Add output file for prior probabilities

src/edu/umich/andykong/ptmshepherd/iterativelocalization/BinPriorProbabilities.java

@@ -27,7 +27,6 @@ public class BinPriorProbabilities {
     int nPsms;
     double priorVectorNorm;
     boolean isConverged;
-    int epoch;
     final double INITVAL = 1.0 / 62.0;
     final char[] AAs = {'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L',
             'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'};
@@ -55,7 +54,6 @@ public BinPriorProbabilities() {
         this.nT1 = 0.0;
         this.cT1 = 0.0;
 
-        this.epoch = 0;
         this.priorVectorNorm = 0.0;
         this.isConverged = false;
 
@@ -71,11 +69,11 @@ public double[] computePriorProbs(String pep, boolean[] allowedPoses) {
             char cAA = pep.charAt(i);
             if (allowedPoses[i] == true) {
                 if (i == 0) { // Pick max probability for N-terminal options
-                    double curProb = Math.max(this.n, Math.max(this.nProbs[cAA-'A'], this.probs[cAA-'A']));
+                    double curProb = (this.n + this.nProbs[cAA-'A'] + this.probs[cAA-'A']) / 3.0;
                     priorProbs[i] = curProb;
                     sumProbs += curProb;
                 } else if (i == pep.length()-1) { // Pick max probability for C-terminal options
-                    double curProb = Math.max(this.c, Math.max(this.cProbs[cAA-'A'], this.probs[cAA-'A']));
+                    double curProb = (this.c + this.cProbs[cAA-'A'] + this.probs[cAA-'A']) / 3.0;
                     priorProbs[i] = curProb;
                     sumProbs += curProb;
                 } else {
@@ -216,6 +214,30 @@ public boolean getIsConverged() {
         return this.isConverged;
     }
 
+    static public String fileHeaderToString() {
+        return new String("mass_shift\tepoch\tlocation\tvalue\n");
+    }
+
+    public String fileLinesToString(float dMass, int epoch) {
+        StringBuffer sb = new StringBuffer();
+
+        sb.append(String.format("%f\t%d\t%s\t%.4f\n", dMass, epoch, "n", this.n));
+        sb.append(String.format("%f\t%d\t%s\t%.4f\n", dMass, epoch, "c", this.c));
+
+        for (Character c : this.AAs) {
+            sb.append(String.format("%f\t%d\tn%c\t%.4f\n", dMass, epoch, c, this.nProbs[c-'A']));
+        }
+
+        for (Character c : this.AAs) {
+            sb.append(String.format("%f\t%d\tc%c\t%.4f\n", dMass, epoch, c, this.cProbs[c-'A']));
+        }
+
+        for (Character c : this.AAs) {
+            sb.append(String.format("%f\t%d\t%c\t%.4f\n", dMass, epoch, c, this.probs[c-'A']));
+        }
+
+        return sb.toString();
+    }
 
     public String toString() {
         StringBuffer sb = new StringBuffer("\nprobs\t");

src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java

@@ -1,6 +1,7 @@
 package edu.umich.andykong.ptmshepherd.iterativelocalization;
 
 import edu.umich.andykong.ptmshepherd.PSMFile;
+import edu.umich.andykong.ptmshepherd.PTMShepherd;
 import edu.umich.andykong.ptmshepherd.core.AAMasses;
 import edu.umich.andykong.ptmshepherd.core.FastLocator;
 import edu.umich.andykong.ptmshepherd.core.MXMLReader;
@@ -9,6 +10,9 @@
 import org.jetbrains.annotations.NotNull;
 
 import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
 import java.lang.reflect.Array;
 import java.text.DecimalFormat;
 import java.util.*;
@@ -211,7 +215,6 @@ private void fitMatchedIonDistribution() throws Exception {
             this.matchedIonDist.calculateLdaWeights();
             this.matchedIonDist.calculateIonPosterior();
             this.matchedIonDist.calculateNegativePredictiveValue();
-            System.out.println(this.matchedIonDist.negPredictiveValue); //XXXQQQ
         }
         if (this.printIonDistribution) {
             //this.matchedIonDist.printIntensityHisto("matched_ion_intensity_distribution.tsv");
@@ -227,6 +230,9 @@ private void fitMatchedIonDistribution() throws Exception {
     private void calculateLocalizationProbabilities() throws Exception {
         System.out.println("\tCalculating PSM-level localization probabilities");
 
+        // Set up bin-wise prior probability string to be updated every epoch
+        StringBuffer priorString = new StringBuffer(BinPriorProbabilities.fileHeaderToString());
+
         // Set up missing spectra error handling
         ArrayList<String> linesWithoutSpectra = new ArrayList<>(); //TODO
 
@@ -450,8 +456,20 @@ private void calculateLocalizationProbabilities() throws Exception {
             if (finalPass)
                 System.out.println("\tUpdating PSM tables with localization information");
 
+            // Update output for prior probabilities
+            for (int i = 0; i < this.peaks[0].length; i++) {
+                if (i == this.zeroBin)
+                    continue;
+                float dMassApex = (float) this.peaks[0][i];
+                priorString.append(this.priorProbs[i].fileLinesToString(dMassApex, epoch));
+            }
+
             epoch++;
         }
+
+        // Output prior probabilities
+        writePriorProbabilitiesOutput("prior_probabilities.tsv", priorString.toString());
+
     }
 
     //todo mods should be parsed here if we don't want to localize on top of var mods
@@ -1430,4 +1448,15 @@ private double safeDivide(int x, int y) {
         else
             return (double) x / (double) y;
     }
+
+    private void writePriorProbabilitiesOutput(String fname, String content) throws IOException {
+        try {
+            PrintWriter out = new PrintWriter(new FileWriter(PTMShepherd.normFName(fname)));
+            out.write(content);
+            out.close();
+        } catch (Exception e) {
+            e.printStackTrace();
+            System.exit(1);
+        }
+    }
 }