New GeometricSeqPhenotype class (#22)

* Created a GeometricSeqPhenotype class that implements Phenotype and uses composition * Maintain translation from nucleotides to amino acids * Precompute vectors from gamma distribution * Made sure nucleotide is being mutated to a different letter. * Test matrix of vectors drawn from the gamma distribution * Remove gamma distribution csv output from repo * Keep mutating until it's not a stop codon * if mutation creates a stop codon, switch index to mutate * represent sequence using a char[] * use inheritance instead of composition * Clean up code, add documentation * finish unit tests for geometricseq * clean up repo * each sentence gets own line. * Address Hugh and Zorian's comments. First round. * Remove SequencePhenotype.java * Fix issue #23 * Remove DMS file requirement * Clean up code and refactor sanity check * Created a GeometricSeqPhenotype class that implements Phenotype and uses composition * Maintain translation from nucleotides to amino acids * Precompute vectors from gamma distribution * Made sure nucleotide is being mutated to a different letter. * Test matrix of vectors drawn from the gamma distribution * Remove gamma distribution csv output from repo * Keep mutating until it's not a stop codon * if mutation creates a stop codon, switch index to mutate * represent sequence using a char[] * use inheritance instead of composition * Clean up code, add documentation * finish unit tests for geometricseq * clean up repo * Address Hugh and Zorian's comments. First round. * Fix issue #23 * Remove DMS file requirement * Clean up code and refactor sanity check * format updates. * remove illegal characters from filename * update readme * Nonfunctional changes to code from Erick's review of PR #22 * Test CodonMap values are correct * Update out.tips for GeometricSeq fields * change names from traitA/B to ag1/2 to consistency * Clean up commented and unused code * print fasta for branches * Add startingSequence and epitopeSites files and output fasta file * Initial commit for testing geometric seq phenotype without predefined dictionary of vectors * Clean up and refactor things * Fix bug with reset and organize/optimize a little more in GeometricSeqPhenotype.java * Make sure that the nucleotide sequence is updated even for synonymous mutations * fasta file rename for pipeline * Update README.md * updates to params for customization of output path * remove .out from outputs * Add headers to fasta file sequences * Update to deme name instead of ID * allow last codon to be a stop * log file creation * file formatting --------- Co-authored-by: Zorian Thornton <[email protected]>
matsengrp · Jun 20, 2023 · 25ad694 · 25ad694
1 parent 0cc19ec
commit 25ad694
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diff --git a/Antigen.java b/Antigen.java
@@ -1,7 +1,9 @@
 /* Implements an individual-based model in which the infection's genealogical history is tracked through time */
 
+import java.io.FileNotFoundException;
+
 class Antigen {
-    public static void main(String[] args) {
+    public static void main(String[] args) throws FileNotFoundException {
 
 		// initialize random number generator
 		cern.jet.random.AbstractDistribution.makeDefaultGenerator();

diff --git a/Biology.java b/Biology.java
diff --git a/GeometricSeqPhenotype.java b/GeometricSeqPhenotype.java
diff --git a/HostPopulation.java b/HostPopulation.java
@@ -17,7 +17,7 @@ public class HostPopulation {
 	private double tmrca;
 	private double netau;	
 	private double serialInterval;
-	private double antigenicDiversity;		
+	private double antigenicDiversity;
 
 	private int newContacts;
 	private int newRecoveries;

diff --git a/Parameters.java b/Parameters.java
diff --git a/PhenotypeFactory.java b/PhenotypeFactory.java
@@ -7,6 +7,7 @@ public class PhenotypeFactory {
 	public static String GEOMETRIC3D = "geometric3d";
 	public static String GEOMETRIC10D = "geometric10d";
 	public static String SEQUENCE = "sequence";
+	public static String GEOMETRIC_SEQ = "geometricSeq";
 
 	// returns newly instantiated Phenotype objects of type according to Parameters.phenotypeSpace
 	public static Phenotype makeVirusPhenotype() {
@@ -15,7 +16,7 @@ public static Phenotype makeVirusPhenotype() {
 		if (GEOMETRIC.equals(Parameters.phenotypeSpace)) { p = new GeometricPhenotype(); }
 		if (GEOMETRIC3D.equals(Parameters.phenotypeSpace)) { p = new GeometricPhenotype3D(); }
 		if (GEOMETRIC10D.equals(Parameters.phenotypeSpace)) { p = new GeometricPhenotype10D(); }
-		if (SEQUENCE.equals(Parameters.phenotypeSpace)) { p = new SequencePhenotype(); }
+		if (GEOMETRIC_SEQ.equals(Parameters.phenotypeSpace)) { p = new GeometricSeqPhenotype(); }
 		return p;
 
 	}
@@ -34,8 +35,13 @@ public static Phenotype makeHostPhenotype() {
 			double[] traits = {Parameters.initialTraitA, 0, 0, 0, 0, 0, 0, 0, 0, 0};
 			p = new GeometricPhenotype10D(traits);
 		}
-		if (SEQUENCE.equals(Parameters.phenotypeSpace)) {
-			p = new SequencePhenotype(Parameters.startingSequence);
+		if (GEOMETRIC_SEQ.equals(Parameters.phenotypeSpace)) {
+			String startingSequence = Parameters.startingSequence;
+			if (startingSequence == null) {
+				p = new GeometricSeqPhenotype(Parameters.initialTraitA, 0);
+			} else {
+				p = new GeometricSeqPhenotype(Parameters.initialTraitA, 0, Parameters.startingSequence.toCharArray());
+			}
 		}
 		return p;
 
@@ -46,6 +52,7 @@ public static Phenotype makeArbitaryPhenotype(double x, double y) {
 
 		Phenotype p = null;
 		if (GEOMETRIC.equals(Parameters.phenotypeSpace)) { p = new GeometricPhenotype(x, y); }
+		if (GEOMETRIC_SEQ.equals(Parameters.phenotypeSpace)) { p = new GeometricSeqPhenotype(x, y); }
 		return p;
 
 	}

diff --git a/README.md b/README.md
@@ -18,10 +18,25 @@ rate of within deme contact.
 
 ## Running
 
+### Setting up Java on Fred Hutch cluster
+
+
+To load Java 11, run these commands:
+
+	source /app/lmod/lmod/init/profile
+	ml Java/11;
+
+
+
 The program can be compiled with:
 
 	javac *.java
 
+
+I (@zorian15) have found that I sometimes need to specify all of the `.jar` files in the compilation command to get things to compile completely, this can be done with::
+
+	javac -classpath ".:lib/classmexer.jar:lib/colt-1.2.0.jar:lib/hamcrest-core-1.3.jar:lib/junit-4.13.1.jar:" *.java
+
 Then to run:
 
 	java -XX:+UseSerialGC -Xmx1G Antigen

diff --git a/Random.java b/Random.java
@@ -1,54 +1,53 @@
 /* Holds random number genator necessities */
-/* Trying to encapsulate this, so the RNG particulars can be changed if necessary */ 
+/* Trying to encapsulate this, so the RNG particulars can be changed if necessary */
 /* Completely static class, allows no instances to be instantiated */
 
-//import cern.jet.random.*;
+import cern.jet.random.*;
 
 public class Random {
-								
+
 	// methods
 
 	public static int nextInt(int from, int to) {
 		return cern.jet.random.Uniform.staticNextIntFromTo(from, to);
-	}	
-	
+	}
+
 	public static double nextDouble() {
-		return cern.jet.random.Uniform.staticNextDouble();		
+		return cern.jet.random.Uniform.staticNextDouble();
 	}
-	
+
 	public static double nextDouble(double from, double to) {
-		return cern.jet.random.Uniform.staticNextDoubleFromTo(from, to);		
-	}	
+		return cern.jet.random.Uniform.staticNextDoubleFromTo(from, to);
+	}
 
 	public static double nextNormal() {
-		return cern.jet.random.Normal.staticNextDouble(0.0,1.0);
+		return cern.jet.random.Normal.staticNextDouble(0.0, 1.0);
 	}
-	
+
 	public static double nextNormal(double mean, double sd) {
-		return cern.jet.random.Normal.staticNextDouble(mean,sd);
-	}	
+		return cern.jet.random.Normal.staticNextDouble(mean, sd);
+	}
 
 	// tuned with mean
 	public static double nextExponential(double lambda) {
-		return cern.jet.random.Exponential.staticNextDouble(1.0/lambda);
+		return cern.jet.random.Exponential.staticNextDouble(1.0 / lambda);
 	}
-	
+
 	// tuned with alpha and beta, matching Mathematica's notation
 	public static double nextGamma(double alpha, double beta) {
-		return cern.jet.random.Gamma.staticNextDouble(alpha, 1/beta);
-	}	
-	
+		return cern.jet.random.Gamma.staticNextDouble(alpha, 1 / beta);
+	}
+
 	public static int nextPoisson(double lambda) {
 		return cern.jet.random.Poisson.staticNextInt(lambda);
 	}
-	
+
 	public static boolean nextBoolean(double p) {
 		boolean x = false;
 		if (nextDouble() < p) {
 			x = true;
 		}
 		return x;
-	}	
-
+	}
 
 }
diff --git a/SequencePhenotype.java b/SequencePhenotype.java