diff --git a/src/main/java/InteractiveInterface.java b/src/main/java/InteractiveInterface.java index b4bf965..0de7a8e 100644 --- a/src/main/java/InteractiveInterface.java +++ b/src/main/java/InteractiveInterface.java @@ -290,7 +290,7 @@ public class InteractiveInterface { else { System.out.println("Reading Sample Plate file: " + plateFile); PlateFileReader plateReader = new PlateFileReader(plateFile); - plate = new Plate(plateReader.getFilename(), plateReader.getWells()); + plate = plateReader.getSamplePlate(); if(BiGpairSEQ.cachePlate()) { BiGpairSEQ.setPlateInMemory(plate, plateFile); } diff --git a/src/main/java/Plate.java b/src/main/java/Plate.java index af37ac0..d0bc1aa 100644 --- a/src/main/java/Plate.java +++ b/src/main/java/Plate.java @@ -10,6 +10,7 @@ import java.util.*; public class Plate { private CellSample cells; private String sourceFile; + private String filename; private List> wells; private final Random rand = BiGpairSEQ.getRand(); private int size; @@ -45,8 +46,9 @@ public class Plate { wells = new ArrayList<>(); } - public Plate(String sourceFileName, List> wells) { - this.sourceFile = sourceFileName; + //constructor for returning a Plate from a PlateFileReader + public Plate(String filename, List> wells) { + this.filename = filename; this.wells = wells; this.size = wells.size(); @@ -176,4 +178,6 @@ public class Plate { public String getSourceFileName() { return sourceFile; } + + public String getFilename() { return filename; } } diff --git a/src/main/java/PlateFileReader.java b/src/main/java/PlateFileReader.java index 7b95cee..27e98b0 100644 --- a/src/main/java/PlateFileReader.java +++ b/src/main/java/PlateFileReader.java @@ -56,11 +56,8 @@ public class PlateFileReader { } - public List> getWells() { - return wells; + public Plate getSamplePlate() { + return new Plate(filename, wells); } - public String getFilename() { - return filename; - } } \ No newline at end of file diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java index 6d3f6eb..0cc6df1 100644 --- a/src/main/java/Simulator.java +++ b/src/main/java/Simulator.java @@ -113,7 +113,7 @@ public class Simulator implements GraphModificationFunctions { distCellsMapAlphaKey, plateVtoAMap, plateVtoBMap, plateAtoVMap, plateBtoVMap, alphaWellCounts, betaWellCounts, time); //Set source file name in graph to name of sample plate - output.setSourceFilename(samplePlate.getSourceFileName()); + output.setSourceFilename(samplePlate.getFilename()); //return GraphWithMapData object return output; }