Many new classes for comparing Kohli CNV and GATK datasets.

Source/edu/utah/kohli/AccuGenGene.java

@@ -0,0 +1,21 @@
+package edu.utah.kohli;
+
+import java.util.ArrayList;
+
+public class AccuGenGene {
+
+	private String geneName;
+	private ArrayList<AccuGenProbe> probes = new ArrayList<AccuGenProbe>();
+
+	public AccuGenGene (String geneName) {
+		this.geneName = geneName;
+	}
+
+	public double meanZScore(double[] testAFs) {
+		return 0;
+	}
+
+	public ArrayList<AccuGenProbe> getProbes() {
+		return probes;
+	}
+}

Source/edu/utah/kohli/AccuGenProbe.java

@@ -1,6 +1,9 @@
 package edu.utah.kohli;
 
+import java.util.ArrayList;
+
 import util.gen.Misc;
+import util.gen.Num;
 
 public class AccuGenProbe {
 
@@ -11,6 +14,9 @@ public class AccuGenProbe {
 	private String alt;
 	private String gene;
 	private boolean ok = true;
+	private ArrayList<Double> ponAfs = new ArrayList<Double>();
+	private double ponAfsMean = Double.NaN;
+	private double ponStdDev = 0;
 
 	public AccuGenProbe (String rep) {
 		//Chr_POS_REF_ALT_GENE
@@ -22,6 +28,16 @@ public AccuGenProbe (String rep) {
 		alt = f[3];
 		gene = f[4];
 	}
+
+	public double calculateZScore (double testAf) {
+		if (Double.isNaN(ponAfsMean)) {
+			double[] afs = Num.arrayListToDoubles(ponAfs);
+			ponAfsMean = Num.mean(afs);
+			ponStdDev = Num.standardDeviation(afs, ponAfsMean);
+		}
+		return (testAf-ponAfsMean)/ponStdDev;
+	}
+
 
 	public String getOriginalInput() {
 		return originalInput;
@@ -51,4 +67,8 @@ public boolean isOk() {
 		return ok;
 	}
 
+	public ArrayList<Double> getPonAfs() {
+		return ponAfs;
+	}
+
 }

Source/edu/utah/kohli/AccuGenProbeCounts.java

@@ -4,11 +4,14 @@
 
 public class AccuGenProbeCounts {
 
+	private AccuGenProbe probe;
 	private int refCounts;
 	private int altCounts;
+	private double scaledAlleleFraction;
 
 
-	public AccuGenProbeCounts(int refCounts, int altCounts) {
+	public AccuGenProbeCounts(AccuGenProbe probe, int refCounts, int altCounts) {
+		this.probe = probe;
 		this.refCounts = refCounts;
 		this.altCounts = altCounts;
 	}
@@ -25,4 +28,24 @@ public String toString() {
 		return refCounts+":"+altCounts+":"+getReadDepth()+":"+Num.formatNumber(getAlleleFraction(), 3);
 	}
 
+	public int getRefCounts() {
+		return refCounts;
+	}
+
+	public int getAltCounts() {
+		return altCounts;
+	}
+
+	public AccuGenProbe getProbe() {
+		return probe;
+	}
+
+	public double getScaledAlleleFraction() {
+		return scaledAlleleFraction;
+	}
+
+	public void setScaledAlleleFraction(double scaledAlleleFraction) {
+		this.scaledAlleleFraction = scaledAlleleFraction;
+	}
+
 }