implement option menu for file caching

src/main/java/BiGpairSEQ.java

@@ -33,12 +33,18 @@ public class BiGpairSEQ {
         return cellSampleInMemory;
     }
 
-    public static void setCellSampleInMemory(CellSample cellSampleInMemory) {
+    public static void setCellSampleInMemory(CellSample cellSample, String filename) {
-        BiGpairSEQ.cellSampleInMemory = cellSampleInMemory;
+        if(cellSampleInMemory != null) {
+            clearCellSampleInMemory();
+        }
+        cellSampleInMemory = cellSample;
+        cellFilename = filename;
+        System.out.println("Cell sample file " + filename + " cached.");
     }
 
     public static void clearCellSampleInMemory() {
         cellSampleInMemory = null;
+        cellFilename = null;
         System.gc();
     }
 
@@ -46,20 +52,22 @@ public class BiGpairSEQ {
         return cellFilename;
     }
 
-    public static void setCellFilename(String cellFilename) {
-        BiGpairSEQ.cellFilename = cellFilename;
-    }
-
     public static Plate getPlateInMemory() {
         return plateInMemory;
     }
 
-    public static void setPlateInMemory(Plate plateInMemory) {
+    public static void setPlateInMemory(Plate plate, String filename) {
-        BiGpairSEQ.plateInMemory = plateInMemory;
+        if(plateInMemory != null) {
+            clearPlateInMemory();
+        }
+        plateInMemory = plate;
+        plateFilename = filename;
+        System.out.println("Sample plate file " + filename + " cached.");
     }
 
     public static void clearPlateInMemory() {
         plateInMemory = null;
+        plateFilename = null;
         System.gc();
     }
 
@@ -67,23 +75,22 @@ public class BiGpairSEQ {
         return plateFilename;
     }
 
-    public static void setPlateFilename(String plateFilename) {
+
-        BiGpairSEQ.plateFilename = plateFilename;
+    public static GraphWithMapData getGraphInMemory() {return graphInMemory;
     }
 
-    public static GraphWithMapData getGraphInMemory() {
+    public static void setGraphInMemory(GraphWithMapData g, String filename) {
-        return graphInMemory;
-    }
-
-    public static void setGraphInMemory(GraphWithMapData g) {
         if (graphInMemory != null) {
             clearGraphInMemory();
         }
         graphInMemory = g;
+        graphFilename = filename;
+        System.out.println("Graph and data file " + filename + " cached.");
     }
 
     public static void clearGraphInMemory() {
         graphInMemory = null;
+        graphFilename = null;
         System.gc();
     }
 
@@ -91,15 +98,16 @@ public class BiGpairSEQ {
         return graphFilename;
     }
 
-    public static void setGraphFilename(String filename) {
-        graphFilename = filename;
-    }
 
     public static boolean cacheCells() {
         return cacheCells;
     }
 
     public static void setCacheCells(boolean cacheCells) {
+        //if not caching, clear the memory
+        if(!cacheCells){
+            BiGpairSEQ.clearCellSampleInMemory();
+        }
         BiGpairSEQ.cacheCells = cacheCells;
     }
 
@@ -108,6 +116,10 @@ public class BiGpairSEQ {
     }
 
     public static void setCachePlate(boolean cachePlate) {
+        //if not caching, clear the memory
+        if(!cachePlate) {
+            BiGpairSEQ.clearPlateInMemory();
+        }
         BiGpairSEQ.cachePlate = cachePlate;
     }
 
@@ -116,6 +128,10 @@ public class BiGpairSEQ {
     }
 
     public static void setCacheGraph(boolean cacheGraph) {
+        //if not caching, clear the memory
+        if(!cacheGraph) {
+            BiGpairSEQ.clearGraphInMemory();
+        }
         BiGpairSEQ.cacheGraph = cacheGraph;
     }
 }

src/main/java/InteractiveInterface.java

@@ -80,11 +80,9 @@ public class InteractiveInterface {
         CellFileWriter writer = new CellFileWriter(filename, sample);
         writer.writeCellsToFile();
         System.out.println("Cell sample written to: " + filename);
-        if(BiGpairSEQ.getCellSampleInMemory() != null) {
+        if(BiGpairSEQ.cacheCells()) {
-            BiGpairSEQ.clearCellSampleInMemory();
+            BiGpairSEQ.setCellSampleInMemory(sample, filename);
         }
-        BiGpairSEQ.setCellSampleInMemory(sample);
-        BiGpairSEQ.setCellFilename(filename);
     }
 
     //Output a CSV of sample plate
@@ -221,9 +219,9 @@ public class InteractiveInterface {
             System.out.println("Reading Cell Sample file: " + cellFile);
             CellFileReader cellReader = new CellFileReader(cellFile);
             cells = cellReader.getCellSample();
-            BiGpairSEQ.clearCellSampleInMemory();
+            if(BiGpairSEQ.cacheCells()) {
-            BiGpairSEQ.setCellSampleInMemory(cells);
+                BiGpairSEQ.setCellSampleInMemory(cells, cellFile);
-            BiGpairSEQ.setCellFilename(cellFile);
+            }
         }
         assert filename != null;
         Plate samplePlate;
@@ -244,8 +242,9 @@ public class InteractiveInterface {
         System.out.println("Writing Sample Plate to file");
         writer.writePlateFile();
         System.out.println("Sample Plate written to file: " + filename);
-        BiGpairSEQ.setPlateInMemory(samplePlate);
+        if(BiGpairSEQ.cachePlate()) {
-        BiGpairSEQ.setPlateFilename(filename);
+            BiGpairSEQ.setPlateInMemory(samplePlate, filename);
+        }
     }
 
     //Output serialized binary of GraphAndMapData object
@@ -273,16 +272,16 @@ public class InteractiveInterface {
         assert cellFile != null;
         CellSample cellSample;
         //check if cells are already in memory
-        if(cellFile.equals(BiGpairSEQ.getCellFilename())) {
+        if(cellFile.equals(BiGpairSEQ.getCellFilename()) && BiGpairSEQ.getCellSampleInMemory() != null) {
             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);
+            if(BiGpairSEQ.cacheCells()) {
-            BiGpairSEQ.setCellFilename(cellFile);
+                BiGpairSEQ.setCellSampleInMemory(cellSample, cellFile);
+            }
         }
 
         assert plateFile != null;
@@ -292,12 +291,12 @@ public class InteractiveInterface {
             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);
+            if(BiGpairSEQ.cachePlate()) {
-            BiGpairSEQ.setPlateFilename(plateFile);
+                BiGpairSEQ.setPlateInMemory(plate, plateFile);
+            }
         }
         if (cellSample.getCells().size() == 0){
             System.out.println("No cell sample found.");
@@ -314,9 +313,10 @@ public class InteractiveInterface {
             GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
             dataWriter.writeDataToFile();
             System.out.println("Graph and Data file written to: " + filename);
-            BiGpairSEQ.setGraphInMemory(data);
+            if(BiGpairSEQ.cacheGraph()) {
-            BiGpairSEQ.setGraphFilename(filename);
+                BiGpairSEQ.setGraphInMemory(data, filename);
-            System.out.println("Graph and Data file " + filename + " cached.");
+
+            }
         }
     }
 
@@ -368,17 +368,15 @@ public class InteractiveInterface {
         assert graphFilename != null;
         //check if this is the same graph we already have in memory.
         GraphWithMapData data;
-        if(!(graphFilename.equals(BiGpairSEQ.getGraphFilename())) || BiGpairSEQ.getGraphInMemory() == null) {
+        if(graphFilename.equals(BiGpairSEQ.getGraphFilename())) {
-            BiGpairSEQ.clearGraphInMemory();
+            data = BiGpairSEQ.getGraphInMemory();
-            //read object data from file
-            GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename);
-            data = dataReader.getData();
-            //set new graph in memory and new filename
-            BiGpairSEQ.setGraphInMemory(data);
-            BiGpairSEQ.setGraphFilename(graphFilename);
         }
         else {
-            data = BiGpairSEQ.getGraphInMemory();
+            GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename);
+            data = dataReader.getData();
+            if(BiGpairSEQ.cacheGraph()) {
+                BiGpairSEQ.setGraphInMemory(data, graphFilename);
+            }
         }
         //simulate matching
         MatchingResult results = Simulator.matchCDR3s(data, graphFilename, lowThreshold, highThreshold, maxOccupancyDiff,
@@ -498,7 +496,7 @@ public class InteractiveInterface {
     private static void options(){
         boolean backToMain = false;
         while(!backToMain) {
-            System.out.println("-------------OPTIONS----------------");
+            System.out.println("--------------OPTIONS---------------");
             System.out.println("1) Turn cell sample file caching " + getOnOff(!BiGpairSEQ.cacheCells()));
             System.out.println("2) Turn sample plate file caching " + getOnOff(!BiGpairSEQ.cachePlate()));
             System.out.println("3) Turn graph/data file caching " + getOnOff(!BiGpairSEQ.cacheGraph()));
@@ -520,12 +518,8 @@ public class InteractiveInterface {
     }
 
     private static String getOnOff(boolean b) {
-        if (b) {
+        if (b) { return "on";}
-            return "on";
+        else { return "off"; }
-        }
-        else {
-            return "off";
-        }
     }
 
     private static void acknowledge(){