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; }
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; }
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; }