From cf771ce57427ac0c81285252daff90db305ca813 Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Wed, 21 Sep 2022 13:15:49 -0500
Subject: [PATCH] parameterized sequence indices

---
 readme.md                    |  2 ++
 src/main/java/Simulator.java | 12 ++++++++----
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/readme.md b/readme.md
index 5c3210b..99da1a3 100644
--- a/readme.md
+++ b/readme.md
@@ -356,6 +356,8 @@ roughly as though it had a constant well population equal to the plate's average
     * Add controllable algorithm-type parameter?
     * This would be fun and valuable, but probably take more time than I have for a hobby project.
 * Implement Vose's alias method for arbitrary statistical distributions of cells
+  * Should probably refactor to use apache commons rng for this
+* Use commons JCS for caching
   
   
 ## CITATIONS
diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 1c62872..933ad0e 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -47,10 +47,11 @@ public class Simulator implements GraphModificationFunctions {
         if(verbose){System.out.println("All betas count: " + betaCount);}
         if(verbose){System.out.println("Well maps made");}
 
-        if(verbose){System.out.println("Removing singleton sequences and sequences present in all wells.");}
-        filterByOccupancyThresholds(allAlphas, 2, numWells - 1);
-        filterByOccupancyThresholds(allBetas, 2, numWells - 1);
-        if(verbose){System.out.println("Sequences removed");}
+
+//        if(verbose){System.out.println("Removing singleton sequences and sequences present in all wells.");}
+//        filterByOccupancyThresholds(allAlphas, 2, numWells - 1);
+//        filterByOccupancyThresholds(allBetas, 2, numWells - 1);
+//        if(verbose){System.out.println("Sequences removed");}
         int pairableAlphaCount = allAlphas.size();
         if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
         int pairableBetaCount = allBetas.size();
@@ -239,6 +240,8 @@ public class Simulator implements GraphModificationFunctions {
         //Metadata comments for CSV file
         String algoType = "LEDA book with heap: " + heapType;
         int min = Math.min(alphaCount, betaCount);
+        //matching weight
+        BigDecimal totalMatchingWeight = maxWeightMatching.getMatchingWeight();
         //rate of attempted matching
         double attemptRate = (double) (trueCount + falseCount) / min;
         BigDecimal attemptRateTrunc = new BigDecimal(attemptRate, mc);
@@ -269,6 +272,7 @@ public class Simulator implements GraphModificationFunctions {
         metadata.put("sample plate filename", data.getSourceFilename());
         metadata.put("graph filename", dataFilename);
         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());