/**
* Given an experiment, we see for each condition if a new growth medium is associated to the cell
* line, and if new media are found, these are added to the medium binding list.
*
* @param experiment
*/
public void addNewMedia(Experiment experiment) {
for (PlateCondition plateCondition : experiment.getPlateConditionList()) {
CellLine cellLine = plateCondition.getCellLine();
String medium = cellLine.getGrowthMedium();
if (!mediumBindingList.contains(medium)) {
mediumBindingList.add(medium);
}
}
}
/**
* Given an experiment, we see for each condition if a new serum is associated to the cell line,
* and if new sera are found, these are added to the serum binding list.
*
* @param experiment
*/
public void addNewSera(Experiment experiment) {
for (PlateCondition plateCondition : experiment.getPlateConditionList()) {
CellLine cellLine = plateCondition.getCellLine();
String serum = cellLine.getSerum();
if (!serumBindingList.contains(serum)) {
serumBindingList.add(serum);
}
}
}
/**
* validate a Plate Condition
*
* @param plateCondition
* @return a list of strings to be concatenated in order to show message to the user
*/
public List<String> validateCondition(PlateCondition plateCondition) {
List<String> messages = new ArrayList<>();
// validate cell line
if (!validateCellLine(plateCondition.getCellLine()).isEmpty()) {
messages.addAll(validateCellLine(plateCondition.getCellLine()));
}
// validate ECM (2D and 3D) input
if (!assayEcmController.validate2DEcm().isEmpty()) {
messages.addAll(assayEcmController.validate2DEcm());
}
if (!assayEcmController.validate3DEcm().isEmpty()) {
messages.addAll(assayEcmController.validate3DEcm());
}
// if validation was OK, validate the condition: check for wells collection
if (messages.isEmpty()) {
if (plateCondition.getWellList().isEmpty()) {
String message = "Conditions must have at least one well";
messages.add(message);
}
}
return messages;
}
/**
* this method assigns default fields to the first Condition created and added to the List
*
* @param firstCondition
*/
private void initFirstCondition(PlateCondition firstCondition) {
// set the name
firstCondition.setName("Condition " + ++conditionIndex);
// set the cell line
CellLine cellLine = new CellLine();
cellLine.setCellLineType(cellLineTypeBindingList.get(0));
cellLine.setSeedingDensity(50000);
cellLine.setSeedingTime("day -1");
cellLine.setGrowthMedium(mediumBindingList.get(0));
cellLine.setSerum(serumBindingList.get(0));
cellLine.setSerumConcentration(10.0);
firstCondition.setCellLine(cellLine);
cellLine.setPlateCondition(firstCondition);
// set the migration assay: Oris platform; matrix dimension: 2D
firstCondition.setAssay(assayEcmController.getAssay2DBindingList().get(0));
// create a new AssayMedium object and set its class members
AssayMedium assayMedium = new AssayMedium();
assayMedium.setMedium(
treatmentsController.getTreatmentsPanel().getAssayMediumComboBox().getItemAt(0).toString());
assayMedium.setSerum(serumBindingList.get(0));
assayMedium.setSerumConcentration(1.0);
assayMedium.setVolume(10.0);
firstCondition.setAssayMedium(assayMedium);
assayMedium.setPlateCondition(firstCondition);
// create a new ECM object and set its class members
Ecm ecm = new Ecm();
ecm.setEcmComposition(assayEcmController.getEcm2DCompositionBindingList().get(0));
ecm.setCoatingTemperature("RT");
ecm.setCoatingTime("60");
ecm.setConcentration(0.04);
ecm.setVolume(100.0);
ecm.setVolumeUnit("\u00B5" + "l");
ecm.setConcentrationUnit("mg/ml");
firstCondition.setEcm(ecm);
// set an empty collection of treatments
List<Treatment> treatmentList = new ArrayList<>();
firstCondition.setTreatmentList(treatmentList);
// set an empty collection of wells
List<Well> wellList = new ArrayList<>();
firstCondition.setWellList(wellList);
}
/**
* this method assigns values for each new condition, from the previously created 8and set-up) one
*
* @param newCondition
*/
private void initNewCondition(PlateCondition newCondition) {
PlateCondition previousCondition = plateConditionBindingList.get(previousConditionIndex);
// set the name
newCondition.setName("Condition " + ++conditionIndex);
// set the cell line (the same as the previous condition)
CellLine cellLine = previousCondition.getCellLine();
CellLine newCellLine =
new CellLine(
cellLine.getSeedingTime(),
cellLine.getSeedingDensity(),
cellLine.getGrowthMedium(),
cellLine.getSerumConcentration(),
cellLine.getCellLineType(),
cellLine.getSerum());
newCondition.setCellLine(newCellLine);
newCellLine.setPlateCondition(newCondition);
// set assay medium (another object, but with the same parameters as previous condition)
String medium =
mediumBindingList.get(
treatmentsController.getTreatmentsPanel().getAssayMediumComboBox().getSelectedIndex());
String serum =
serumBindingList.get(
treatmentsController.getTreatmentsPanel().getSerumComboBox().getSelectedIndex());
Double serumConcentration =
Double.parseDouble(
treatmentsController.getTreatmentsPanel().getSerumConcentrationTextField().getText());
Double volume =
Double.parseDouble(
treatmentsController.getTreatmentsPanel().getMediumVolumeTextField().getText());
AssayMedium assayMedium = new AssayMedium(medium, serum, serumConcentration, volume);
newCondition.setAssayMedium(assayMedium);
assayMedium.setPlateCondition(newCondition);
// set assay and ecm (get the values according to the last selected ones)
Ecm ecm = new Ecm();
Assay assay = null;
BottomMatrix bottomMatrix = null;
// need to set different values according to matrix dimension: 2D or 3D or 2.5D
switch (assayEcmController
.getMatrixDimensionBindingList()
.get(setupConditionsPanel.getEcmDimensionComboBox().getSelectedIndex())
.getDimension()) {
case "2D":
// set assay
assay =
assayEcmController
.getAssay2DBindingList()
.get(assayEcmController.getAssayEcm2DPanel().getAssayComboBox().getSelectedIndex());
// 2D matrix: set ecm 2D fields
ecm.setEcmComposition(
assayEcmController
.getEcm2DCompositionBindingList()
.get(
assayEcmController
.getAssayEcm2DPanel()
.getCompositionComboBox()
.getSelectedIndex()));
ecm.setConcentration(
Double.parseDouble(
assayEcmController.getAssayEcm2DPanel().getConcentrationTextField().getText()));
ecm.setVolume(
Double.parseDouble(
assayEcmController.getAssayEcm2DPanel().getVolumeTextField().getText()));
ecm.setCoatingTime(
assayEcmController.getAssayEcm2DPanel().getCoatingTimeTextField().getText());
ecm.setCoatingTemperature(
assayEcmController.getAssayEcm2DPanel().getCoatingTemperatureTextField().getText());
ecm.setVolumeUnit(assayEcmController.getAssayEcm2DPanel().getVolumeUnitLabel().getText());
ecm.setConcentrationUnit(
assayEcmController
.getAssayEcm2DPanel()
.getConcentrationUnitOfMeasure()
.getSelectedItem()
.toString());
break;
case "3D":
// set assay
assay =
assayEcmController
.getAssay3DBindingList()
.get(assayEcmController.getAssayEcm3DPanel().getAssayComboBox().getSelectedIndex());
// 3D matrix: set ecm 3D fields
ecm.setEcmComposition(
assayEcmController
.getEcm3DCompositionBindingList()
.get(
assayEcmController
.getAssayEcm3DPanel()
.getCompositionComboBox()
.getSelectedIndex()));
ecm.setEcmDensity(
assayEcmController
.getEcmDensityBindingList()
.get(
assayEcmController
.getAssayEcm3DPanel()
.getDensityComboBox()
.getSelectedIndex()));
// bottom matrix
bottomMatrix =
assayEcmController
.getBottomMatrixBindingList()
.get(
assayEcmController
.getAssayEcm3DPanel()
.getBottomMatrixTypeComboBox()
.getSelectedIndex());
ecm.setBottomMatrix(bottomMatrix);
switch (bottomMatrix.getType()) {
case "gel":
// both top and bottom matrix volumes
String text =
assayEcmController.getAssayEcm3DPanel().getTopMatrixVolumeTextField().getText();
if (!text.isEmpty()) {
ecm.setTopMatrixVolume(Double.parseDouble(text));
} else {
ecm.setTopMatrixVolume(40.0);
}
ecm.setBottomMatrixVolume(
Double.parseDouble(
assayEcmController
.getAssayEcm3DPanel()
.getBottomMatrixVolumeTextField()
.getText()));
break;
case "thin gel coating":
// top matrix but no bottom matrix volume
ecm.setTopMatrixVolume(
Double.parseDouble(
assayEcmController
.getAssayEcm3DPanel()
.getTopMatrixVolumeTextField()
.getText()));
break;
}
ecm.setPolymerisationTime(
assayEcmController.getAssayEcm3DPanel().getPolymerizationTimeTextField().getText());
ecm.setPolymerisationTemperature(
assayEcmController
.getAssayEcm3DPanel()
.getPolymerizationTemperatureTextField()
.getText());
ecm.setPolymerisationPh(
assayEcmController
.getPolymerisationPhBindingList()
.get(
assayEcmController
.getAssayEcm3DPanel()
.getPolymerizationPhComboBox()
.getSelectedIndex()));
break;
case "2.5D":
// set assay
assay =
assayEcmController
.getAssay25DBindingList()
.get(
assayEcmController.getAssayEcm25DPanel().getAssayComboBox().getSelectedIndex());
// 3D matrix: set ecm 2.5D fields
ecm.setEcmComposition(
assayEcmController
.getEcm25DCompositionBindingList()
.get(
assayEcmController
.getAssayEcm25DPanel()
.getCompositionComboBox()
.getSelectedIndex()));
ecm.setEcmDensity(
assayEcmController
.getEcmDensityBindingList()
.get(
assayEcmController
.getAssayEcm25DPanel()
.getDensityComboBox()
.getSelectedIndex()));
// bottom matrix
bottomMatrix =
assayEcmController
.getBottomMatrixBindingList()
.get(
assayEcmController
.getAssayEcm25DPanel()
.getBottomMatrixTypeComboBox()
.getSelectedIndex());
ecm.setBottomMatrix(bottomMatrix);
switch (bottomMatrix.getType()) {
case "gel":
// bottom matrix volume
ecm.setBottomMatrixVolume(
Double.parseDouble(
assayEcmController
.getAssayEcm25DPanel()
.getBottomMatrixVolumeTextField()
.getText()));
break;
}
ecm.setPolymerisationTime(
assayEcmController.getAssayEcm25DPanel().getPolymerizationTimeTextField().getText());
ecm.setPolymerisationTemperature(
assayEcmController
.getAssayEcm25DPanel()
.getPolymerizationTemperatureTextField()
.getText());
ecm.setPolymerisationPh(
assayEcmController
.getPolymerisationPhBindingList()
.get(
assayEcmController
.getAssayEcm25DPanel()
.getPolymerizationPhComboBox()
.getSelectedIndex()));
break;
}
newCondition.setAssay(assay);
newCondition.setEcm(ecm);
// create new treatment with same parameters as ones from previous condition
List<Treatment> treatmentList = new ArrayList<>();
ObservableList<Treatment> treatmentBindingList = treatmentsController.getTreatmentBindingList();
for (Treatment treatment : treatmentBindingList) {
Double concentration = treatment.getConcentration();
String concentrationUnit = treatment.getConcentrationUnit();
String timing = treatment.getTiming();
String drugSolvent = treatment.getDrugSolvent();
Double drugSolventConcentration = treatment.getDrugSolventConcentration();
TreatmentType treatmentType = treatment.getTreatmentType();
Treatment newTreatment =
new Treatment(
concentration,
concentrationUnit,
timing,
drugSolvent,
drugSolventConcentration,
treatmentType);
newTreatment.setPlateCondition(newCondition);
treatmentList.add(newTreatment);
}
newCondition.setTreatmentList(treatmentList);
// set an empty collection of wells (wells are not recalled from previous condition)
List<Well> wellList = new ArrayList<>();
newCondition.setWellList(wellList);
}
