From 33250766b0b18608f756403554291bdb399c3b03 Mon Sep 17 00:00:00 2001
From: Fengchao <fyuab@connect.ust.hk>
Date: Wed, 4 Oct 2017 15:27:19 +0800
Subject: [PATCH] Increase PTM mass decimal point to three.

---
 src/main/java/proteomics/Index/BuildIndex.java | 4 ++--
 src/main/java/proteomics/Search/Search.java    | 4 ++--
 src/main/java/proteomics/Types/AA.java         | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/java/proteomics/Index/BuildIndex.java b/src/main/java/proteomics/Index/BuildIndex.java
index 075c151..fc23239 100644
--- a/src/main/java/proteomics/Index/BuildIndex.java
+++ b/src/main/java/proteomics/Index/BuildIndex.java
@@ -326,7 +326,7 @@ private Set<VarSequence> generateModSeq(String seq, Set<Short> modFreeListSites,
                     for (int i = 0; i < seq.length(); ++i) {
                         sb.append(seq.substring(i, i + 1));
                         if (idxBinaryModMassMap.containsKey(i)) {
-                            sb.append(String.format(Locale.US, "[%.2f]", idxBinaryModMassMap.get(i).get(0)));
+                            sb.append(String.format(Locale.US, "[%.3f]", idxBinaryModMassMap.get(i).get(0)));
                         }
                     }
                     varSeqSet.add(new VarSequence(sb.toString(), linkSite, binaryModParam.hashCode()));
@@ -445,7 +445,7 @@ private Set<VarSequence> generateModSeqSub(String seq, int[] idxCombination, Map
             for (int i = 0; i < seq.length(); ++i) {
                 sb.append(seq.charAt(i));
                 if (localIdxModMassMap.containsKey(i)) {
-                    sb.append(String.format(Locale.US, "[%.2f]", localIdxModMassMap.get(i)));
+                    sb.append(String.format(Locale.US, "[%.3f]", localIdxModMassMap.get(i)));
                 }
             }
             outputSet.add(new VarSequence(sb.toString(), linkSite, binaryModType));
diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java
index cf95164..769a49f 100644
--- a/src/main/java/proteomics/Search/Search.java
+++ b/src/main/java/proteomics/Search/Search.java
@@ -375,10 +375,10 @@ private String addFixMod(String seq, int linkSite) {
             if (i == linkSite) { // priority order: linkSite > fixMod > varMod
                 sb.append(aa.aa);
             } else if (Math.abs(fix_mod_map.get(aa.aa)) > 1e-6) {
-                sb.append(String.format(Locale.US, "%c[%.2f]", aa.aa, fix_mod_map.get(aa.aa)));
+                sb.append(String.format(Locale.US, "%c[%.3f]", aa.aa, fix_mod_map.get(aa.aa)));
             } else {
                 if (Math.abs(aa.delta_mass) > 1e-6) {
-                    sb.append(String.format(Locale.US, "%c[%.2f]", aa.aa, aa.delta_mass));
+                    sb.append(String.format(Locale.US, "%c[%.3f]", aa.aa, aa.delta_mass));
                 } else {
                     sb.append(aa.aa);
                 }
diff --git a/src/main/java/proteomics/Types/AA.java b/src/main/java/proteomics/Types/AA.java
index f19a1a2..a7aea84 100644
--- a/src/main/java/proteomics/Types/AA.java
+++ b/src/main/java/proteomics/Types/AA.java
@@ -13,7 +13,7 @@ public AA(char aa, float delta_mass) {
         this.aa = aa;
         this.delta_mass = delta_mass;
         if (Math.abs(delta_mass) > 1e-6) {
-            toString = String.format(Locale.US, "%c[%.2f]", aa, delta_mass);
+            toString = String.format(Locale.US, "%c[%.3f]", aa, delta_mass);
         } else {
             toString = String.valueOf(aa);
         }