring.ajax.RunControllerHelperService
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