Fix a bug triggered by empty spectrum.

fcyu · Feb 5, 2018 · a3262e0 · a3262e0
1 parent b07b34c
commit a3262e0
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Showing 3 changed files with 13 additions and 0 deletions.
diff --git a/src/main/java/proteomics/Search/SearchWrap.java b/src/main/java/proteomics/Search/SearchWrap.java
@@ -60,6 +60,11 @@ public Entry call() throws IOException, JMzReaderException, SQLException {
         }
 
         SparseVector xcorrPL = preSpectrumObj.preSpectrum(rawPLMap, precursorMass, scanId);
+
+        if (xcorrPL == null) {
+            return null;
+        }
+
         if (ECL2.debug) {
             BufferedWriter writer = new BufferedWriter(new FileWriter(scanId + ".xcorr.spectrum.csv"));
             writer.write("bin_idx,intensity\n");

diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java
@@ -79,6 +79,10 @@ public PreSpectra(JMzReader spectra_parser, double ms1Tolerance, double leftInve
 
             Map<Double, Double> raw_mz_intensity_map = spectrum.getPeakList();
 
+            if (raw_mz_intensity_map.size() < 5) {
+                continue;
+            }
+
             if (ECL2.debug) {
                 BufferedWriter writer = new BufferedWriter(new FileWriter(Integer.valueOf(spectrum.getId()) + ".raw.spectrum.csv"));
                 writer.write("mz,intensity\n");

diff --git a/src/main/java/proteomics/Spectrum/PreSpectrum.java b/src/main/java/proteomics/Spectrum/PreSpectrum.java
@@ -30,6 +30,10 @@ public SparseVector preSpectrum (Map<Double, Double> peaks_map, double precursor
             }
         }
 
+        if (sqrt_pl_map.isEmpty()) {
+            return null;
+        }
+
         // digitize the spectrum
         double[] pl_array = digitizeSpec(sqrt_pl_map);