private boolean isValidAnalysis(DatasetTimp[] datasets, GtaModelReference gtaModelReference) {
Tgm tgm = getModel(gtaModelReference);
String feedback = null;
boolean run = true;
for (DatasetTimp dataset : datasets) {
if (dataset == null) {
run = false;
}
}
if (!tgm.getDat().getIrfparPanel().isMirf()) {
if (tgm.getDat().getIrfparPanel().getParmu() != null
|| tgm.getDat().getIrfparPanel().getPartau() != null) {
if (!tgm.getDat().getIrfparPanel().getParmu().isEmpty()
|| !tgm.getDat().getIrfparPanel().getPartau().isEmpty()) {
Double testLamda = tgm.getDat().getIrfparPanel().getLamda();
if (testLamda == null || testLamda.isNaN()) {
run = false;
feedback = "Parmu or Partau specified but no center wavelength was specified.";
}
}
}
}
if (feedback != null) {
NotifyDescriptor errorMessage =
new NotifyDescriptor.Exception(
new Exception(
"Invalid Model: \n" + "" + feedback + "\n" + "Analysis was not started."));
DialogDisplayer.getDefault().notify(errorMessage);
}
return run;
}
private static String get_oscillations(Tgm tgm) {
String oscSpecStr = null;
if (tgm.getDat().getOscspecPanel() != null) {
OscspecPanelModel oscspecPanel = tgm.getDat().getOscspecPanel();
String typeOsc = oscspecPanel.getOscspec().getType();
if (typeOsc != null) {
oscSpecStr = "oscspec = list(type = \"" + typeOsc + "\"";
if (typeOsc.equalsIgnoreCase("harmonic")) {
oscSpecStr = oscSpecStr + ",";
// ArrayList<Double> seqstart = (ArrayList<Double>)
// tgm.getDat().getOscspecPanel().getOscpar();
ArrayList<Double> seqstart =
(ArrayList<Double>) tgm.getDat().getOscspecPanel().getOscspec().getStart();
if (seqstart != null && !seqstart.isEmpty()) {
oscSpecStr = oscSpecStr + "start = c(";
for (int i = 0; i < seqstart.size(); i++) {
if (i > 0) {
oscSpecStr = oscSpecStr + ",";
}
oscSpecStr = oscSpecStr + seqstart.get(i);
}
oscSpecStr = oscSpecStr + ")";
}
}
}
if (oscSpecStr != null) {
oscSpecStr = oscSpecStr + ")";
}
} else {
}
return oscSpecStr;
}
private static String get_measured_irf(Tgm tgm) {
String meaIrfString = null;
// System.out.println("DDD"+Current.GetcurrMIRF());
IrfparPanelModel irfparPanel = tgm.getDat().getIrfparPanel();
if (irfparPanel.isMirf()) {
int conv = irfparPanel.getConvalg();
meaIrfString = "measured_irf= c( " + tgm.getDat().getIrfparPanel().getMeasuredIrf();
meaIrfString = meaIrfString + " ), convalg= ";
meaIrfString = meaIrfString.concat(String.valueOf(conv));
if (conv == 3) {
meaIrfString = meaIrfString.concat(", reftau = ");
meaIrfString = meaIrfString.concat(String.valueOf(irfparPanel.getReftau()));
}
}
return meaIrfString;
}
private static String get_clpequspec(Tgm tgm) {
String clpequspecCall = null;
String clpequCall = null;
int count = 0;
KMatrixPanelModel kMatrixPanel = tgm.getDat().getKMatrixPanel();
int size = kMatrixPanel.getContrainsMatrix().getData().size();
for (int i = 0; i < size; i++) { // to
for (int j = 0; j < size; j++) { // from
Double min = kMatrixPanel.getContrainsMatrix().getData().get(i).getMin().get(j);
Double max = kMatrixPanel.getContrainsMatrix().getData().get(i).getMax().get(j);
Double scal;
if (!kMatrixPanel.getContrainsMatrix().getData().get(i).getScal().isEmpty()) {
scal = kMatrixPanel.getContrainsMatrix().getData().get(i).getScal().get(j);
} else {
scal = 1.0;
}
if (min != null && max != null) {
if (count == 0) {
clpequspecCall = "clpequspec = list(";
clpequCall = "clpequ = c(";
}
clpequspecCall =
clpequspecCall
+ "list("
+ "to="
+ String.valueOf(i + 1)
+ ",from="
+ String.valueOf(j + 1)
+ ",low="
+ String.valueOf(min)
+ ",high="
+ String.valueOf(max)
+ "),";
if (scal != null) {
clpequCall = clpequCall + String.valueOf(scal) + ',';
} else {
clpequCall = clpequCall + "1,";
}
count++;
}
}
}
// Removes last comma:
if (count > 0) {
clpequspecCall = clpequspecCall.substring(0, clpequspecCall.length() - 1);
clpequCall = clpequCall.substring(0, clpequCall.length() - 1);
clpequspecCall = clpequspecCall + ")";
clpequCall = clpequCall + ")";
clpequspecCall = clpequspecCall + "," + clpequCall;
}
if (addToFixed == null) {
addToFixed = "clpequ=1:" + count;
} else {
addToFixed = addToFixed + ", clpequ=1:" + count;
}
return clpequspecCall;
}
// private static String get_constrained(Tgm tgm) {
// Dat dat = tgm.getDat();
// KinparPanelModel kinparPanelModel = dat.getKinparPanel();
// String constrained = "constrained = list(";
// double cc;
// int count=0;
// for (int i = 0; i < kinparPanelModel.getKinpar().size(); i++) {
// if(kinparPanelModel.getKinpar().get(i).isConstrained()){
// if(kinparPanelModel.getKinpar().get(i).getMin() != null) {
// if(count > 0)
// constrained = constrained + ",";
// cc = kinparPanelModel.getKinpar().get(i).getMin();
// constrained = constrained + "list(what=\"kinpar\", ind = "+
// Integer.toString(i+1) +", low=" + cc + ")";
// count++;
// }
// else if(kinparPanelModel.getKinpar().get(i).getMax() != null) {
// if(count > 0)
// constrained = constrained + ",";
// cc = kinparPanelModel.getKinpar().get(i).getMax();
// constrained = constrained + "list(what=\"kinpar\", ind = "+
// Integer.toString(i+1) +", high=" + cc + ")";
// count++;
// }
// }
// }
// constrained = constrained + ")";
// // need to fill in other parameters here, once we have panels for them
// return constrained;
// }
private static String get_seqmod(Tgm tgm) {
KinparPanelModel kinparPanelModel = tgm.getDat().getKinparPanel();
if (kinparPanelModel.isSeqmod()) {
return "seqmod = TRUE";
} else {
return "seqmod = FALSE";
}
}
private static String get_cohArtefact(Tgm tgm) {
String cohSpecStr = null;
CohspecPanelModel cohspecPanel = tgm.getDat().getCohspecPanel();
String typeCoh = cohspecPanel.getCohspec().getType();
if (typeCoh != null) {
cohSpecStr = "cohspec = list(type = \"" + typeCoh + "\"";
if (typeCoh.equalsIgnoreCase("seq") || typeCoh.equalsIgnoreCase("mix")) {
cohSpecStr = cohSpecStr + ",";
ArrayList<Double> seqstart =
(ArrayList<Double>) tgm.getDat().getCohspecPanel().getCohspec().getSeqstart();
if (seqstart != null && !seqstart.isEmpty()) {
cohSpecStr = cohSpecStr + "start = c(";
for (int i = 0; i < seqstart.size(); i++) {
if (i > 0) {
cohSpecStr = cohSpecStr + ",";
}
cohSpecStr = cohSpecStr + seqstart.get(i);
}
cohSpecStr = cohSpecStr + ")";
}
}
if (typeCoh.equalsIgnoreCase("xpm")) {
cohSpecStr = cohSpecStr + ") ,";
ArrayList<Double> seqstart =
(ArrayList<Double>) tgm.getDat().getCohspecPanel().getCohspec().getSeqstart();
if (seqstart != null && !seqstart.isEmpty()) {
cohSpecStr = cohSpecStr + "coh = c(";
for (int i = 0; i < seqstart.size(); i++) {
if (i > 0) {
cohSpecStr = cohSpecStr + ",";
}
cohSpecStr = cohSpecStr + seqstart.get(i);
}
}
}
if (typeCoh.equalsIgnoreCase("freeirfdisp")) {
// TODO: implement freeirfdisp etc.
System.out.println("coh = c( " + cohspecPanel.getCoh() + ")");
}
}
if (cohSpecStr != null) {
cohSpecStr = cohSpecStr + ")";
}
return cohSpecStr;
}
private static String get_irf(Tgm tgm) {
IrfparPanelModel irfparPanel = tgm.getDat().getIrfparPanel();
String irfStr = null;
if (irfparPanel.isMirf() != null && irfparPanel.isMirf()) {
irfStr = get_measured_irf(tgm);
} else {
IrfparPanelModel irfPanel = tgm.getDat().getIrfparPanel();
int count = 0;
if (irfPanel.getIrf().size() > 0) {
if (irfPanel.getIrf().size() == 2) {
irfStr = "irffun = \"gaus\",";
} else {
if (irfPanel.getIrf().size() == 4) {
irfStr = "irffun = \"doublegaus\",";
} else {
irfStr = "irffun = \"multiplegaus\",";
}
}
irfStr = irfStr + "irfpar = ";
for (int i = 0; i < irfPanel.getIrf().size(); i++) {
if (count > 0) {
irfStr = irfStr + ",";
} else {
irfStr = irfStr + "c(";
}
irfStr = irfStr + Double.toString(irfPanel.getIrf().get(i));
count++;
}
irfStr = irfStr + ")";
if (irfPanel.getIrf().size() == 4) {
irfStr = irfStr + ", doublegaus = TRUE";
}
if (irfPanel.isBacksweepEnabled() != null && irfPanel.isBacksweepEnabled()) {
irfStr =
irfStr
+ ", streak = TRUE, streakT = "
+ String.valueOf(irfPanel.getBacksweepPeriod());
}
}
}
return irfStr;
}
public static String get_weightpar(Tgm tgm) {
WeightParPanelModel weightParPanelModel = tgm.getDat().getWeightParPanel();
String weightpar = null;
int size = weightParPanelModel.getWeightpar().size();
if (size > 0) {
weightpar = "weightpar = list(";
for (int i = 0; i < size; i++) {
if ((i > 0) && (i < size)) {
weightpar = weightpar + ",";
}
weightpar = weightpar + "c(";
WeightPar wp = weightParPanelModel.getWeightpar().get(i);
Double[] temparray = {
wp.getMin1(), wp.getMax1(), wp.getMin2(), wp.getMax2(), wp.getWeight()
};
for (int j = 0; j < temparray.length; j++) {
if (temparray[j] != null && !temparray[j].isNaN()) {
weightpar = weightpar + String.valueOf(temparray[j]);
} else {
weightpar = weightpar + "NA";
}
if (j < temparray.length - 1) {
weightpar = weightpar + ",";
}
}
weightpar = weightpar + ")";
}
}
if (weightParPanelModel.isPoisson() != null && weightParPanelModel.isPoisson()) {
if (weightpar == null) {
weightpar = "";
}
if (weightpar.isEmpty()) {
weightpar = "weightpar = list(poisson = TRUE";
} else {
weightpar = weightpar + ", poisson = TRUE";
}
}
if (weightpar != null) {
if (!weightpar.isEmpty()) {
weightpar = weightpar + ")";
}
}
return weightpar;
}
public static String get_kinpar(Tgm tgm) {
KinparPanelModel kinparPanelModel = tgm.getDat().getKinparPanel();
String kinpar = null;
int size = kinparPanelModel.getKinpar().size();
if (size > 0) {
kinpar = "kinpar = c(";
double k;
for (int i = 0; i < size; i++) {
if (i > 0) {
kinpar = kinpar + ",";
}
k = kinparPanelModel.getKinpar().get(i).getStart();
kinpar = kinpar + Double.toString(k);
}
kinpar = kinpar + ")";
}
return kinpar;
}
private static String get_positivepar(Tgm tgm) {
KinparPanelModel kinparPanelModel = tgm.getDat().getKinparPanel();
int count = 0;
String positivepar = null;
if (kinparPanelModel.isPositivepar()) {
count++;
positivepar = "positivepar = c(\"kinpar\"";
}
// need to fill in other parameters here, once we have panels for them
// if(count>0)
// positivepar = positivepar + ",";
if (count < 1) {
positivepar = "positivepar=vector()";
} else {
positivepar = positivepar + ")";
}
return positivepar;
}
private static String get_relations(Tgm tgm) {
String relationsCall = null;
String fixed = null;
KMatrixPanelModel kMatrixPanel = tgm.getDat().getKMatrixPanel();
int size = kMatrixPanel.getRelationsMatrix().getData().size();
// prelspec = list(list(what1="kinpar", what2="kinpar",ind1=6,ind2=1, start=c(0.05,0))),
Double c0, c1;
Boolean fc0, fc1;
int count = 0;
for (int i = 0; i < size; i++) {
for (int j = 0; j < size; j++) {
c0 = kMatrixPanel.getRelationsMatrix().getData().get(i).getC0().get(j);
c1 = kMatrixPanel.getRelationsMatrix().getData().get(i).getC1().get(j);
fc0 = kMatrixPanel.getRelationsMatrix().getData().get(i).getC0Fixed().get(j);
fc1 = kMatrixPanel.getRelationsMatrix().getData().get(i).getC1Fixed().get(j);
if ((!Double.isNaN(c0)) && (!Double.isNaN(c1))) {
if (count == 0) {
relationsCall = "prelspec = list(";
} else {
relationsCall = relationsCall + ",";
}
relationsCall =
relationsCall
+ "list(what1=\"kinpar\", what2=\"kinpar\",ind1="
+ (i + 1)
+ ", ind2="
+ (j + 1)
+ ", start=c("
+ c1
+ ","
+ c0
+ "))";
if (fc1) {
if (fixed == null) {
fixed = "prel = c(";
} else if (count != 0) {
fixed = fixed + ",";
}
fixed = fixed + (2 * count + 1);
}
if (fc0) {
if (fixed == null) {
fixed = "prel = c(";
} else {
if ((count != 0) || ((count == 0) && (fc0))) {
fixed = fixed + ",";
}
}
fixed = fixed + (2 * count + 2);
}
count++;
}
}
}
if (relationsCall != null) {
relationsCall = relationsCall + ")";
}
if (fixed != null) {
fixed = fixed + ")";
if (addToFixed != null) {
addToFixed = addToFixed + "," + fixed;
} else {
addToFixed = fixed;
}
}
return relationsCall;
}
private static String get_mod_type(Tgm tgm) {
addToFixed = null;
String mod_type = "mod_type = \"" + tgm.getDat().getModType() + "\"";
return mod_type;
}
private static String get_clp0(Tgm tgm) {
String clp0Call = null;
int indexOfComponent = 0;
KMatrixPanelModel kMatrix = tgm.getDat().getKMatrixPanel();
int size = kMatrix.getSpectralContraints().getMax().size();
if (size > 0) {
int count = 0;
for (int i = 0; i < size; i++) {
Double min = kMatrix.getSpectralContraints().getMin().get(i);
Double max = kMatrix.getSpectralContraints().getMax().get(i);
if (min != null && max != null) {
if (count == 0) {
clp0Call = "clp0 = list(";
} else {
clp0Call = clp0Call + ",";
}
clp0Call =
clp0Call
+ "list(low = "
+ Double.valueOf(min)
+ ", high ="
+ Double.valueOf(max)
+ ", comp = "
+ (i + 1)
+ ")";
count++;
}
}
}
if (tgm.getDat().getCohspecPanel().isClp0Enabled() != null) {
if (tgm.getDat().getCohspecPanel().isClp0Enabled()) {
if (clp0Call != null) {
clp0Call = clp0Call + ",";
} else {
clp0Call = "clp0 = list(";
}
if (kMatrix.getJVector() != null) {
if (kMatrix.getJVector().getVector().size() > 0) {
indexOfComponent = kMatrix.getJVector().getVector().size() + 1;
} else {
indexOfComponent = (tgm.getDat().getKinparPanel().getKinpar().size() + 1);
}
} else {
indexOfComponent = (tgm.getDat().getKinparPanel().getKinpar().size() + 1);
}
clp0Call =
clp0Call
+ "list(low = "
+ tgm.getDat().getCohspecPanel().getClp0Min()
+ ", high = "
+ tgm.getDat().getCohspecPanel().getClp0Max()
+ ", comp = "
+ indexOfComponent
+ ")";
}
}
if (clp0Call != null) {
clp0Call = clp0Call + ")";
}
return clp0Call;
}
private static String get_parmu(Tgm tgm) {
String parmuStr = null;
IrfparPanelModel irfPanel = tgm.getDat().getIrfparPanel();
if (irfPanel.getParmu() != null) {
if (irfPanel.getParmu().trim().length() != 0) {
if (irfPanel.getLamda() != null) {
if (irfPanel.getLamda() > 0) {
parmuStr = "lambdac = " + String.valueOf(irfPanel.getLamda());
}
}
if (parmuStr == null) {
parmuStr = "parmu = list(";
} else {
parmuStr = parmuStr.concat(", parmu = list(");
}
parmuStr = parmuStr + "c(" + irfPanel.getParmu() + "))";
}
if (irfPanel.getDispmufun() != null) {
if (parmuStr != null) {
if (irfPanel.getDispmufun().equals("poly")) {
parmuStr = parmuStr.concat(", dispmufun = \"poly\"");
} else if (irfPanel.getDispmufun().equals("discrete")) {
parmuStr = parmuStr.concat(", dispmufun = \"discrete\"");
}
} else {
if (irfPanel.getDispmufun().equals("poly")) {
parmuStr = "dispmufun = \"poly\"";
} else if (irfPanel.getDispmufun().equals("discrete")) {
parmuStr = "dispmufun = \"discrete\"";
}
}
}
}
if (irfPanel.getPartau() != null) {
if (irfPanel.getPartau().trim().length() != 0) {
if (irfPanel.getLamda() != null) {
if (irfPanel.getLamda() > 0) {
parmuStr = "lambdac = " + String.valueOf(irfPanel.getLamda());
}
}
if (parmuStr == null) {
parmuStr = "partau= list(";
} else {
parmuStr = parmuStr.concat(", partau= list(");
}
parmuStr = parmuStr + "c(" + irfPanel.getPartau() + "))";
}
if (irfPanel.getDisptaufun() != null && parmuStr != null) {
if (irfPanel.getDisptaufun().equals("poly")) {
parmuStr = parmuStr.concat(", disptaufun = \"poly\"");
} else if (irfPanel.getDisptaufun().equals("discrete")) {
parmuStr = parmuStr.concat(", disptaufun = \"discrete\"");
}
} else {
if (irfPanel.getDisptaufun().equals("poly")) {
parmuStr = "disptaufun = \"poly\"";
} else if (irfPanel.getDisptaufun().equals("discrete")) {
parmuStr = "disptaufun = \"discrete\"";
}
}
}
return parmuStr;
}
// Private classes
public static String get_kmatrix(Tgm tgm) {
String kMatrixCall = null;
KMatrixPanelModel kMatrix = tgm.getDat().getKMatrixPanel();
int matrixSize = kMatrix.getJVector().getVector().size();
if (matrixSize > 0) {
kMatrixCall = "kmat = array(c(";
kMatrixCall =
kMatrixCall.concat(String.valueOf(kMatrix.getKMatrix().getData().get(0).getRow().get(0)));
for (int j = 1; j < matrixSize; j++) {
kMatrixCall =
kMatrixCall.concat(
"," + String.valueOf(kMatrix.getKMatrix().getData().get(j).getRow().get(0)));
}
for (int i = 1; i < matrixSize; i++) {
for (int j = 0; j < matrixSize; j++) {
kMatrixCall =
kMatrixCall.concat(
"," + String.valueOf(kMatrix.getKMatrix().getData().get(j).getRow().get(i)));
}
}
for (int i = 0; i < matrixSize; i++) {
for (int j = 0; j < matrixSize; j++) {
kMatrixCall =
kMatrixCall.concat(
","
+ String.valueOf(
kMatrix.getKMatrix().getData().get(j + matrixSize).getRow().get(i)));
}
}
kMatrixCall = kMatrixCall.concat("), dim = c(");
kMatrixCall =
kMatrixCall.concat(
String.valueOf(matrixSize) + "," + String.valueOf(matrixSize) + ",2))");
kMatrixCall = kMatrixCall.concat(", jvec = c(");
// TODO: verify jVector
kMatrixCall = kMatrixCall.concat(String.valueOf(kMatrix.getJVector().getVector().get(0)));
for (int j = 1; j < matrixSize; j++) {
kMatrixCall =
kMatrixCall.concat("," + String.valueOf(kMatrix.getJVector().getVector().get(j)));
}
kMatrixCall = kMatrixCall.concat(")");
int size = kMatrix.getKinScal().size();
if (size > 0) {
kMatrixCall = kMatrixCall.concat(", kinscal = c(");
double k;
for (int i = 0; i < size; i++) {
if (i > 0) {
kMatrixCall = kMatrixCall + ",";
}
k = kMatrix.getKinScal().get(i).getStart();
kMatrixCall = kMatrixCall + Double.toString(k);
}
kMatrixCall = kMatrixCall + ")";
}
}
return kMatrixCall;
}
private void writeResults(
TimpResultDataset[] results, GtaModelReference modelReference, String[] nlsprogressResult) {
Tgm model = getModel(modelReference);
GtaResult newResultsObject = new GtaResult();
String freeResultsFilename =
FileUtil.findFreeFileName(resultsfolder, resultsfolder.getName(), "summary");
try {
writeSummary(resultsfolder, freeResultsFilename);
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
if (nlsprogressResult != null) {
for (int i = 0; i < nlsprogressResult.length; i++) {
NlsProgress progress = new NlsProgress();
progress.setRss(nlsprogressResult[i]);
newResultsObject.getNlsprogress().add(progress);
}
}
for (int i = 0; i < results.length; i++) {
TimpResultDataset timpResultDataset = results[i];
timpResultDataset.setType(datasets[i].getType());
newResultsObject.getDatasets().add(new Dataset());
newResultsObject.getDatasets().get(i).setDatasetFile(new OutputFile());
newResultsObject
.getDatasets()
.get(i)
.getDatasetFile()
.setFilename(datasetContainer.getDatasets().get(i).getFilename());
newResultsObject
.getDatasets()
.get(i)
.getDatasetFile()
.setPath(datasetContainer.getDatasets().get(i).getPath());
newResultsObject.getDatasets().get(i).getDatasetFile().setFiletype(datasets[i].getType());
newResultsObject.getDatasets().get(i).setId(String.valueOf(i + 1));
if (model.getDat().getIrfparPanel().getLamda() != null) {
timpResultDataset.setLamdac(model.getDat().getIrfparPanel().getLamda());
}
if (datasets[i].getType().equalsIgnoreCase("flim")) {
timpResultDataset.setOrheigh(datasets[i].getOriginalHeight());
timpResultDataset.setOrwidth(datasets[i].getOriginalWidth());
timpResultDataset.setIntenceIm(datasets[i].getIntenceIm().clone());
timpResultDataset.setMaxInt(datasets[i].getMaxInt());
timpResultDataset.setMinInt(datasets[i].getMinInt());
timpResultDataset.setX(datasets[i].getX().clone());
timpResultDataset.setX2(datasets[i].getX2().clone());
}
try {
String freeFilename =
FileUtil.findFreeFileName(
resultsfolder,
resultsfolder.getName() + "_d" + (i + 1) + "_" + timpResultDataset.getDatasetName(),
"timpres");
timpResultDataset.setDatasetName(freeFilename);
writeTo = resultsfolder.createData(freeFilename, "timpres");
ObjectOutputStream stream = new ObjectOutputStream(writeTo.getOutputStream());
stream.writeObject(timpResultDataset);
stream.close();
newResultsObject.getDatasets().get(i).setResultFile(new OutputFile());
newResultsObject.getDatasets().get(i).getResultFile().setFilename(freeFilename);
newResultsObject
.getDatasets()
.get(i)
.getResultFile()
.setPath(FileUtil.getRelativePath(project.getProjectDirectory(), resultsfolder));
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
try {
writeResultsXml(newResultsObject);
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
private static String get_fixed(Tgm tgm) {
String fixedStr = null;
KinparPanelModel kinparPanelModel = tgm.getDat().getKinparPanel();
int count = 0;
for (int i = 0; i < kinparPanelModel.getKinpar().size(); i++) {
if (kinparPanelModel.getKinpar().get(i).isFixed()) {
if (count > 0) {
fixedStr = fixedStr + ",";
} else {
fixedStr = "fixed = list(kinpar=c(";
}
fixedStr = fixedStr + String.valueOf(i + 1);
count++;
}
}
if (count > 0) {
fixedStr = fixedStr + ")";
}
count = 0;
KMatrixPanelModel kmatPanel = tgm.getDat().getKMatrixPanel();
for (int i = 0; i < kmatPanel.getKinScal().size(); i++) {
if (kmatPanel.getKinScal().get(i).isFixed()) {
if (count > 0) {
fixedStr = fixedStr + ",";
} else {
if (fixedStr != null) {
fixedStr = fixedStr + ", kinscal=c(";
} else {
fixedStr = "fixed = list(kinscal=c(";
}
}
fixedStr = fixedStr + String.valueOf(i + 1);
count++;
}
}
if (count > 0) {
fixedStr = fixedStr + ")";
}
count = 0;
IrfparPanelModel irfPanel = tgm.getDat().getIrfparPanel();
for (int i = 0; i < irfPanel.getFixed().size(); i++) {
if (irfPanel.getFixed().get(i)) {
if (count > 0) {
fixedStr = fixedStr + ",";
} else {
if (fixedStr != null) {
fixedStr = fixedStr + ", irfpar=c(";
} else {
fixedStr = "fixed = list(irfpar=c(";
}
}
fixedStr = fixedStr + String.valueOf(i + 1);
count++;
}
}
if (count > 0) {
fixedStr = fixedStr + ")";
}
if (irfPanel.getParmu() != null) {
if (irfPanel.isParmufixed() != null && irfPanel.isParmufixed()) {
if (fixedStr != null) {
fixedStr = fixedStr + ", parmu=c(";
} else {
fixedStr = "fixed = list(parmu=c(";
}
String[] doubles = irfPanel.getParmu().split(",");
fixedStr = fixedStr + "1:" + String.valueOf(doubles.length);
fixedStr = fixedStr + ")";
}
}
if (irfPanel.getPartau() != null) {
if (irfPanel.isPartaufixed()) {
if (fixedStr != null) {
fixedStr = fixedStr + ", partau=c(";
} else {
fixedStr = "fixed = list(partau=c(";
}
String[] doubles = irfPanel.getPartau().split(",");
fixedStr = fixedStr + "1:" + String.valueOf(doubles.length);
fixedStr = fixedStr + ")";
}
}
count = 0;
for (int i = 0; i < tgm.getDat().getCohspecPanel().getCohspec().getFixed().size(); i++) {
if (tgm.getDat().getCohspecPanel().getCohspec().getFixed().get(i)) {
if (count > 0) {
fixedStr = fixedStr + ",";
} else {
if (fixedStr != null) {
fixedStr = fixedStr + ", coh=c(";
} else {
fixedStr = "fixed = list(coh=c(";
}
}
fixedStr = fixedStr + String.valueOf(i + 1);
count++;
}
}
if (count > 0) {
fixedStr = fixedStr + ")";
}
if (tgm.getDat().getOscspecPanel() != null) {
if (tgm.getDat().getOscspecPanel().getOscspec() != null) {
count = 0;
for (int i = 0; i < tgm.getDat().getOscspecPanel().getOscspec().getFixed().size(); i++) {
if (tgm.getDat().getOscspecPanel().getOscspec().getFixed().get(i)) {
if (count > 0) {
fixedStr = fixedStr + ",";
} else {
if (fixedStr != null) {
fixedStr = fixedStr + ", oscpar=c(";
} else {
fixedStr = "fixed = list(oscpar=c(";
}
}
fixedStr = fixedStr + String.valueOf(i + 1);
count++;
}
}
if (count > 0) {
fixedStr = fixedStr + ")";
}
}
}
count = 0;
KMatrixPanelModel kMatrix = tgm.getDat().getKMatrixPanel();
for (int i = 0; i < kMatrix.getJVector().getFixed().size(); i++) {
if (kMatrix.getJVector().getFixed().get(i)) {
if (count > 0) {
fixedStr = fixedStr + ",";
} else {
if (fixedStr != null) {
fixedStr = fixedStr + ", jvec=c(";
} else {
fixedStr = "fixed = list(jvec=c(";
}
}
fixedStr = fixedStr + String.valueOf(i + 1);
count++;
}
}
if (count > 0) {
fixedStr = fixedStr + ")";
}
// TODO: add additional paramters for fixed here:
// This closes the "fixed" argument
if (fixedStr != null) {
if (addToFixed != null) {
fixedStr = fixedStr + "," + addToFixed + ")";
} else {
fixedStr = fixedStr + ")";
}
} else {
if (addToFixed != null) {
fixedStr = "fixed = list(" + addToFixed + ")";
}
}
return fixedStr;
}