예제 #1
0
 /*
  * This method gets reportType for BudgetCumulativeNonPersonnel by setting
  * parameters data to reportType
  */
 private ReportType getReportTypeForBudgetCumulativeNonPersonnel(
     ScaleTwoDecimal calculatedCost, ReportTypeVO reportTypeVO) {
   ReportType reportType = ReportType.Factory.newInstance();
   reportType.setBudgetCategoryDescription(reportTypeVO.getBudgetCategoryDesc());
   reportType.setCostElementDescription(reportTypeVO.getCostElementDesc());
   reportType.setCalculatedCost(calculatedCost.doubleValue());
   return reportType;
 }
예제 #2
0
 /*
  * This method gets reportType for CumulativeBudgetSalary by setting data to
  * reportType from passed parameters
  */
 private ReportType getReportTypeForCumulativeBudgetSalary(
     ScaleTwoDecimal vacationRate,
     ScaleTwoDecimal empBenefitRate,
     ScaleTwoDecimal fringe,
     ReportTypeVO reportTypeVO) {
   ReportType reportType = ReportType.Factory.newInstance();
   reportType.setStartDate(reportTypeVO.getStartDate().toString());
   reportType.setEndDate(reportTypeVO.getEndDate().toString());
   reportType.setBudgetCategoryDescription(reportTypeVO.getBudgetCategoryDesc());
   reportType.setPersonName(reportTypeVO.getPersonName());
   reportType.setVacationRate(vacationRate.toString().concat(PERCENTAGE));
   reportType.setEmployeeBenefitRate(empBenefitRate.toString().concat(PERCENTAGE));
   reportType.setFringe(fringe.doubleValue());
   reportType.setCostElementDescription(reportTypeVO.getCostElementDesc());
   reportType.setInvestigatorFlag(reportTypeVO.getInvestigatorFlag());
   if (reportTypeVO.getBudgetCategoryCode() != null) {
     reportType.setBudgetCategoryCode(Integer.parseInt(reportTypeVO.getBudgetCategoryCode()));
   }
   reportType.setSalaryRequested(reportTypeVO.getSalaryRequested().doubleValue());
   return reportType;
 }
예제 #3
0
  /**
   * Marshalls the additional parameters and returns them as a string.
   *
   * @return A string holding the marshalled parameters
   */
  private String marshallAdditionalParameters() {
    String parameters = "";

    if (accessions != null && accessions.size() > 0) {
      parameters += "ACCESSION=";
      for (int i = 0; i < accessions.size(); i++)
        parameters += ((i > 0) ? "," : "") + "\"" + accessions.get(i) + "\"";
      parameters += "\n";
    }

    if (charge != null) parameters += "CHARGE=" + charge + "\n";

    if (enzyme != null) parameters += "CLE=" + enzyme + "\n";

    if (searchTitle != null) parameters += "COM=" + searchTitle + "\n";

    if (precursorRemoval != null) parameters += "CUTOUT=" + precursorRemoval + "\n";

    if (database != null) parameters += "DB=" + database + "\n";

    if (performDecoySearch != null)
      parameters += "DECOY=" + ((performDecoySearch) ? "1" : "0") + "\n";

    if (isErrorTolerant != null)
      parameters += "ERRORTOLERANT=" + ((isErrorTolerant) ? "1" : "0") + "\n";

    if (format != null) parameters += "FORMAT=" + format + "\n";

    if (frames != null && frames.size() > 0) {
      parameters += "FRAMES=";
      for (int i = 0; i < frames.size(); i++)
        parameters += ((i > 0) ? "," : "") + frames.get(i).toString();
      parameters += "\n";
    }

    if (instrument != null) parameters += "INSTRUMENT=" + instrument + "\n";

    if (variableModifications != null) parameters += "IT_MODS=" + variableModifications + "\n";

    if (fragmentIonTolerance != null)
      parameters += "ITOL=" + fragmentIonTolerance.toString() + "\n";

    if (fragmentIonToleranceUnit != null)
      parameters +=
          "ITOLU="
              + ((fragmentIonToleranceUnit == FragmentToleranceUnits.MMU) ? "mmu" : "Da")
              + "\n";

    if (massType != null)
      parameters += "MASS=" + ((massType == MassType.AVERAGE) ? "Average" : "Monoisotopic") + "\n";

    if (fixedMofications != null) parameters += "MODS=" + fixedMofications + "\n";

    if (peptideIsotopeError != null)
      parameters += "PEP_ISOTOPE_ERROR=" + peptideIsotopeError.toString() + "\n";

    if (partials != null) parameters += "PFA=" + partials.toString() + "\n";

    if (precursor != null) parameters += "PRECURSOR=" + precursor.toString() + "\n";

    if (quantitation != null) parameters += "QUANTITATION=" + quantitation + "\n";

    if (maxHitsToReport != null) parameters += "REPORT=" + maxHitsToReport + "\n";

    if (reportType != null) parameters += "REPTYPE=" + reportType.toString() + "\n";

    if (searchType != null) parameters += "SEARCH=" + searchType.toString() + "\n";

    if (proteinMass != null) parameters += "SEG=" + proteinMass + "\n";

    if (taxonomy != null) parameters += "TAXONOMY=" + taxonomy + "\n";

    if (peptideMassTolerance != null) parameters += "TOL=" + peptideMassTolerance.toString() + "\n";

    if (peptideMassToleranceUnit != null)
      parameters += "TOLU=" + peptideMassToleranceUnit.toString() + "\n";

    if (userMail != null) parameters += "USEREMAIL=" + userMail + "\n";

    if (userName != null) parameters += "USERNAME="******"\n";

    if (userParameter != null) {
      for (Integer i = 0; i < userParameter.size(); i++) {
        parameters +=
            "USER" + ((i < 10) ? "0" : "") + i.toString() + "=" + userParameter.get(i) + "\n";
      }
    }

    return parameters;
  }