From a4ef245c9578630df3d6a37d1af5da761cda0d69 Mon Sep 17 00:00:00 2001 From: Fengchao Date: Sun, 21 May 2017 20:07:53 +0800 Subject: [PATCH] Add flanking peak. --- src/main/java/proteomics/ECL2.java | 1 + src/main/java/proteomics/Spectrum/PreSpectrum.java | 8 ++++++++ 2 files changed, 9 insertions(+) diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java index 96478dd..2ab7e61 100644 --- a/src/main/java/proteomics/ECL2.java +++ b/src/main/java/proteomics/ECL2.java @@ -24,6 +24,7 @@ public class ECL2 { public static final double delta_c_t = 0; public static final int score_point_t = 15000; public static final int random_score_point_t = 2; + public static final boolean flankingPeaks = true; private static final Logger logger = LoggerFactory.getLogger(ECL2.class); private static final String version = "2.1.3"; diff --git a/src/main/java/proteomics/Spectrum/PreSpectrum.java b/src/main/java/proteomics/Spectrum/PreSpectrum.java index 4af5f4a..b7a4821 100644 --- a/src/main/java/proteomics/Spectrum/PreSpectrum.java +++ b/src/main/java/proteomics/Spectrum/PreSpectrum.java @@ -76,6 +76,14 @@ private SparseVector prepareXcorr(double[] pl_array) { for (int i = 1; i < pl_array.length; ++i) { double temp = pl_array[i] - tempArray[i]; + + if (ECL2.flankingPeaks) { + temp += (pl_array[i - 1] - tempArray[i - 1]) * 0.5; + if (i + 1 < pl_array.length) { + temp += (pl_array[i + 1] - tempArray[i + 1]) * 0.5; + } + } + if (Math.abs(temp) > 1e-6) { xcorr_pl.put(i, (float) temp); }