From a3262e0e16a13cd47d41815b586c9de33c50cd8f Mon Sep 17 00:00:00 2001
From: Fengchao <fyuab@connect.ust.hk>
Date: Mon, 5 Feb 2018 21:14:27 +0800
Subject: [PATCH] Fix a bug triggered by empty spectrum.

---
 src/main/java/proteomics/Search/SearchWrap.java    | 5 +++++
 src/main/java/proteomics/Spectrum/PreSpectra.java  | 4 ++++
 src/main/java/proteomics/Spectrum/PreSpectrum.java | 4 ++++
 3 files changed, 13 insertions(+)

diff --git a/src/main/java/proteomics/Search/SearchWrap.java b/src/main/java/proteomics/Search/SearchWrap.java
index b729105..6cc3ded 100644
--- 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
index ceb6c46..db8ca8d 100644
--- 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
index 6669ffe..ef09298 100644
--- 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);