efischer/BiGpairSEQ
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efischer
2022-02-23 10:30:42 -06:00
parent 74ffbfd8ac
commit decdb147a9
5 changed files with 96 additions and 29 deletions
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85
src/main/java/InteractiveInterface.java
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@@ -74,8 +74,15 @@ public class InteractiveInterface {
}
CellSample sample = Simulator.generateCellSample(numCells, cdr1Freq);
assert filename != null;
System.out.println("Writing cells to file");
CellFileWriter writer = new CellFileWriter(filename, sample);
writer.writeCellsToFile();
System.out.println("Cell sample written to: " + filename);
if(BiGpairSEQ.getCellSampleInMemory() != null) {
BiGpairSEQ.clearCellSampleInMemory();
}
BiGpairSEQ.setCellSampleInMemory(sample);
BiGpairSEQ.setCellFilename(filename);
}
//Output a CSV of sample plate
@@ -203,27 +210,40 @@ public class InteractiveInterface {
System.out.println(ex);
sc.next();
}
System.out.println("Reading Cell Sample file: " + cellFile);
assert cellFile != null;
CellFileReader cellReader = new CellFileReader(cellFile);
CellSample cells;
if (cellFile.equals(BiGpairSEQ.getCellFilename())){
cells = BiGpairSEQ.getCellSampleInMemory();
}
else {
System.out.println("Reading Cell Sample file: " + cellFile);
CellFileReader cellReader = new CellFileReader(cellFile);
cells = cellReader.getCellSample();
BiGpairSEQ.clearCellSampleInMemory();
BiGpairSEQ.setCellSampleInMemory(cells);
BiGpairSEQ.setCellFilename(cellFile);
}
assert filename != null;
Plate samplePlate;
PlateFileWriter writer;
if(exponential){
Plate samplePlate = new Plate(numWells, dropOutRate, populations);
samplePlate.fillWellsExponential(cellReader.getFilename(), cellReader.getCells(), lambda);
PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
writer.writePlateFile();
samplePlate = new Plate(numWells, dropOutRate, populations);
samplePlate.fillWellsExponential(cellFile, cells.getCells(), lambda);
writer = new PlateFileWriter(filename, samplePlate);
}
else {
if (poisson) {
stdDev = Math.sqrt(cellReader.getCellCount()); //gaussian with square root of elements approximates poisson
stdDev = Math.sqrt(cells.getCellCount()); //gaussian with square root of elements approximates poisson
}
Plate samplePlate = new Plate(numWells, dropOutRate, populations);
samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells(), stdDev);
assert filename != null;
PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
System.out.println("Writing Sample Plate to file");
writer.writePlateFile();
System.out.println("Sample Plate written to file: " + filename);
samplePlate = new Plate(numWells, dropOutRate, populations);
samplePlate.fillWells(cellFile, cells.getCells(), stdDev);
writer = new PlateFileWriter(filename, samplePlate);
}
System.out.println("Writing Sample Plate to file");
writer.writePlateFile();
System.out.println("Sample Plate written to file: " + filename);
BiGpairSEQ.setPlateInMemory(samplePlate);
BiGpairSEQ.setPlateFilename(filename);
}
//Output serialized binary of GraphAndMapData object
@@ -247,14 +267,37 @@ public class InteractiveInterface {
System.out.println(ex);
sc.next();
}
System.out.println("Reading Cell Sample file: " + cellFile);
assert cellFile != null;
CellFileReader cellReader = new CellFileReader(cellFile);
System.out.println("Reading Sample Plate file: " + plateFile);
CellSample cellSample;
//check if cells are already in memory
if(cellFile.equals(BiGpairSEQ.getCellFilename())) {
cellSample = BiGpairSEQ.getCellSampleInMemory();
}
else {
BiGpairSEQ.clearCellSampleInMemory();
System.out.println("Reading Cell Sample file: " + cellFile);
CellFileReader cellReader = new CellFileReader(cellFile);
cellSample = cellReader.getCellSample();
BiGpairSEQ.setCellSampleInMemory(cellSample);
BiGpairSEQ.setCellFilename(cellFile);
}
assert plateFile != null;
PlateFileReader plateReader = new PlateFileReader(plateFile);
Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
if (cellReader.getCells().size() == 0){
Plate plate;
//check if plate is already in memory
if(plateFile.equals(BiGpairSEQ.getPlateFilename())){
plate = BiGpairSEQ.getPlateInMemory();
}
else {
BiGpairSEQ.clearPlateInMemory();
System.out.println("Reading Sample Plate file: " + plateFile);
PlateFileReader plateReader = new PlateFileReader(plateFile);
plate = new Plate(plateReader.getFilename(), plateReader.getWells());
BiGpairSEQ.setPlateInMemory(plate);
BiGpairSEQ.setPlateFilename(plateFile);
}
if (cellSample.getCells().size() == 0){
System.out.println("No cell sample found.");
System.out.println("Returning to main menu.");
}
@@ -263,7 +306,7 @@ public class InteractiveInterface {
System.out.println("Returning to main menu.");
}
else{
List<Integer[]> cells = cellReader.getCells();
List<Integer[]> cells = cellSample.getCells();
GraphWithMapData data = Simulator.makeGraph(cells, plate, true);
assert filename != null;
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);