update ToDos

.idea/artifacts/BiGpairSEQ_Sim_jar.xml

@@ -1,16 +1,27 @@
 <component name="ArtifactManager">
-  <artifact type="jar" build-on-make="true" name="BiGpairSEQ_Sim:jar">
+  <artifact type="jar" name="BiGpairSEQ_Sim:jar">
     <output-path>$PROJECT_DIR$/out/artifacts/BiGpairSEQ_Sim_jar</output-path>
     <root id="archive" name="BiGpairSEQ_Sim.jar">
       <element id="directory" name="META-INF">
-        <element id="file-copy" path="$PROJECT_DIR$/src/main/java/META-INF/MANIFEST.MF" />
+        <element id="file-copy" path="$PROJECT_DIR$/META-INF/MANIFEST.MF" />
       </element>
-      <element id="module-output" name="BigPairSEQ" />
+      <element id="module-output" name="BiGpairSEQ_Sim" />
-      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.1/jgrapht-core-1.5.1.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.2/jgrapht-core-1.5.2.jar" path-in-jar="/" />
-      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.13/jheaps-0.13.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-sampling/1.6/commons-rng-sampling-1.6.jar" path-in-jar="/" />
-      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.5.0/commons-cli-1.5.0.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.14.0/commons-csv-1.14.0.jar" path-in-jar="/" />
-      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.9.0/commons-csv-1.9.0.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jetbrains/annotations/26.0.2/annotations-26.0.2.jar" path-in-jar="/" />
-      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jetbrains/annotations/23.0.0/annotations-23.0.0.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-io/1.5.2/jgrapht-io-1.5.2.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-simple/1.6/commons-rng-simple-1.6.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-io/commons-io/2.18.0/commons-io-2.18.0.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-core/1.6/commons-rng-core-1.6.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.18.0/commons-codec-1.18.0.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-rng-client-api/1.6/commons-rng-client-api-1.6.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.9.0/commons-cli-1.9.0.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-lang3/3.12.0/commons-lang3-3.12.0.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/antlr/antlr4-runtime/4.12.0/antlr4-runtime-4.12.0.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apfloat/apfloat/1.10.1/apfloat-1.10.1.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/apache/commons/commons-text/1.10.0/commons-text-1.10.0.jar" path-in-jar="/" />
+      <element id="extracted-dir" path="$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.14/jheaps-0.14.jar" path-in-jar="/" />
     </root>
   </artifact>
 </component>

.idea/compiler.xml

@@ -7,6 +7,7 @@
         <sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
         <outputRelativeToContentRoot value="true" />
         <module name="BigPairSEQ" />
+        <module name="BiGpairSEQ_Sim" />
       </profile>
     </annotationProcessing>
   </component>

.idea/jarRepositories.xml

@@ -1,20 +1,35 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
   <component name="RemoteRepositoriesConfiguration">
+    <remote-repository>
+      <option name="id" value="my-internal-site" />
+      <option name="name" value="my-internal-site" />
+      <option name="url" value="https://myserver/repo" />
+    </remote-repository>
+    <remote-repository>
+      <option name="id" value="central" />
+      <option name="name" value="Central Repository" />
+      <option name="url" value="https://repo1.maven.org/maven2" />
+    </remote-repository>
+    <remote-repository>
+      <option name="id" value="central repo" />
+      <option name="name" value="central repo" />
+      <option name="url" value="https://repo1.maven.org/maven2/" />
+    </remote-repository>
     <remote-repository>
       <option name="id" value="central" />
       <option name="name" value="Central Repository" />
       <option name="url" value="https://repo.maven.apache.org/maven2" />
     </remote-repository>
-    <remote-repository>
-      <option name="id" value="central" />
-      <option name="name" value="Maven Central repository" />
-      <option name="url" value="https://repo1.maven.org/maven2" />
-    </remote-repository>
     <remote-repository>
       <option name="id" value="jboss.community" />
       <option name="name" value="JBoss Community repository" />
       <option name="url" value="https://repository.jboss.org/nexus/content/repositories/public/" />
     </remote-repository>
+    <remote-repository>
+      <option name="id" value="34d16bdc-85f0-48ee-8e8b-144091765be1" />
+      <option name="name" value="34d16bdc-85f0-48ee-8e8b-144091765be1" />
+      <option name="url" value="https://repository.mulesoft.org/nexus/content/repositories/public/" />
+    </remote-repository>
   </component>
 </project>

.idea/libraries/apache_commons_csv.xml

@@ -1,8 +1,10 @@
 <component name="libraryTable">
   <library name="apache.commons.csv" type="repository">
-    <properties maven-id="org.apache.commons:commons-csv:1.9.0" />
+    <properties maven-id="org.apache.commons:commons-csv:1.14.0" />
     <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.9.0/commons-csv-1.9.0.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.14.0/commons-csv-1.14.0.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/commons-io/commons-io/2.18.0/commons-io-2.18.0.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.18.0/commons-codec-1.18.0.jar!/" />
     </CLASSES>
     <JAVADOC />
     <SOURCES />

.idea/libraries/commons_cli.xml

@@ -1,8 +1,8 @@
 <component name="libraryTable">
   <library name="commons.cli" type="repository">
-    <properties maven-id="commons-cli:commons-cli:1.5.0" />
+    <properties maven-id="commons-cli:commons-cli:1.9.0" />
     <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.5.0/commons-cli-1.5.0.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/commons-cli/commons-cli/1.9.0/commons-cli-1.9.0.jar!/" />
     </CLASSES>
     <JAVADOC />
     <SOURCES />

.idea/libraries/commons_rng_1.xml

@@ -1,13 +0,0 @@
-<component name="libraryTable">
-  <library name="commons-rng-1">
-    <CLASSES>
-      <root url="file://$USER_HOME$/Downloads/commons-rng-1.6" />
-    </CLASSES>
-    <JAVADOC />
-    <SOURCES>
-      <root url="file://$USER_HOME$/Downloads/commons-rng-1.6" />
-    </SOURCES>
-    <jarDirectory url="file://$USER_HOME$/Downloads/commons-rng-1.6" recursive="false" />
-    <jarDirectory url="file://$USER_HOME$/Downloads/commons-rng-1.6" recursive="false" type="SOURCES" />
-  </library>
-</component>

.idea/libraries/jgrapht_core.xml

@@ -1,9 +1,10 @@
 <component name="libraryTable">
   <library name="jgrapht.core" type="repository">
-    <properties maven-id="org.jgrapht:jgrapht-core:1.5.1" />
+    <properties maven-id="org.jgrapht:jgrapht-core:1.5.2" />
     <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.1/jgrapht-core-1.5.1.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.2/jgrapht-core-1.5.2.jar!/" />
-      <root url="jar://$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.13/jheaps-0.13.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.14/jheaps-0.14.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/apfloat/apfloat/1.10.1/apfloat-1.10.1.jar!/" />
     </CLASSES>
     <JAVADOC />
     <SOURCES />

.idea/libraries/jgrapht_io.xml

@@ -1,13 +1,14 @@
 <component name="libraryTable">
   <library name="jgrapht.io" type="repository">
-    <properties maven-id="org.jgrapht:jgrapht-io:1.5.1" />
+    <properties maven-id="org.jgrapht:jgrapht-io:1.5.2" />
     <CLASSES>
-      <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-io/1.5.1/jgrapht-io-1.5.1.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-io/1.5.2/jgrapht-io-1.5.2.jar!/" />
-      <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.1/jgrapht-core-1.5.1.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/jgrapht/jgrapht-core/1.5.2/jgrapht-core-1.5.2.jar!/" />
-      <root url="jar://$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.13/jheaps-0.13.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/jheaps/jheaps/0.14/jheaps-0.14.jar!/" />
-      <root url="jar://$MAVEN_REPOSITORY$/org/antlr/antlr4-runtime/4.8-1/antlr4-runtime-4.8-1.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/apfloat/apfloat/1.10.1/apfloat-1.10.1.jar!/" />
-      <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-text/1.8/commons-text-1.8.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/antlr/antlr4-runtime/4.12.0/antlr4-runtime-4.12.0.jar!/" />
-      <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-lang3/3.9/commons-lang3-3.9.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-text/1.10.0/commons-text-1.10.0.jar!/" />
+      <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-lang3/3.12.0/commons-lang3-3.12.0.jar!/" />
     </CLASSES>
     <JAVADOC />
     <SOURCES />

pom.xml

@@ -5,7 +5,7 @@
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>org.example</groupId>
-    <artifactId>TCellSim</artifactId>
+    <artifactId>BiGpairSEQ_Sim</artifactId>
     <version>1.0-SNAPSHOT</version>
     <build>
         <plugins>
@@ -26,8 +26,48 @@
             <version>RELEASE</version>
             <scope>compile</scope>
         </dependency>
+        <!-- https://mvnrepository.com/artifact/org.apache.commons/commons-rng-simple -->
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-rng-simple</artifactId>
+            <version>1.6</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-rng-sampling</artifactId>
+            <version>1.6</version>
+        </dependency>
+        <!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-csv</artifactId>
+            <version>1.14.0</version>
+        </dependency>
+        <!-- https://mvnrepository.com/artifact/org.jgrapht/jgrapht-core -->
+        <dependency>
+            <groupId>org.jgrapht</groupId>
+            <artifactId>jgrapht-core</artifactId>
+            <version>1.5.2</version>
+        </dependency>
+        <!-- https://mvnrepository.com/artifact/org.jgrapht/jgrapht-io -->
+        <dependency>
+            <groupId>org.jgrapht</groupId>
+            <artifactId>jgrapht-io</artifactId>
+            <version>1.5.2</version>
+        </dependency>
+        <!-- https://mvnrepository.com/artifact/org.jheaps/jheaps -->
+        <dependency>
+            <groupId>org.jheaps</groupId>
+            <artifactId>jheaps</artifactId>
+            <version>0.14</version>
+        </dependency>
+        <!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
+        <dependency>
+            <groupId>commons-cli</groupId>
+            <artifactId>commons-cli</artifactId>
+            <version>1.9.0</version>
+        </dependency>
     </dependencies>
-
     <properties>
         <maven.compiler.source>11</maven.compiler.source>
         <maven.compiler.target>11</maven.compiler.target>

readme.md

@@ -634,7 +634,10 @@ a means of exploring some very beautiful math.
 
 ## TODO
 
-* Update CLI option text in this readme to include Zipf distribution options
+* Consider whether a graph database might be a better option than keeping things in memory.
+* Look at fastUtil for more performant maps and arrays. Note that there is an optional jGraphT library to work with fastUtil (see FastutilMapIntVertexGraph, for example).
+* Consider implementing an option to use the jGrapht sparse graph representation for a lower memory cost with very large graphs (tens or hundreds of thousands of distinct sequences).
+* ~~Update CLI option text in this readme to include Zipf distribution options~~
 * ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE
 * ~~Hold graph data in memory until another graph is read-in? ABANDONED UNABANDONED~~ DONE
     * ~~*No, this won't work, because BiGpairSEQ simulations alter the underlying graph based on filtering constraints. Changes would cascade with multiple experiments.*~~

src/main/java/BiGpairSEQ.java

@@ -13,7 +13,7 @@ public class BiGpairSEQ {
     private static boolean cacheCells = false;
     private static boolean cachePlate = false;
     private static boolean cacheGraph = false;
-    private static AlgorithmType matchingAlgoritmType = AlgorithmType.HUNGARIAN;
+    private static AlgorithmType matchingAlgorithmType = AlgorithmType.HUNGARIAN;
     private static HeapType priorityQueueHeapType = HeapType.PAIRING;
     private static DistributionType distributionType = DistributionType.ZIPF;
     private static boolean outputBinary = true;
@@ -166,13 +166,13 @@ public class BiGpairSEQ {
         return priorityQueueHeapType;
     }
 
-    public static AlgorithmType getMatchingAlgoritmType() { return matchingAlgoritmType; }
+    public static AlgorithmType getMatchingAlgorithmType() { return matchingAlgorithmType; }
 
-    public static void setHungarianAlgorithm() { matchingAlgoritmType = AlgorithmType.HUNGARIAN; }
+    public static void setHungarianAlgorithm() { matchingAlgorithmType = AlgorithmType.HUNGARIAN; }
 
-    public static void setIntegerWeightScalingAlgorithm() { matchingAlgoritmType = AlgorithmType.INTEGER_WEIGHT_SCALING; }
+    public static void setIntegerWeightScalingAlgorithm() { matchingAlgorithmType = AlgorithmType.INTEGER_WEIGHT_SCALING; }
 
-    public static void setAuctionAlgorithm() { matchingAlgoritmType = AlgorithmType.AUCTION; }
+    public static void setAuctionAlgorithm() { matchingAlgorithmType = AlgorithmType.AUCTION; }
 
     public static void setPairingHeap() {
         priorityQueueHeapType = HeapType.PAIRING;

src/main/java/GraphModificationFunctions.java

@@ -1,72 +1,54 @@
 import org.jgrapht.graph.DefaultWeightedEdge;
 import org.jgrapht.graph.SimpleWeightedGraph;
 
-import java.util.ArrayList;
+import java.util.*;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
 
 public interface GraphModificationFunctions {
 
     //remove over- and under-weight edges, return removed edges
-    static Map<Vertex[], Integer> filterByOverlapThresholds(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
+    static Map<DefaultWeightedEdge, Vertex[]> filterByOverlapThresholds(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
-                                                            int low, int high, boolean saveEdges) {
+                                                              int low, int high, boolean saveEdges) {
-        Map<Vertex[], Integer> removedEdges = new HashMap<>();
+        Map<DefaultWeightedEdge, Vertex[]> removedEdges = new HashMap<>();
+        Set<DefaultWeightedEdge> edgesToRemove = new HashSet<>();
         for (DefaultWeightedEdge e : graph.edgeSet()) {
             if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)) {
                 if(saveEdges) {
-                    Vertex source = graph.getEdgeSource(e);
+                    Vertex[] vertices = {graph.getEdgeSource(e), graph.getEdgeTarget(e)};
-                    Vertex target = graph.getEdgeTarget(e);
+                    removedEdges.put(e, vertices);
-                    Integer weight = (int) graph.getEdgeWeight(e);
-                    Vertex[] edge = {source, target};
-                    removedEdges.put(edge, weight);
-                }
-                else {
-                    graph.setEdgeWeight(e, 0.0);
                 }
+                edgesToRemove.add(e);
             }
         }
-        if(saveEdges) {
+        edgesToRemove.forEach(graph::removeEdge);
-            for (Vertex[] edge : removedEdges.keySet()) {
-                graph.removeEdge(edge[0], edge[1]);
-            }
-        }
         return removedEdges;
     }
 
     //Remove edges for pairs with large occupancy discrepancy, return removed edges
-    static Map<Vertex[], Integer> filterByRelativeOccupancy(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
+    static Map<DefaultWeightedEdge, Vertex[]> filterByRelativeOccupancy(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
                                                   Integer maxOccupancyDifference, boolean saveEdges) {
-        Map<Vertex[], Integer> removedEdges = new HashMap<>();
+        Map<DefaultWeightedEdge, Vertex[]> removedEdges = new HashMap<>();
+        Set<DefaultWeightedEdge> edgesToRemove = new HashSet<>();
         for (DefaultWeightedEdge e : graph.edgeSet()) {
             Integer alphaOcc = graph.getEdgeSource(e).getOccupancy();
             Integer betaOcc = graph.getEdgeTarget(e).getOccupancy();
             if (Math.abs(alphaOcc - betaOcc) >= maxOccupancyDifference) {
                 if (saveEdges) {
-                    Vertex source = graph.getEdgeSource(e);
+                    Vertex[] vertices = {graph.getEdgeSource(e), graph.getEdgeTarget(e)};
-                    Vertex target = graph.getEdgeTarget(e);
+                    removedEdges.put(e, vertices);
-                    Integer weight = (int) graph.getEdgeWeight(e);
-                    Vertex[] edge = {source, target};
-                    removedEdges.put(edge, weight);
-                }
-                else {
-                    graph.setEdgeWeight(e, 0.0);
                 }
+                edgesToRemove.add(e);
             }
         }
-        if(saveEdges) {
+        edgesToRemove.forEach(graph::removeEdge);
-            for (Vertex[] edge : removedEdges.keySet()) {
-                graph.removeEdge(edge[0], edge[1]);
-            }
-        }
         return removedEdges;
     }
 
     //Remove edges for pairs where overlap size is significantly lower than the well occupancy, return removed edges
-    static Map<Vertex[], Integer> filterByOverlapPercent(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
+    static Map<DefaultWeightedEdge, Vertex[]> filterByOverlapPercent(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
                                                          Integer minOverlapPercent,
                                                          boolean saveEdges) {
-        Map<Vertex[], Integer> removedEdges = new HashMap<>();
+        Map<DefaultWeightedEdge, Vertex[]> removedEdges = new HashMap<>();
+        Set<DefaultWeightedEdge> edgesToRemove = new HashSet<>();
         for (DefaultWeightedEdge e : graph.edgeSet()) {
             Integer alphaOcc = graph.getEdgeSource(e).getOccupancy();
             Integer betaOcc = graph.getEdgeTarget(e).getOccupancy();
@@ -74,22 +56,13 @@ public interface GraphModificationFunctions {
             double min = minOverlapPercent / 100.0;
             if ((weight / alphaOcc < min) || (weight / betaOcc < min)) {
                 if (saveEdges) {
-                    Vertex source = graph.getEdgeSource(e);
+                    Vertex[] vertices = {graph.getEdgeSource(e), graph.getEdgeTarget(e)};
-                    Vertex target = graph.getEdgeTarget(e);
+                    removedEdges.put(e, vertices);
-                    Integer intWeight = (int) graph.getEdgeWeight(e);
-                    Vertex[] edge = {source, target};
-                    removedEdges.put(edge, intWeight);
-                }
-                else {
-                    graph.setEdgeWeight(e, 0.0);
                 }
+                edgesToRemove.add(e);
             }
         }
-        if(saveEdges) {
+        edgesToRemove.forEach(graph::removeEdge);
-            for (Vertex[] edge : removedEdges.keySet()) {
-                graph.removeEdge(edge[0], edge[1]);
-            }
-        }
         return removedEdges;
     }
 
@@ -126,10 +99,10 @@ public interface GraphModificationFunctions {
     }
 
     static void addRemovedEdges(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
-                                Map<Vertex[], Integer> removedEdges) {
+                                Map<DefaultWeightedEdge, Vertex[]> removedEdges) {
-        for (Vertex[] edge : removedEdges.keySet()) {
+        for (DefaultWeightedEdge edge : removedEdges.keySet()) {
-            DefaultWeightedEdge e = graph.addEdge(edge[0], edge[1]);
+            Vertex[] vertices = removedEdges.get(edge);
-            graph.setEdgeWeight(e, removedEdges.get(edge));
+            graph.addEdge(vertices[0], vertices[1], edge);
         }
     }
 

src/main/java/Plate.java

@@ -13,8 +13,7 @@ TODO: Implement discrete frequency distributions using Vose's Alias Method
  */
 
 
-import org.apache.commons.rng.UniformRandomProvider;
+
-import org.apache.commons.rng.core.BaseProvider;
 import org.apache.commons.rng.sampling.distribution.RejectionInversionZipfSampler;
 import org.apache.commons.rng.simple.JDKRandomWrapper;
 
@@ -242,7 +241,7 @@ public class Plate {
                                     sequencesAndMisreads.put(currentSequence, new ArrayList<>());
                                 }
                                 //The specific misread hasn't happened before
-                                if (rand.nextDouble() >= errorCollisionRate || sequencesAndMisreads.get(currentSequence).size() == 0) {
+                                if (rand.nextDouble() >= errorCollisionRate || sequencesAndMisreads.get(currentSequence).isEmpty()) {
                                     //The misread doesn't collide with a real sequence already on the plate and some sequences have already been read
                                     if(rand.nextDouble() >= realSequenceCollisionRate || !sequenceMap.isEmpty()){
                                         StringBuilder spurious = new StringBuilder(currentSequence);

src/main/java/Simulator.java

@@ -1,9 +1,8 @@
+import org.jgrapht.Graphs;
 import org.jgrapht.alg.interfaces.MatchingAlgorithm;
 import org.jgrapht.alg.matching.MaximumWeightBipartiteMatching;
-import org.jgrapht.generate.SimpleWeightedBipartiteGraphMatrixGenerator;
 import org.jgrapht.graph.DefaultWeightedEdge;
 import org.jgrapht.graph.SimpleWeightedGraph;
-import org.jheaps.tree.FibonacciHeap;
 import org.jheaps.tree.PairingHeap;
 
 import java.math.BigDecimal;
@@ -70,58 +69,104 @@ public class Simulator implements GraphModificationFunctions {
             if(verbose){System.out.println("Total beta sequence wells removed: " + betaWellsRemoved);}
         }
 
-        //construct the graph. For simplicity, going to make
+        /*
-        if(verbose){System.out.println("Making vertex maps");}
+         * The commented out code below works beautifully for small enough graphs. However, after implementing a
-        //For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
+         * Zipf distribution and attempting to simulate Experiment 3 from the paper again, I discovered that
-        //distinct numbers associated with them. Since I'm using a 2D array, that means
+         * this method uses too much memory. Even a 120GB heap is not enough to build this adjacency matrix.
-        //distinct indices between the rows and columns. vertexStartValue lets me track where I switch
+         * So I'm going to attempt to build this graph directly and see if that is less memory intensive
-        //from numbering rows to columns, so I can assign unique numbers to every vertex, and then
+         */
-        //subtract the vertexStartValue from betas to use their vertex labels as array indices
+//        //construct the graph. For simplicity, going to make
-        int vertexStartValue = 0;
+//        if(verbose){System.out.println("Making vertex maps");}
-        //keys are sequential integer vertices, values are alphas
+//        //For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
-        Map<String, Integer> plateAtoVMap = makeSequenceToVertexMap(alphaSequences, vertexStartValue);
+//        //distinct numbers associated with them. Since I'm using a 2D array, that means
-        //new start value for vertex to beta map should be one more than final vertex value in alpha map
+//        //distinct indices between the rows and columns. vertexStartValue lets me track where I switch
-        vertexStartValue += plateAtoVMap.size();
+//        //from numbering rows to columns, so I can assign unique numbers to every vertex, and then
-        //keys are betas, values are sequential integers
+//        //subtract the vertexStartValue from betas to use their vertex labels as array indices
-        Map<String, Integer> plateBtoVMap = makeSequenceToVertexMap(betaSequences, vertexStartValue);
+//        int vertexStartValue = 0;
-        if(verbose){System.out.println("Vertex maps made");}
+//        //keys are sequential integer vertices, values are alphas
-        //make adjacency matrix for bipartite graph generator
+//        Map<String, Integer> plateAtoVMap = makeSequenceToVertexMap(alphaSequences, vertexStartValue);
-        //(technically this is only 1/4 of an adjacency matrix, but that's all you need
+//        //new start value for vertex to beta map should be one more than final vertex value in alpha map
-        //for a bipartite graph, and all the SimpleWeightedBipartiteGraphMatrixGenerator class expects.)
+//        vertexStartValue += plateAtoVMap.size();
-        if(verbose){System.out.println("Making adjacency matrix");}
+//        //keys are betas, values are sequential integers
-        double[][] weights = new double[plateAtoVMap.size()][plateBtoVMap.size()];
+//        Map<String, Integer> plateBtoVMap = makeSequenceToVertexMap(betaSequences, vertexStartValue);
-        fillAdjacencyMatrix(weights, vertexStartValue, alphaSequences, betaSequences, plateAtoVMap, plateBtoVMap);
+//        if(verbose){System.out.println("Vertex maps made");}
-        if(verbose){System.out.println("Adjacency matrix made");}
+//        //make adjacency matrix for bipartite graph generator
+//        //(technically this is only 1/4 of an adjacency matrix, but that's all you need
+//        //for a bipartite graph, and all the SimpleWeightedBipartiteGraphMatrixGenerator class expects.)
+//        if(verbose){System.out.println("Making adjacency matrix");}
+//        double[][] weights = new double[plateAtoVMap.size()][plateBtoVMap.size()];
+//        fillAdjacencyMatrix(weights, vertexStartValue, alphaSequences, betaSequences, plateAtoVMap, plateBtoVMap);
+//        if(verbose){System.out.println("Adjacency matrix made");}
+//        //make bipartite graph
+//        if(verbose){System.out.println("Making bipartite weighted graph");}
+//        //the graph object
+//        SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph =
+//                new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
+//        //the graph generator
+//        SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
+//        //the list of alpha vertices
+//        List<Vertex> alphaVertices = new ArrayList<>();
+//        for (String seq : plateAtoVMap.keySet()) {
+//            Vertex alphaVertex = new Vertex(alphaSequences.get(seq), plateAtoVMap.get(seq));
+//            alphaVertices.add(alphaVertex);
+//        }
+//        //Sort to make sure the order of vertices in list matches the order of the adjacency matrix
+//        Collections.sort(alphaVertices);
+//        //Add ordered list of vertices to the graph
+//        graphGenerator.first(alphaVertices);
+//        //the list of beta vertices
+//        List<Vertex> betaVertices = new ArrayList<>();
+//        for (String seq : plateBtoVMap.keySet()) {
+//            Vertex betaVertex = new Vertex(betaSequences.get(seq), plateBtoVMap.get(seq));
+//            betaVertices.add(betaVertex);
+//        }
+//        //Sort to make sure the order of vertices in list matches the order of the adjacency matrix
+//        Collections.sort(betaVertices);
+//        //Add ordered list of vertices to the graph
+//        graphGenerator.second(betaVertices);
+//        //use adjacency matrix of weight created previously
+//        graphGenerator.weights(weights);
+//        graphGenerator.generateGraph(graph);
+
         //make bipartite graph
         if(verbose){System.out.println("Making bipartite weighted graph");}
         //the graph object
         SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph =
                 new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
-        //the graph generator
+        int vertexLabelValue = 0;
-        SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
+        //create and add alpha sequence vertices
-        //the list of alpha vertices
         List<Vertex> alphaVertices = new ArrayList<>();
-        for (String seq : plateAtoVMap.keySet()) {
+        for (Map.Entry<String, SequenceRecord> entry: alphaSequences.entrySet()) {
-            Vertex alphaVertex = new Vertex(alphaSequences.get(seq), plateAtoVMap.get(seq));
+            alphaVertices.add(new Vertex(entry.getValue(), vertexLabelValue));
-            alphaVertices.add(alphaVertex);
+            vertexLabelValue++;
         }
-        //Sort to make sure the order of vertices in list matches the order of the adjacency matrix
+        alphaVertices.forEach(graph::addVertex);
-        Collections.sort(alphaVertices);
+        //add beta sequence vertices
-        //Add ordered list of vertices to the graph
-        graphGenerator.first(alphaVertices);
-        //the list of beta vertices
         List<Vertex> betaVertices = new ArrayList<>();
-        for (String seq : plateBtoVMap.keySet()) {
+        for (Map.Entry<String, SequenceRecord> entry: betaSequences.entrySet()) {
-            Vertex betaVertex = new Vertex(betaSequences.get(seq), plateBtoVMap.get(seq));
+            betaVertices.add(new Vertex(entry.getValue(), vertexLabelValue));
-            betaVertices.add(betaVertex);
+            vertexLabelValue++;
+        }
+        betaVertices.forEach(graph::addVertex);
+        //add edges (best so far)
+        int edgesAddedCount = 0;
+        for(Vertex a: alphaVertices) {
+            Set<Integer> a_wells = a.getRecord().getWells();
+            for(Vertex b: betaVertices) {
+                Set<Integer> sharedWells = new HashSet<>(a_wells);
+                sharedWells.retainAll(b.getRecord().getWells());
+                if (!sharedWells.isEmpty()) {
+                    Graphs.addEdge(graph, a, b, (double) sharedWells.size());
+                }
+                edgesAddedCount++;
+                if (edgesAddedCount % 10000000 == 0) { //collect garbage every 10,000,000 edges
+                    System.out.println(edgesAddedCount + " edges added");
+                    //request garbage collection
+                    System.gc();
+                    System.out.println("Garbage collection requested");
+                }
+            }
         }
-        //Sort to make sure the order of vertices in list matches the order of the adjacency matrix
-        Collections.sort(betaVertices);
-        //Add ordered list of vertices to the graph
-        graphGenerator.second(betaVertices);
-        //use adjacency matrix of weight created previously
-        graphGenerator.weights(weights);
-        graphGenerator.generateGraph(graph);
         if(verbose){System.out.println("Graph created");}
         //stop timing
         Instant stop = Instant.now();
@@ -145,7 +190,7 @@ public class Simulator implements GraphModificationFunctions {
                                             Integer minOverlapPercent, boolean verbose, boolean calculatePValue) {
         Instant start = Instant.now();
         SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph = data.getGraph();
-        Map<Vertex[], Integer> removedEdges = new HashMap<>();
+        Map<DefaultWeightedEdge, Vertex[]> removedEdges = new HashMap<>();
         boolean saveEdges = BiGpairSEQ.cacheGraph();
         int numWells = data.getNumWells();
         //Integer alphaCount = data.getAlphaCount();
@@ -163,6 +208,7 @@ public class Simulator implements GraphModificationFunctions {
         }
         Integer graphAlphaCount = alphas.size();
         Integer graphBetaCount = betas.size();
+        Integer graphEdgeCount = graph.edgeSet().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");}
@@ -182,12 +228,14 @@ public class Simulator implements GraphModificationFunctions {
         if(verbose){System.out.println("Edges between vertices of with excessively different occupancy values " +
                 "removed");}
 
+        Integer filteredGraphEdgeCount = graph.edgeSet().size();
+
         //Find Maximum Weight Matching
         if(verbose){System.out.println("Finding maximum weight matching");}
         //The matching object
         MatchingAlgorithm<Vertex, DefaultWeightedEdge> maxWeightMatching;
         //Determine algorithm type
-        AlgorithmType algorithm = BiGpairSEQ.getMatchingAlgoritmType();
+        AlgorithmType algorithm = BiGpairSEQ.getMatchingAlgorithmType();
         switch (algorithm) { //Only two options now, but I have room to add more algorithms in the future this way
             case AUCTION -> {
                 //create a new MaximumIntegerWeightBipartiteAuctionMatching
@@ -333,8 +381,10 @@ public class Simulator implements GraphModificationFunctions {
         metadata.put("real sequence collision rate", data.getRealSequenceCollisionRate().toString());
         metadata.put("total alphas read from plate", data.getAlphaCount().toString());
         metadata.put("total betas read from plate", data.getBetaCount().toString());
+        metadata.put("initial edges in graph", graphEdgeCount.toString());
         metadata.put("alphas in graph (after pre-filtering)", graphAlphaCount.toString());
         metadata.put("betas in graph (after pre-filtering)", graphBetaCount.toString());
+        metadata.put("final edges in graph (after pre-filtering)", filteredGraphEdgeCount.toString());
         metadata.put("high overlap threshold for pairing", highThreshold.toString());
         metadata.put("low overlap threshold for pairing", lowThreshold.toString());
         metadata.put("minimum overlap percent for pairing", minOverlapPercent.toString());