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parameterized sequence indices

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eugenefischer
2022-09-21 13:15:49 -05:00
parent 1df86f01df
commit cf771ce574
2 changed files with 10 additions and 4 deletions
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2
readme.md
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@@ -356,6 +356,8 @@ roughly as though it had a constant well population equal to the plate's average
* Add controllable algorithm-type parameter? * Add controllable algorithm-type parameter?
* This would be fun and valuable, but probably take more time than I have for a hobby project. * 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 * 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 ## CITATIONS

12
src/main/java/Simulator.java
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@@ -47,10 +47,11 @@ public class Simulator implements GraphModificationFunctions {
if(verbose){System.out.println("All betas count: " + betaCount);} if(verbose){System.out.println("All betas count: " + betaCount);}
if(verbose){System.out.println("Well maps made");} 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); // if(verbose){System.out.println("Removing singleton sequences and sequences present in all wells.");}
filterByOccupancyThresholds(allBetas, 2, numWells - 1); // filterByOccupancyThresholds(allAlphas, 2, numWells - 1);
if(verbose){System.out.println("Sequences removed");} // filterByOccupancyThresholds(allBetas, 2, numWells - 1);
// if(verbose){System.out.println("Sequences removed");}
int pairableAlphaCount = allAlphas.size(); int pairableAlphaCount = allAlphas.size();
if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);} if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
int pairableBetaCount = allBetas.size(); int pairableBetaCount = allBetas.size();
@@ -239,6 +240,8 @@ public class Simulator implements GraphModificationFunctions {
//Metadata comments for CSV file //Metadata comments for CSV file
String algoType = "LEDA book with heap: " + heapType; String algoType = "LEDA book with heap: " + heapType;
int min = Math.min(alphaCount, betaCount); int min = Math.min(alphaCount, betaCount);
//matching weight
BigDecimal totalMatchingWeight = maxWeightMatching.getMatchingWeight();
//rate of attempted matching //rate of attempted matching
double attemptRate = (double) (trueCount + falseCount) / min; double attemptRate = (double) (trueCount + falseCount) / min;
BigDecimal attemptRateTrunc = new BigDecimal(attemptRate, mc); BigDecimal attemptRateTrunc = new BigDecimal(attemptRate, mc);
@@ -269,6 +272,7 @@ public class Simulator implements GraphModificationFunctions {
metadata.put("sample plate filename", data.getSourceFilename()); metadata.put("sample plate filename", data.getSourceFilename());
metadata.put("graph filename", dataFilename); metadata.put("graph filename", dataFilename);
metadata.put("algorithm type", algoType); metadata.put("algorithm type", algoType);
metadata.put("matching weight", totalMatchingWeight.toString());
metadata.put("well populations", wellPopulationsString); metadata.put("well populations", wellPopulationsString);
metadata.put("total alphas found", alphaCount.toString()); metadata.put("total alphas found", alphaCount.toString());
metadata.put("total betas found", betaCount.toString()); metadata.put("total betas found", betaCount.toString());