/*
* 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;
}
/*
* 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;
}
/**
* 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;
}
