fix for 2nd round which includes the bad qualtiy compounds

Author: marcus-ludwig

gibbs_sampling/src/main/java/de/unijena/bioinf/GibbsSampling/model/scorer/CommonFragmentAndLossScorer.java

@@ -36,7 +36,9 @@ private void prepare(FragmentsCandidate[][] candidates, double minimum_number_ma
         System.out.println("prepare.");
 
 
-        if (normalizationMap==null & (used_minimum_number_matched_peaks_losses != minimum_number_matched_peaks_losses)){
+        if (normalizationMap==null || (used_minimum_number_matched_peaks_losses != minimum_number_matched_peaks_losses)
+                || !containsAllCompounds(normalizationMap, Arrays.stream(candidates).map(c->c[0].getExperiment()).toArray(s->new Ms2Experiment[s]))){
+            //something changed, so recompute all.
             long start = System.currentTimeMillis();
             used_minimum_number_matched_peaks_losses = minimum_number_matched_peaks_losses;
             norm = this.normalization(candidates, minimum_number_matched_peaks_losses);
@@ -102,9 +104,12 @@ private void prepare(FragmentsCandidate[][] candidates, double minimum_number_ma
         if (GibbsMFCorrectionNetwork.DEBUG) System.out.println("compounds: " + this.maybeSimilar.length + " | maybeSimilar: " + sum + " | threshold was "+threshold);
     }
 
-//    private void prepareData(){
-//
-//    }
+    private boolean containsAllCompounds(TObjectDoubleHashMap<Ms2Experiment> normalizationMap, Ms2Experiment[] ms2Experiments) {
+        for (Ms2Experiment ms2Experiment : ms2Experiments) {
+            if (!normalizationMap.containsKey(ms2Experiment)) return false;
+        }
+        return true;
+    }