Finish reverting back to wells-as-rows

src/main/java/PlateFileWriter.java

@@ -99,7 +99,7 @@ public class PlateFileWriter {
             else {
                 printer.printComment("Std. dev.: " + stdDev);
             }
-            printer.printRecords(rows);
+            printer.printRecords(wellsAsStrings);
         } catch(IOException ex){
             System.out.println("Could not make new file named "+filename);
             System.err.println(ex);

src/main/java/UserInterface.java

@@ -681,17 +681,6 @@ public class UserInterface {
         System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation");
         System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences.");
         System.out.println();
-        System.out.println("Unlike pairSEQ, which calculates p-values for every TCR alpha/beta overlap and compares");
-        System.out.println("against a null distribution, BiGpairSEQ does not do any statistical calculations");
-        System.out.println("directly. Instead, BiGpairSEQ creates a simple bipartite weighted graph representing");
-        System.out.println("the sample plate. The distinct TCRA and TCRB sequences form the two sets of vertices.");
-        System.out.println("Every TCRA/TCRB pair that share a well are connected by an edge, with the edge weight");
-        System.out.println("set to the number of wells in which both sequences appear. (Sequences in all wells are");
-        System.out.println("filtered out prior to creating the graph, as there is no signal in their occupancy");
-        System.out.println("pattern.) The problem of pairing TCRA/TCRB sequences thus reduces to the \"assignment");
-        System.out.println("problem\" of finding a maximum weight matching on a bipartite graph--the subset of");
-        System.out.println("vertex-disjoint edges whose weights sum to the maximum possible value.");
-        System.out.println();
         System.out.println("For full documentation, see: https://gitea.ejsf.synology.me/efischer/BiGpairSEQ");
         System.out.println();
         System.out.println("pairSEQ citation:");