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Clean up interactive text, bugfix

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efischer
2022-02-19 22:21:09 -06:00
parent 0026d8cdfe
commit 5b2ed165d0
3 changed files with 20 additions and 8 deletions
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12
src/main/java/Simulator.java
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@@ -72,9 +72,9 @@ public class Simulator {
Map<Integer, Integer> allAlphas = samplePlate.assayWellsPeptideP(alphaIndex);
Map<Integer, Integer> allBetas = samplePlate.assayWellsPeptideP(betaIndex);
int alphaCount = allAlphas.size();
if(verbose){System.out.println("all alphas count: " + alphaCount);}
if(verbose){System.out.println("All alphas count: " + alphaCount);}
int betaCount = allBetas.size();
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");}
@@ -87,9 +87,9 @@ public class Simulator {
filterByOccupancyThreshold(allBetas, lowThreshold, numWells - 1);
if(verbose){System.out.println("Peptides removed");}
int pairableAlphaCount = allAlphas.size();
if(verbose){System.out.println("Remaining alpha count: " + pairableAlphaCount);}
if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
int pairableBetaCount = allBetas.size();
if(verbose){System.out.println("Remaining beta count: " + pairableBetaCount);}
if(verbose){System.out.println("Remaining betas count: " + pairableBetaCount);}
if(verbose){System.out.println("Making vertex maps");}
//For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
@@ -119,10 +119,10 @@ public class Simulator {
double[][] weights = new double[plateVtoAMap.size()][plateVtoBMap.size()];
countPeptidesAndFillMatrix(samplePlate, allAlphas, allBetas, plateAtoVMap,
plateBtoVMap, alphaIndex, betaIndex, alphaWellCounts, betaWellCounts, weights);
if(verbose){System.out.println("matrix created");}
if(verbose){System.out.println("Matrix created");}
//create bipartite graph
if(verbose){System.out.println("creating graph");}
if(verbose){System.out.println("Creating graph");}
//the graph object
SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph =
new SimpleWeightedGraph<>(DefaultWeightedEdge.class);