All working, able to be built to .jar

2021-11-12 10:41:44 -06:00
parent d39fdbee3b
commit e15cbc6672
21 changed files with 1003 additions and 12 deletions
--- a/.idea/.gitignore
+++ b/.idea/.gitignore
@@ -0,0 +1,3 @@
+# Default ignored files
+/shelf/
+/workspace.xml
--- a/.idea/artifacts/TCellSim_jar.xml
+++ b/.idea/artifacts/TCellSim_jar.xml
@@ -0,0 +1,15 @@
+<component name="ArtifactManager">
+  <artifact type="jar" name="TCellSim:jar">
+    <output-path>$PROJECT_DIR$/out/artifacts/TCellSim_jar</output-path>
+    <root id="archive" name="TCellSim.jar">
+      <element id="directory" name="META-INF">
+        <element id="file-copy" path="$PROJECT_DIR$/src/main/java/META-INF/MANIFEST.MF" />
+      </element>
+      <element id="module-output" name="TCellSim" />
+      <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/23.0.0/annotations-23.0.0.jar" path-in-jar="/" />
+      <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/jheaps/jheaps/0.13/jheaps-0.13.jar" path-in-jar="/" />
+    </root>
+  </artifact>
+</component>
--- a/.idea/artifacts/TCellSim_jar2.xml
+++ b/.idea/artifacts/TCellSim_jar2.xml
@@ -0,0 +1,15 @@
+<component name="ArtifactManager">
+  <artifact type="jar" name="TCellSim:jar2">
+    <output-path>$PROJECT_DIR$/out/artifacts/TCellSim_jar2</output-path>
+    <root id="archive" name="TCellSim.jar">
+      <element id="directory" name="META-INF">
+        <element id="file-copy" path="$PROJECT_DIR$/src/main/java/META-INF/MANIFEST.MF" />
+      </element>
+      <element id="module-output" name="TCellSim" />
+      <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/23.0.0/annotations-23.0.0.jar" path-in-jar="/" />
+      <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/jheaps/jheaps/0.13/jheaps-0.13.jar" path-in-jar="/" />
+    </root>
+  </artifact>
+</component>
--- a/.idea/compiler.xml
+++ b/.idea/compiler.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="CompilerConfiguration">
+    <annotationProcessing>
+      <profile name="Maven default annotation processors profile" enabled="true">
+        <sourceOutputDir name="target/generated-sources/annotations" />
+        <sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
+        <outputRelativeToContentRoot value="true" />
+        <module name="TCellSim" />
+      </profile>
+    </annotationProcessing>
+  </component>
+</project>
--- a/.idea/jarRepositories.xml
+++ b/.idea/jarRepositories.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="RemoteRepositoriesConfiguration">
+    <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>
+  </component>
+</project>
--- a/.idea/libraries/apache_commons_csv.xml
+++ b/.idea/libraries/apache_commons_csv.xml
@@ -0,0 +1,10 @@
+<component name="libraryTable">
+  <library name="apache.commons.csv" type="repository">
+    <properties maven-id="org.apache.commons:commons-csv:1.9.0" />
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-csv/1.9.0/commons-csv-1.9.0.jar!/" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES />
+  </library>
+</component>
--- a/.idea/libraries/jgrapht_core.xml
+++ b/.idea/libraries/jgrapht_core.xml
@@ -0,0 +1,11 @@
+<component name="libraryTable">
+  <library name="jgrapht.core" type="repository">
+    <properties maven-id="org.jgrapht:jgrapht-core:1.5.1" />
+    <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/jheaps/jheaps/0.13/jheaps-0.13.jar!/" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES />
+  </library>
+</component>
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ExternalStorageConfigurationManager" enabled="true" />
+  <component name="MavenProjectsManager">
+    <option name="originalFiles">
+      <list>
+        <option value="$PROJECT_DIR$/pom.xml" />
+      </list>
+    </option>
+  </component>
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_17" default="true" project-jdk-name="17" project-jdk-type="JavaSDK">
+    <output url="file://$PROJECT_DIR$/out" />
+  </component>
+</project>
--- a/.idea/runConfigurations.xml
+++ b/.idea/runConfigurations.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="RunConfigurationProducerService">
+    <option name="ignoredProducers">
+      <set>
+        <option value="com.android.tools.idea.compose.preview.runconfiguration.ComposePreviewRunConfigurationProducer" />
+      </set>
+    </option>
+  </component>
+</project>
--- a/.idea/uiDesigner.xml
+++ b/.idea/uiDesigner.xml
@@ -0,0 +1,124 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Palette2">
+    <group name="Swing">
+      <item class="com.intellij.uiDesigner.HSpacer" tooltip-text="Horizontal Spacer" icon="/com/intellij/uiDesigner/icons/hspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="1" hsize-policy="6" anchor="0" fill="1" />
+      </item>
+      <item class="com.intellij.uiDesigner.VSpacer" tooltip-text="Vertical Spacer" icon="/com/intellij/uiDesigner/icons/vspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="1" anchor="0" fill="2" />
+      </item>
+      <item class="javax.swing.JPanel" icon="/com/intellij/uiDesigner/icons/panel.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3" />
+      </item>
+      <item class="javax.swing.JScrollPane" icon="/com/intellij/uiDesigner/icons/scrollPane.png" removable="false" auto-create-binding="false" can-attach-label="true">
+        <default-constraints vsize-policy="7" hsize-policy="7" anchor="0" fill="3" />
+      </item>
+      <item class="javax.swing.JButton" icon="/com/intellij/uiDesigner/icons/button.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="3" anchor="0" fill="1" />
+        <initial-values>
+          <property name="text" value="Button" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JRadioButton" icon="/com/intellij/uiDesigner/icons/radioButton.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
+        <initial-values>
+          <property name="text" value="RadioButton" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JCheckBox" icon="/com/intellij/uiDesigner/icons/checkBox.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
+        <initial-values>
+          <property name="text" value="CheckBox" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JLabel" icon="/com/intellij/uiDesigner/icons/label.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="0" anchor="8" fill="0" />
+        <initial-values>
+          <property name="text" value="Label" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JTextField" icon="/com/intellij/uiDesigner/icons/textField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+          <preferred-size width="150" height="-1" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JPasswordField" icon="/com/intellij/uiDesigner/icons/passwordField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+          <preferred-size width="150" height="-1" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JFormattedTextField" icon="/com/intellij/uiDesigner/icons/formattedTextField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+          <preferred-size width="150" height="-1" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTextArea" icon="/com/intellij/uiDesigner/icons/textArea.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTextPane" icon="/com/intellij/uiDesigner/icons/textPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JEditorPane" icon="/com/intellij/uiDesigner/icons/editorPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JComboBox" icon="/com/intellij/uiDesigner/icons/comboBox.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="2" anchor="8" fill="1" />
+      </item>
+      <item class="javax.swing.JTable" icon="/com/intellij/uiDesigner/icons/table.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JList" icon="/com/intellij/uiDesigner/icons/list.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="2" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTree" icon="/com/intellij/uiDesigner/icons/tree.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTabbedPane" icon="/com/intellij/uiDesigner/icons/tabbedPane.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3">
+          <preferred-size width="200" height="200" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JSplitPane" icon="/com/intellij/uiDesigner/icons/splitPane.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3">
+          <preferred-size width="200" height="200" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JSpinner" icon="/com/intellij/uiDesigner/icons/spinner.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
+      </item>
+      <item class="javax.swing.JSlider" icon="/com/intellij/uiDesigner/icons/slider.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
+      </item>
+      <item class="javax.swing.JSeparator" icon="/com/intellij/uiDesigner/icons/separator.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3" />
+      </item>
+      <item class="javax.swing.JProgressBar" icon="/com/intellij/uiDesigner/icons/progressbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1" />
+      </item>
+      <item class="javax.swing.JToolBar" icon="/com/intellij/uiDesigner/icons/toolbar.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1">
+          <preferred-size width="-1" height="20" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JToolBar$Separator" icon="/com/intellij/uiDesigner/icons/toolbarSeparator.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="0" anchor="0" fill="1" />
+      </item>
+      <item class="javax.swing.JScrollBar" icon="/com/intellij/uiDesigner/icons/scrollbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="0" anchor="0" fill="2" />
+      </item>
+    </group>
+  </component>
+</project>
--- a/.idea/vcs.xml
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
--- a/pom.xml
+++ b/pom.xml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>org.example</groupId>
+    <artifactId>TCellSim</artifactId>
+    <version>1.0-SNAPSHOT</version>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <configuration>
+                    <source>14</source>
+                    <target>14</target>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+    <dependencies>
+        <dependency>
+            <groupId>org.jetbrains</groupId>
+            <artifactId>annotations</artifactId>
+            <version>RELEASE</version>
+            <scope>compile</scope>
+        </dependency>
+    </dependencies>
+
+    <properties>
+        <maven.compiler.source>11</maven.compiler.source>
+        <maven.compiler.target>11</maven.compiler.target>
+    </properties>
+
+</project>
--- a/src/main/java/CellFileReader.java
+++ b/src/main/java/CellFileReader.java
@@ -0,0 +1,50 @@
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVParser;
+import org.apache.commons.csv.CSVRecord;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
+
+public class CellFileReader {
+
+    private List<Integer[]> distinctCells = new ArrayList<>();
+
+    public CellFileReader(String filename) {
+
+        if(!filename.matches(".*\\.csv")){
+            filename = filename + ".csv";
+        }
+
+        CSVFormat cellFileFormat = CSVFormat.Builder.create()
+                .setHeader("Alpha", "Beta")
+                .setSkipHeaderRecord(true)
+                .build();
+
+        try(//don't need to close reader bc of try-with-resources auto-closing
+            BufferedReader reader = Files.newBufferedReader(Path.of(filename));
+            CSVParser parser = new CSVParser(reader, cellFileFormat);
+        ){
+            for(CSVRecord record: parser.getRecords()) {
+                Integer[] cell = new Integer[2];
+                cell[0] = Integer.valueOf(record.get("Alpha"));
+                cell[1] = Integer.valueOf(record.get("Beta"));
+                distinctCells.add(cell);
+            }
+        } catch(IOException ex){
+            System.out.println("cell file " + filename + " not found.");
+            System.err.println(ex);
+        }
+    }
+
+    public List<Integer[]> getCells(){
+        return distinctCells;
+    }
+
+    public Integer getCellCount() {
+        return distinctCells.size();
+    }
+}
--- a/src/main/java/CellFileWriter.java
+++ b/src/main/java/CellFileWriter.java
@@ -0,0 +1,38 @@
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVPrinter;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
+import java.util.List;
+
+public class CellFileWriter {
+
+    private String[] headers = {"Alpha", "Beta"};
+    List<Integer[]> cells;
+    String filename;
+
+    public CellFileWriter(String filename, CellSample cells) {
+        if(!filename.matches(".*\\.csv")){
+            filename = filename + ".csv";
+        }
+        this.filename = filename;
+        this.cells = cells.getCells();
+    }
+
+    public void writeCellsToFile() {
+        CSVFormat cellFileFormat = CSVFormat.Builder.create()
+                .setHeader(headers)
+                .build();
+        try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
+            CSVPrinter printer = new CSVPrinter(writer, cellFileFormat);
+        ){
+            printer.printRecords(cells);
+        } catch(IOException ex){
+            System.out.println("Could not make new file named "+filename);
+            System.err.println(ex);
+        }
+    }
+}
--- a/src/main/java/CellSample.java
+++ b/src/main/java/CellSample.java
@@ -0,0 +1,19 @@
+import java.util.List;
+
+public class CellSample {
+
+    private List<Integer[]> cells;
+
+    public CellSample(List<Integer[]> cells){
+        this.cells = cells;
+    }
+
+    public List<Integer[]> getCells(){
+        return cells;
+    }
+
+    public Integer population(){
+        return cells.size();
+    }
+
+}
--- a/src/main/java/MatchingFileWriter.java
+++ b/src/main/java/MatchingFileWriter.java
@@ -0,0 +1,52 @@
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVPrinter;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
+import java.util.List;
+
+
+public class MatchingFileWriter {
+
+    private String filename;
+    private List<String> comments;
+    private List<String> headers;
+    private List<List<String>> results;
+
+    public MatchingFileWriter(String filename, List<String> comments, List<String> headers, List<List<String>> results){
+        if(!filename.matches(".*\\.csv")){
+            filename = filename + ".csv";
+        }
+        this.filename = filename;
+        this.comments = comments;
+        this.headers = headers;
+        this.results = results;
+    }
+
+    public void writeResultsToFile(){
+        String[] headerStrings = new String[headers.size()];
+        for(int i = 0; i < headers.size(); i++){
+            headerStrings[i] = headers.get(i);
+        }
+        CSVFormat resultsFileFormat = CSVFormat.Builder.create()
+                .setCommentMarker('#')
+                //.setHeader(headerStrings)
+                .build();
+        try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
+            CSVPrinter printer = new CSVPrinter(writer, resultsFileFormat);
+        ){
+            for(String comment: comments){
+                printer.printComment(comment);
+            }
+            results.add(0, headers);
+            printer.printRecords(results);
+
+        } catch(IOException ex){
+            System.out.println("Could not make new file named "+filename);
+            System.err.println(ex);
+        }
+    }
+}
--- a/src/main/java/Plate.java
+++ b/src/main/java/Plate.java
@@ -8,14 +8,23 @@ public class Plate {
    private Random rand = new Random();
    private int size;
    private double error;
+    private Integer[] concentrations;
+    private double stdDev;

-    public Plate (int size, double error) {
+    public Plate (int size, double error, Integer[] concentrations, double stdDev) {
        this.size = size;
        this.error = error;
+        this.concentrations = concentrations;
+        this.stdDev = stdDev;
        wells = new ArrayList<>();
    }

-    public void fillWells(List<Integer[]> cells, int[] concentrations, double stdDev) {
+    public Plate(List<List<Integer[]>> wells){
+        this.wells = wells;
+        this.size = wells.size();
+    }
+
+    public void fillWells(List<Integer[]> cells) {
        int numSections = concentrations.length;
        int section = 0;
        double m;
@@ -26,8 +35,8 @@ public class Plate {
                List<Integer[]> well = new ArrayList<>();
                for (int j = 0; j < concentrations[section]; j++) {
                    do {
-                        m = Math.abs(rand.nextGaussian()) * stdDev;
-                    } while (m >= cells.size());
+                        m = (rand.nextGaussian() * stdDev) + (cells.size() / 2);
+                    } while (m >= cells.size() || m < 0);
                    n = (int) Math.floor(m);
                    Integer[] cellToAdd = cells.get(n).clone();
                    drop = Math.abs(rand.nextDouble()) < error;
@@ -46,6 +55,31 @@ public class Plate {
        }
    }

+    public void writePlateToFile(String filename) {
+
+
+    }
+
+    public Integer[] getConcentrations(){
+        return concentrations;
+    }
+
+    public int getSize(){
+        return size;
+    }
+
+    public double getStdDev() {
+        return stdDev;
+    }
+
+    public double getError() {
+        return error;
+    }
+
+    public List<List<Integer[]>> getWells() {
+        return wells;
+    }
+
    public Map<Integer, Integer> assayWellsAlpha() {
        return this.assayWellsAlpha(0, size);
    }
--- a/src/main/java/PlateFileReader.java
+++ b/src/main/java/PlateFileReader.java
@@ -0,0 +1,61 @@
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVParser;
+import org.apache.commons.csv.CSVRecord;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.sql.Array;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Pattern;
+
+public class PlateFileReader {
+
+    private List<List<Integer[]>> wells = new ArrayList<>();
+
+    public PlateFileReader(String filename){
+
+        if(!filename.matches(".*\\.csv")){
+            filename = filename + ".csv";
+        }
+
+        CSVFormat plateFileFormat = CSVFormat.Builder.create()
+                .setCommentMarker('#')
+                .build();
+
+        try(//don't need to close reader bc of try-with-resources auto-closing
+            BufferedReader reader = Files.newBufferedReader(Path.of(filename));
+            CSVParser parser = new CSVParser(reader, plateFileFormat);
+        ){
+            for(CSVRecord record: parser.getRecords()) {
+                List<Integer[]> well = new ArrayList<>();
+                for(String s: record) {
+                    if(!"".equals(s)) {
+                        String[] intString = s.replaceAll("\\[", "")
+                                .replaceAll("]", "")
+                                .replaceAll(" ", "")
+                                .split(",");
+                        //System.out.println(intString);
+                        Integer[] arr = new Integer[intString.length];
+                        for (int i = 0; i < intString.length; i++) {
+                            arr[i] = Integer.valueOf(intString[i]);
+                        }
+                        well.add(arr);
+                    }
+                }
+                wells.add(well);
+            }
+        } catch(IOException ex){
+            System.out.println("plate file " + filename + " not found.");
+            System.err.println(ex);
+        }
+
+    }
+
+    public List<List<Integer[]>> getWells() {
+        return wells;
+    }
+
+}
--- a/src/main/java/PlateFileWriter.java
+++ b/src/main/java/PlateFileWriter.java
@@ -0,0 +1,93 @@
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVPrinter;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
+import java.util.*;
+import java.util.regex.Pattern;
+
+public class PlateFileWriter {
+    private int size;
+    private List<List<Integer[]>> wells;
+    private double stdDev;
+    private Double error;
+    private String filename;
+    private String[] headers;
+    private List<Integer> concentrations;
+
+    public PlateFileWriter(String filename, Plate plate) {
+        if(!filename.matches(".*\\.csv")){
+            filename = filename + ".csv";
+        }
+        this.filename = filename;
+        this.size = plate.getSize();
+        this.stdDev = plate.getStdDev();
+        this.error = plate.getError();
+        this.wells = plate.getWells();
+        this.concentrations = Arrays.asList(plate.getConcentrations());
+        concentrations.sort(Comparator.reverseOrder());
+    }
+
+    public void writePlateFile(){
+        //works as is, but too many columns in csv, need to make them all rows.
+
+        //will now redo it so that every column is a well, with well names as headers
+        //need to give plate error, sample pop size, stdDev, num sections, concentration per section as comments
+        Comparator<List<Integer[]>> listLengthDescending = Comparator.comparingInt(List::size);
+        wells.sort(listLengthDescending.reversed());
+        int maxLength = wells.get(0).size();
+        List<List<String>> wellsAsStrings = new ArrayList<>();
+        for (List<Integer[]> w: wells){
+            List<String> tmp = new ArrayList<>();
+            for(Integer[] c: w) {
+                tmp.add(Arrays.toString(c));
+            }
+            wellsAsStrings.add(tmp);
+        }
+        for(List<String> w: wellsAsStrings){
+            while(w.size() < maxLength){
+                w.add("");
+            }
+        }
+
+        //this took forever
+        List<List<String>> rows = new ArrayList<>();
+        List<String> tmp = new ArrayList<>();
+        for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
+            tmp.add("well " + (i+1));
+        }
+        rows.add(tmp);
+        for(int row = 0; row < maxLength; row++){
+            tmp = new ArrayList<>();
+            for(List<String> c: wellsAsStrings){
+                tmp.add(c.get(row));
+            }
+            rows.add(tmp);
+        }
+        StringBuilder concen = new StringBuilder();
+        for(Integer i: concentrations){
+            concen.append(i.toString());
+            concen.append(" ");
+        }
+        String concenString = concen.toString();
+
+        CSVFormat plateFileFormat = CSVFormat.Builder.create().setCommentMarker('#').build();
+
+        try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
+            CSVPrinter printer = new CSVPrinter(writer, plateFileFormat);
+        ){
+            printer.printComment("Each row represents one well on the plate.");
+            printer.printComment("Plate size: " + size);
+            printer.printComment("Error rate: " + error);
+            printer.printComment("Concentrations: " + concenString);
+            printer.printComment("Std. dev.: " + stdDev);
+            printer.printRecords(wellsAsStrings);
+        } catch(IOException ex){
+            System.out.println("Could not make new file named "+filename);
+            System.err.println(ex);
+        }
+    }
+}
--- a/src/main/java/Simulation.java
+++ b/src/main/java/Simulation.java
@@ -13,21 +13,196 @@ import java.time.Instant;
 import java.util.*;
 import java.util.stream.IntStream;

-public class Simulation {
-    private static Integer numDistinctCells = 15_000_000;
-    private static double stdDeviation = 1000; //square root of numDistCells would approximate poisson dist, supposedly
+public class Simulator {
+    private static Integer numDistinctCells = 2_000_000;
+    private static double stdDeviation = 200; //square root of numDistCells would approximate poisson dist
    private static int numWells = 96;
    private static int numConcentrations = 1;
    private static double errorRate = 0.1;
-    private static int[] concentrations = {500};
+    private static Integer[] concentrations = {500};
    private static int lowThreshold = 2; //min number of shared wells to attempt pairing
    private static int highThreshold = numWells - 3; //max number of shared wells to attempt pairing
    private static boolean use2DArrayForGraph = true; //Doing this is much faster for larger graphs
    private static boolean useJGraphTGraphMatrixGenerator = true; //fastest option

-    public static void main(String[] args) {
-        Instant start = Instant.now();

+    public static CellSample generateCellSample(Integer numDistinctCells) {
+        List<Integer> numbers = new ArrayList<>();
+        IntStream.range(1, (2 * numDistinctCells) + 1).forEach(i -> numbers.add(i));
+        Collections.shuffle(numbers);
+
+        //Each cell represented by two numbers from the random permutation
+        //These represent unique alpha and beta peptides
+        List<Integer[]> distinctCells = new ArrayList<>();
+        for(int i = 0; i < numbers.size() - 1; i = i + 2) {
+            Integer tmp1 = numbers.get(i);
+            Integer tmp2 = numbers.get(i+1);
+            Integer[] tmp = {tmp1, tmp2};
+            distinctCells.add(tmp);
+        }
+        return new CellSample(distinctCells);
+    }
+
+    public static void matchCells(String filename, List<Integer[]> distinctCells, Plate samplePlate, Integer lowThreshold, Integer highThreshold){
+        System.out.println("Cells: " + distinctCells.size());
+
+        System.out.println("Making cell maps");
+        //HashMap keyed to Alphas, values Betas
+        Map<Integer, Integer> distCellsMapAlphaKey = new HashMap<>();
+        for (Integer[] cell : distinctCells) {
+            distCellsMapAlphaKey.put(cell[0], cell[1]);
+        }
+        //HashMap keyed to Betas, values Alphas
+        Map<Integer, Integer> distCellsMapBetaKey = new HashMap<>();
+        for (Integer[] cell : distinctCells) {
+            distCellsMapBetaKey.put(cell[1], cell[0]);
+        }
+        System.out.println("Cell maps made");
+
+        System.out.println("Making well maps");
+        Map<Integer, Integer> allAlphas = samplePlate.assayWellsAlpha();
+        Map<Integer, Integer> allBetas = samplePlate.assayWellsBeta();
+        int alphaCount = allAlphas.size();
+        System.out.println("all alphas count: " + alphaCount);
+        int betaCount = allBetas.size();
+        System.out.println("all betas count: " + betaCount);
+
+        System.out.println("Well maps made");
+
+        System.out.println("Making vertex maps");
+        //Using Integers instead of Strings to label vertices so I can do clever stuff with indices if I need to
+        // when I refactor to use a 2d array to make the graph
+        //For the autogenerator, all vertices must have distinct numbers associated with them
+        Integer vertexStartValue = 0;
+        //keys are sequential integer vertices, values are alphas
+        Map<Integer, Integer> plateVtoAMap = getVertexToPeptideMap(allAlphas, vertexStartValue);
+        //New start value for vertex to beta map should be one more than final vertex value in alpha map
+        vertexStartValue += plateVtoAMap.size();
+        //keys are sequential integers vertices, values are betas
+        Map<Integer, Integer> plateVtoBMap = getVertexToPeptideMap(allBetas, vertexStartValue);
+        //keys are alphas, values are sequential integer vertices from previous map
+        Map<Integer, Integer> plateAtoVMap = invertVertexMap(plateVtoAMap);
+        System.out.println(plateAtoVMap.size());
+        //keys are betas, values are sequential integer vertices from previous map
+        Map<Integer, Integer> plateBtoVMap = invertVertexMap(plateVtoBMap);
+        System.out.println(plateAtoVMap.size());
+        System.out.println("Vertex maps made");
+
+        System.out.println("Creating Graph");
+        //Count how many wells each alpha appears in
+        Map<Integer, Integer> alphaWellCounts = new HashMap<>();
+        //count how many wells each beta appears in
+        Map<Integer, Integer> betaWellCounts = new HashMap<>();
+        //add edges, where weights are number of wells the peptides share in common.
+        //If this is too slow, can make a 2d array and use the SimpleWeightedGraphMatrixGenerator class
+        Map<Integer, Integer> wellNAlphas = null;
+        Map<Integer, Integer> wellNBetas = null;
+        SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph =
+                new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
+        double[][] weights = new double[plateVtoAMap.size()][plateVtoBMap.size()];
+        for (int n = 0; n < numWells; n++) {
+            wellNAlphas = samplePlate.assayWellsAlpha(n);
+            for (Integer a : wellNAlphas.keySet()) {
+                alphaWellCounts.merge(a, 1, (oldValue, newValue) -> oldValue + newValue);
+            }
+            wellNBetas = samplePlate.assayWellsBeta(n);
+            for (Integer b : wellNBetas.keySet()) {
+                betaWellCounts.merge(b, 1, (oldValue, newValue) -> oldValue + newValue);
+            }
+            for (Integer i : wellNAlphas.keySet()) {
+                for (Integer j : wellNBetas.keySet()) {
+                    weights[plateAtoVMap.get(i)][plateBtoVMap.get(j) - vertexStartValue] += 1.0;
+                }
+            }
+        }
+        SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
+        List<Integer> alphaVertices = new ArrayList<>();
+        alphaVertices.addAll(plateVtoAMap.keySet()); //This will work because LinkedHashMap preserves order of entry
+        graphGenerator.first(alphaVertices);
+        List<Integer> betaVertices = new ArrayList<>();
+        betaVertices.addAll(plateVtoBMap.keySet());
+        graphGenerator.second(betaVertices); //This will work because LinkedHashMap preserves order of entry
+        graphGenerator.weights(weights);
+        graphGenerator.generateGraph(graph);
+        System.out.println("Graph created");
+
+        System.out.println("Finding maximum weighted matching");
+        MaximumWeightBipartiteMatching maxWeightMatching =
+                new MaximumWeightBipartiteMatching(graph, plateVtoAMap.keySet(), plateVtoBMap.keySet());
+        MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = maxWeightMatching.getMatching();
+        System.out.println("Matching completed");
+
+        //Header for CSV file
+        List<String> header = new ArrayList<>();
+        header.add("Alpha");
+        header.add("Alpha well count");
+        header.add("Beta");
+        header.add("Beta well count");
+        header.add("Overlap well count");
+        header.add("Matched correctly?");
+        header.add("P-value");
+
+
+        //Results for csv file
+        List<List<String>> allResults = new ArrayList<>();
+        int size = samplePlate.getSize();
+        Iterator<DefaultWeightedEdge> weightIter = graphMatching.iterator();
+        DefaultWeightedEdge e = null;
+        int trueCount = 0;
+        int falseCount = 0;
+        boolean check = false;
+        while(weightIter.hasNext()) {
+            e = weightIter.next();
+            if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
+                continue;
+            }
+            Integer source = graph.getEdgeSource(e);
+            Integer target = graph.getEdgeTarget(e);
+            check = plateVtoBMap.get(target).equals(distCellsMapAlphaKey.get(plateVtoAMap.get(source)));
+            if(check) {
+                trueCount++;
+            }
+            else {
+                falseCount++;
+            }
+            List<String> result = new ArrayList<>();
+            result.add(plateVtoAMap.get(source).toString());
+            //alpha well count
+            result.add(alphaWellCounts.get(plateVtoAMap.get(source)).toString());
+            result.add(plateVtoBMap.get(target).toString());
+            //beta well count
+            result.add(betaWellCounts.get(plateVtoBMap.get(target)).toString());
+            //overlap count
+            result.add(Double.toString(graph.getEdgeWeight(e)));
+            result.add(Boolean.toString(check));
+            result.add(Double.toString(Equations.pValue(size, alphaWellCounts.get(plateVtoAMap.get(source)),
+                    betaWellCounts.get(plateVtoBMap.get(target)), graph.getEdgeWeight(e))));
+            allResults.add(result);
+        }
+
+        //Metadate comments for CSV file
+        int min = alphaCount > betaCount ? betaCount : alphaCount;
+        double attemptRate = (double) (trueCount + falseCount) / min;
+        double pairingErrorRate = (double) falseCount / (trueCount + falseCount);
+
+        List<String> comments = new ArrayList<>();
+        comments.add("Total alphas found: " + alphaCount);
+        comments.add("Total betas found: " + betaCount);
+        comments.add("Pairing attempt rate: " + attemptRate);
+        comments.add("Correct pairings: " + trueCount);
+        comments.add("Incorrect pairings: " + falseCount);
+        comments.add("Pairing error rate: " + pairingErrorRate);
+
+        //result writer
+        MatchingFileWriter writer = new MatchingFileWriter(filename, comments, header, allResults);
+        writer.writeResultsToFile();
+    }
+
+
+
+
+    public static void Simulate() {
+        Instant start = Instant.now();
        //Four things to try to improve this
        //1. Run it on hardware with more memory
        //2. implement p-values and just check exhaustively for strictly-bounded weights
@@ -76,8 +251,8 @@ public class Simulation {
            distCellsMapBetaKey.put(cell[1], cell[0]);
        }

-        Plate samplePlate = new Plate(numWells, errorRate);
-        samplePlate.fillWells(distinctCells, concentrations, stdDeviation);
+        Plate samplePlate = new Plate(numWells, errorRate, concentrations, stdDeviation);
+        samplePlate.fillWells(distinctCells);

        //OUTPUT
        System.out.println("Wells filled");
--- a/src/main/java/UserInterface.java
+++ b/src/main/java/UserInterface.java
@@ -0,0 +1,192 @@
+import java.util.List;
+import java.util.Scanner;
+import java.util.ArrayList;
+import java.util.InputMismatchException;
+
+//
+public class UserInterface {
+
+    final static Scanner sc = new Scanner(System.in);
+    static int input;
+    static boolean quit = false;
+
+    public static void main(String args[]) {
+        while(!quit) {
+            System.out.println("\nALPHA/BETA T-CELL RECEPTOR MATCHING SIMULATOR");
+            System.out.println("Please select and option:");
+            System.out.println("1) Generate a population of distinct cells");
+            System.out.println("2) Generate a sample plate of T-cells");
+            System.out.println("3) Simulate T-Cell matching");
+            System.out.println("4) Acknowledgements");
+            System.out.println("0) Exit");
+            try {
+                input = sc.nextInt();
+                switch(input){
+                    case 1 -> makeCells();
+                    case 2 -> makePlate();
+                    case 3 -> matchCells();
+                    //case 4 -> //method call goes here
+                    case 0 -> quit = true;
+                    default -> throw new InputMismatchException("Invalid input.");
+                }
+            }catch(InputMismatchException ex){
+                System.out.println(ex);
+                sc.next();
+            }
+        }
+        sc.close();
+    }
+
+    private static void makeCells() {
+        String filename = null;
+        Integer numCells = 0;
+        try {
+            System.out.println("\nSimulated T-Cells consist of matched pairs of alpha and beta peptides, " +
+                    "represented by unique integer values.");
+            System.out.println("(Note: peptide values are unique within a simulated population, " +
+                    "but repeated between simulated populations.)");
+            System.out.println("\nThe cells will be written to a file.");
+            System.out.print("Please enter a file name: ");
+            filename = sc.next();
+            System.out.print("Please enter the number of T-cells to generate: ");
+            numCells = sc.nextInt();
+            if(numCells <= 0){
+                throw new InputMismatchException("Number of cells must be a positive integer.");
+            }
+        } catch (InputMismatchException ex) {
+            System.out.println(ex);
+            sc.next();
+        }
+        CellSample sample = Simulator.generateCellSample(numCells);
+        CellFileWriter writer = new CellFileWriter(filename, sample);
+        writer.writeCellsToFile();
+    }
+
+    //method to output a CSV of
+    private static void makePlate() {
+        String cellFile = null;
+        String filename = null;
+        Double stdDev = 0.0;
+        Integer numWells = 0;
+        Integer numSections = 0;
+        Integer[] concentrations = {1};
+        Double dropOutRate = 0.0;
+        boolean poisson = false;
+        try {
+            System.out.println("\nMaking a sample plate requires a population of distinct cells");
+            System.out.println("Please enter name of an existing cell sample file: ");
+            cellFile = sc.next();
+            System.out.println("\nThe sample plate will be written to file");
+            System.out.print("Please enter a name for the output file: ");
+            filename = sc.next();
+            System.out.println("Select T-cell frequency distribution function");
+            System.out.println("1) Poisson");
+            System.out.println("2) Gaussian");
+            System.out.println("(Note: wider distributions are more memory intensive to match)");
+            System.out.print("Enter selection value: ");
+            input = sc.nextInt();
+            switch(input) {
+                case 1:
+                    poisson = true;
+                    break;
+                case 2:
+                    System.out.println("How many distinct T-cells within one standard deviation of peak frequency?");
+                    System.out.println("(Note: wider distributions are more memory intensive to match)");
+                    stdDev = sc.nextDouble();
+                    if(stdDev <= 0.0){
+                        throw new InputMismatchException("Value must be positive.");
+                    }
+                    break;
+                default:
+                    System.out.println("Invalid input. Defaulting to Poisson.");
+                    poisson = true;
+            }
+            System.out.print("Number of wells on plate: ");
+            numWells = sc.nextInt();
+            if(numWells < 1){
+                throw new InputMismatchException("No wells on plate");
+            }
+            System.out.println("The plate can be evenly sectioned to allow multiple concentrations of T-cells/well");
+            System.out.println("How many sections would you like to make (minimum 1)?");
+            numSections = sc.nextInt();
+            if(numSections < 1) {
+                throw new InputMismatchException("Too few sections.");
+            }
+            else if (numSections > numWells) {
+                throw new InputMismatchException("Cannot have more sections than wells.");
+            }
+            int i = 1;
+            concentrations = new Integer[numSections];
+            while(numSections > 0) {
+                System.out.print("Enter number of T-cells per well in section " + i +": ");
+                concentrations[i - 1] = sc.nextInt();
+                i++;
+                numSections--;
+            }
+            System.out.println("Errors in amplification can induce a well dropout rate for peptides");
+            System.out.print("Enter well dropout rate (0.0 to 1.0): ");
+            dropOutRate = sc.nextDouble();
+            if(dropOutRate < 0.0 || dropOutRate > 1.0) {
+                throw new InputMismatchException("The well dropout rate must be in the range [0.0, 1.0]");
+            }
+        }catch(InputMismatchException ex){
+            System.out.println(ex);
+            sc.next();
+        }
+        CellFileReader cellReader = new CellFileReader(cellFile);
+        if(poisson) {
+            stdDev = Math.sqrt(cellReader.getCellCount()); //gaussian with square root of elements approximates poisson
+        }
+        Plate samplePlate = new Plate(numWells, dropOutRate, concentrations, stdDev);
+        samplePlate.fillWells(cellReader.getCells());
+        PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
+        writer.writePlateFile();
+    }
+
+    private static void matchCells() {
+        String filename = null;
+        String cellFile = null;
+        String plateFile = null;
+        Integer lowThreshold = 0;
+        Integer highThreshold = Integer.MAX_VALUE;
+        try {
+            System.out.println("\nSimulated experiment requires a cell sample file and a sample plate file.");
+            System.out.print("Please enter name of an existing cell sample file: ");
+            cellFile = sc.next();
+            System.out.print("Please enter name of an existing sample plate file: ");
+            plateFile = sc.next();
+            System.out.println("The matching results will be written to a file.");
+            System.out.print("Please enter a name for the output file: ");
+            filename = sc.next();
+            System.out.println("What is the minimum number of alpha/beta overlap wells to attempt matching?");
+            lowThreshold = sc.nextInt();
+            if(lowThreshold < 1){
+                throw new InputMismatchException("Minimum value for low threshold is 1");
+            }
+            System.out.println("What is the maximum number of alpha/beta overlap wells to attempt matching?");
+            highThreshold = sc.nextInt();
+        } catch (InputMismatchException ex) {
+            System.out.println(ex);
+            sc.next();
+        }
+        CellFileReader cellReader = new CellFileReader(cellFile);
+        PlateFileReader plateReader = new PlateFileReader(plateFile);
+        Plate plate = new Plate(plateReader.getWells());
+        if (cellReader.getCells().size() == 0){
+            System.out.println("No cell sample found.");
+            System.out.println("Returning to main menu.");
+        }
+        else if(plate.getWells().size() == 0){
+            System.out.println("No sample plate found.");
+            System.out.println("Returning to main menu.");
+
+        }
+        else{
+            if(highThreshold > plate.getSize()){
+                highThreshold = plate.getSize();
+            }
+            List<Integer[]> cells = cellReader.getCells();
+            Simulator.matchCells(filename, cells, plate, lowThreshold, highThreshold);
+        }
+    }
+}