Fb bilinear regression fit

src/org/labkey/targetedms/TargetedMSModule.java

@@ -60,6 +60,7 @@
 import org.labkey.panoramapremium.PanoramaPremiumController;
 import org.labkey.panoramapremium.QCNotificationSender;
 import org.labkey.panoramapremium.View.QCSummaryMenuCustomizer;
+import org.labkey.targetedms.calculations.quantification.RegressionFit;
 import org.labkey.targetedms.chart.ComparisonCategory;
 import org.labkey.targetedms.chart.ReplicateLabelMinimizer;
 import org.labkey.targetedms.datasource.MsDataSourceUtil;
@@ -667,7 +668,7 @@ public Set<Class> getUnitTests()
             TargetedMSController.TestCase.class,
             PrecursorManager.TestCase.class,
             CrossLinkedPeptideInfo.TestCase.class,
-            Protein.TestCase.class
+            RegressionFit.TestCase.class
         );
     }
 

src/org/labkey/targetedms/calculations/quantification/CalibrationCurve.java

@@ -14,13 +14,21 @@
  */
 package org.labkey.targetedms.calculations.quantification;
 
-public class CalibrationCurve {
+import org.jetbrains.annotations.Nullable;
+
+public class CalibrationCurve implements Cloneable {
     private Double slope;
     private Double intercept;
+    private Double turningPoint;
     private Integer pointCount;
     private Double quadraticCoefficient;
     private Double rSquared;
     private String errorMessage;
+    private RegressionFit regressionFit;
+
+    public CalibrationCurve(RegressionFit regressionFit) {
+        this.regressionFit = regressionFit;
+    }
 
     public double getSlope() {
         return slope == null ? 0 : slope;
@@ -38,13 +46,25 @@ public double getIntercept() {
         return intercept == null ? 0 : intercept;
     }
 
+
     public boolean hasIntercept() {
         return intercept != null;
     }
 
     public void setIntercept(Double intercept) {
         this.intercept = intercept;
     }
+    public double getTurningPoint()
+    {
+        return turningPoint  == null ? 0 : turningPoint;
+    }
+    public boolean hasTurningPoint() {
+        return turningPoint != null;
+    }
+    public void setTurningPoint(Double turningPoint)
+    {
+        this.turningPoint = turningPoint;
+    }
 
     public int getPointCount() {
         return pointCount == null ? 0 : pointCount;
@@ -88,30 +108,25 @@ public void setErrorMessage(String errorMessage) {
 
     public Double getY(double x)
     {
-        if (hasQuadraticCoefficient())
-        {
-            return x*x*getQuadraticCoefficient() + x*getSlope() + getIntercept();
-        }
-        return x*getSlope() + getIntercept();
+        return regressionFit.getY(this, x);
     }
 
+    @Nullable
     public Double getX(double y)
     {
-        if (hasQuadraticCoefficient())
-        {
-            double discriminant = getSlope()*getSlope()- 4*getQuadraticCoefficient()*(getIntercept() - y);
-            if (discriminant < 0)
-            {
-                return Double.NaN;
-            }
-            double sqrtDiscriminant = Math.sqrt(discriminant);
-            return (-getSlope() + sqrtDiscriminant)/2/getQuadraticCoefficient();
-        }
-        return (y - getIntercept())/getSlope();
+        return regressionFit.getX(this, y);
+    }
+
+    public RegressionFit getRegressionFit() {
+        return regressionFit;
+    }
+
+    public void setRegressionFit(RegressionFit regressionFit) {
+        this.regressionFit = regressionFit;
     }
 
     public static CalibrationCurve forNoExternalStandards() {
-        CalibrationCurve calibrationCurve = new CalibrationCurve();
+        CalibrationCurve calibrationCurve = new CalibrationCurve(RegressionFit.NONE);
         calibrationCurve.setPointCount(0);
         calibrationCurve.setSlope(1.0);
         return calibrationCurve;

src/org/labkey/targetedms/calculations/quantification/CalibrationCurveDataSet.java

@@ -15,6 +15,7 @@
 package org.labkey.targetedms.calculations.quantification;
 
 import org.apache.commons.math3.fitting.WeightedObservedPoint;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -100,6 +101,7 @@ public TransitionKeys getFeaturesToQuantifyOn(String label) {
         return transitionKeys;
     }
 
+    @Nullable
     public Double getCalculatedConcentration(String label, CalibrationCurve calibrationCurve, Replicate replicate) {
         if (calibrationCurve == null) {
             return null;
@@ -108,7 +110,11 @@ public Double getCalculatedConcentration(String label, CalibrationCurve calibrat
         if (y == null) {
             return null;
         }
-        return calibrationCurve.getX(y) * replicate.getSampleDilutionFactor();
+        Double x = calibrationCurve.getX(y);
+        if (x == null) {
+            return null;
+        }
+        return x * replicate.getSampleDilutionFactor();
     }
 
     /**