From 8a77d53f1f24e5b9c306a86da8d9cf655f8f1684 Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Sun, 25 Sep 2022 17:20:50 -0500
Subject: [PATCH] Output sequence counts before and after pre-filtering
 (currently pre-filtering only sequences present in all wells)

---
 src/main/java/GraphWithMapData.java | 18 +++++++++---------
 src/main/java/Simulator.java        | 14 ++++++++------
 2 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/src/main/java/GraphWithMapData.java b/src/main/java/GraphWithMapData.java
index 8f9ab03..aad6c2f 100644
--- a/src/main/java/GraphWithMapData.java
+++ b/src/main/java/GraphWithMapData.java
@@ -25,9 +25,9 @@ public class GraphWithMapData implements java.io.Serializable {
     private final Duration time;
 
     public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer[] wellConcentrations,
-                            Map<Integer, Integer> distCellsMapAlphaKey, Duration time){
+                            Map<Integer, Integer> distCellsMapAlphaKey, Integer alphaCount, Integer betaCount, Duration time){
 
-//                            Map<Integer, Integer> plateVtoAMap, Integer alphaCount, Integer betaCount,
+//                            Map<Integer, Integer> plateVtoAMap,
 //                            Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
 //                            Map<Integer, Integer> plateBtoVMap, Map<Integer, Integer> alphaWellCounts,
 //                            Map<Integer, Integer> betaWellCounts,) {
@@ -58,13 +58,13 @@ public class GraphWithMapData implements java.io.Serializable {
         return wellPopulations;
     }
 
-//    public Integer getAlphaCount() {
-//        return alphaCount;
-//    }
-//
-//    public Integer getBetaCount() {
-//        return betaCount;
-//    }
+    public Integer getAlphaCount() {
+        return alphaCount;
+    }
+
+    public Integer getBetaCount() {
+        return betaCount;
+    }
 
     public Map<Integer, Integer> getDistCellsMapAlphaKey() {
         return distCellsMapAlphaKey;
diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 0d9e17b..28dd8ff 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -129,7 +129,7 @@ public class Simulator implements GraphModificationFunctions {
         Duration time = Duration.between(start, stop);
 
         //create GraphWithMapData object
-        GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), distCellsMapAlphaKey, time);
+        GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), distCellsMapAlphaKey, alphaCount, betaCount, time);
         //Set source file name in graph to name of sample plate
         output.setSourceFilename(samplePlate.getFilename());
         //return GraphWithMapData object
@@ -158,8 +158,8 @@ public class Simulator implements GraphModificationFunctions {
                 betas.add(v);
             }
         }
-        Integer alphaCount = alphas.size();
-        Integer betaCount = betas.size();
+        Integer graphAlphaCount = alphas.size();
+        Integer graphBetaCount = betas.size();
 
         //remove edges with weights outside given overlap thresholds, add those to removed edge list
         if(verbose){System.out.println("Eliminating edges with weights outside overlap threshold values");}
@@ -266,7 +266,7 @@ public class Simulator implements GraphModificationFunctions {
 
         //Metadata comments for CSV file
         String algoType = "LEDA book with heap: " + heapType;
-        int min = Math.min(alphaCount, betaCount);
+        int min = Math.min(graphAlphaCount, graphBetaCount);
         //matching weight
         BigDecimal totalMatchingWeight = maxWeightMatching.getMatchingWeight();
         //rate of attempted matching
@@ -301,8 +301,10 @@ public class Simulator implements GraphModificationFunctions {
         metadata.put("algorithm type", algoType);
         metadata.put("matching weight", totalMatchingWeight.toString());
         metadata.put("well populations", wellPopulationsString);
-        metadata.put("total alphas found", alphaCount.toString());
-        metadata.put("total betas found", betaCount.toString());
+        metadata.put("total alphas on plate", data.getAlphaCount().toString());
+        metadata.put("total betas on plate", data.getBetaCount().toString());
+        metadata.put("alphas in graph (after pre-filtering)", graphAlphaCount.toString());
+        metadata.put("betas in graph (after pre-filtering)", graphBetaCount.toString());
         metadata.put("high overlap threshold", highThreshold.toString());
         metadata.put("low overlap threshold", lowThreshold.toString());
         metadata.put("minimum overlap percent", minOverlapPercent.toString());