Remove an error in the mzIdentML output when no mods are used, and add Java 9 compatibility via 2 additional dependencies

Java 9 compatibility does cause a warning message when running on Java 9, but does not change behavior with previous versions of Java (tested with Java 8)

Author: FarmGeek4Life

doc/Changelog.html

@@ -13,6 +13,15 @@ <h1 class="pagetitle">MS-GF+ ChangeLog</h1>
         <a href="index.html">MS-GF+ Documentation home</a>
     </p>
 
+    <p>
+        <b>01/30/2018 v2018.01.30</b>
+    </p>
+    <ul>
+        <li>MzIdentML creation: Don't output an empty ModificationParams element when there are no modifications (because not including it complies with the XML Schema, while including it with no child nodes does not)</li>
+        <li>Java 9 compatibility: add dependencies on com.sun.xml.bind:jaxb-impl and jaxb:activation to support use with Java 9 (with some warnings). Without this change, users must supply the Java VM argument "--add-modules=java.xml.bind,java.activation"</li>
+        <li>Fix a type in the usage output of ComputeFDR (thanks to GitHub user Jong-hun-Park)</li>
+    </ul>
+
     <p>
         <b>08/23/2017 v2017.08.23</b>
     </p>

pom.xml

@@ -190,6 +190,16 @@
             <scope>test</scope>
             <type>jar</type>
         </dependency>
+        <dependency>
+            <groupId>com.sun.xml.bind</groupId>
+            <artifactId>jaxb-impl</artifactId>
+            <version>2.2.7</version>
+        </dependency>
+        <dependency>
+            <groupId>jaxb</groupId>
+            <artifactId>activation</artifactId>
+            <version>1.0.2</version>
+        </dependency>
     </dependencies>
 
     <repositories>

src/main/java/edu/ucsd/msjava/mzid/AnalysisProtocolCollectionGen.java

@@ -24,6 +24,8 @@ public AnalysisProtocolCollectionGen(SearchParams params, AminoAcidSet aaSet) {
         this.params = params;
         this.aaSet = aaSet;
         analysisProtocolCollection = new AnalysisProtocolCollection();
+        modMap = new HashMap<edu.ucsd.msjava.msutil.Modification, uk.ac.ebi.jmzidml.model.mzidml.SearchModification>();
+        fixedModMap = new HashMap<String, List<edu.ucsd.msjava.msutil.Modification>>();
         generateSpectrumIdentificationProtocol();
     }
 
@@ -108,8 +110,10 @@ private void generateSpectrumIdentificationProtocol() {
         userParamList.add(Constants.makeUserParam("ChargeCarrierMass", String.valueOf(params.getChargeCarrierMass())));
         spectrumIdentificationProtocol.setAdditionalSearchParams(additionalSearchParams);
 
-        ModificationParams modParams = getModificationParam();
-        spectrumIdentificationProtocol.setModificationParams(modParams);
+        if (!aaSet.getModifications().isEmpty()) {
+            ModificationParams modParams = getModificationParam();
+            spectrumIdentificationProtocol.setModificationParams(modParams);
+        }
 
 //        enzymes.setIndependent(false);
 //        if(enzyme == null || enzyme == edu.ucsd.msjava.msutil.Enzyme.NOENZYME)
@@ -188,9 +192,6 @@ private void generateSpectrumIdentificationProtocol() {
     }
 
     public ModificationParams getModificationParam() {
-        modMap = new HashMap<edu.ucsd.msjava.msutil.Modification, uk.ac.ebi.jmzidml.model.mzidml.SearchModification>();
-        fixedModMap = new HashMap<String, List<edu.ucsd.msjava.msutil.Modification>>();
-
         ModificationParams modParams = new ModificationParams();
         List<SearchModification> searchModList = modParams.getSearchModification();
 

src/main/java/edu/ucsd/msjava/ui/MSGFPlus.java

@@ -21,8 +21,8 @@
 
 
 public class MSGFPlus {
-    public static final String VERSION = "Release (v2017.08.23)";
-    public static final String RELEASE_DATE = "23 August 2017";
+    public static final String VERSION = "Release (v2018.01.30)";
+    public static final String RELEASE_DATE = "30 January 2018";
 
     public static final String DECOY_DB_EXTENSION = ".revCat.fasta";
     public static final String DECOY_PROTEIN_PREFIX = "XXX";