Update mzml and mzidentml reading dependencies to get their performance improvements

On a test file the conversion from mzid to tsv was 4x faster
Also bump the version

Author: FarmGeek4Life

doc/Changelog.html

@@ -13,6 +13,13 @@ <h1 class="pagetitle">MS-GF+ ChangeLog</h1>
         <a href="index.html">MS-GF+ Documentation home</a>
     </p>
 
+    <p>
+        <b>07/21/2017 v2017.07.21</b>
+    </p>
+    <ul>
+        <li>Performance improvements when reading mzML and mzIdentML files</li>
+    </ul>
+
     <p>
         <b>05/18/2017 v2017.05.18</b>
     </p>

pom.xml

@@ -168,63 +168,16 @@
     </build>
     <dependencies>
         <dependency>
-            <groupId>uk.ac.ebi.pride.tools</groupId>
-            <artifactId>jmzreader</artifactId>
-            <version>1.2.4</version>
-            <type>jar</type>
-        </dependency>
-        <dependency>
-            <groupId>uk.ac.ebi.pride.tools</groupId>
-            <artifactId>pkl-parser</artifactId>
-            <version>1.2.5</version>
-            <type>jar</type>
-        </dependency>
-        <dependency>
-            <groupId>uk.ac.ebi.pride.tools</groupId>
-            <artifactId>dta-parser</artifactId>
-            <version>1.2.5</version>
-            <type>jar</type>
-        </dependency>
-        <dependency>
-            <groupId>uk.ac.ebi.pride.tools</groupId>
-            <artifactId>ms2-parser</artifactId>
-            <version>1.2.6</version>
-            <type>jar</type>
-        </dependency>
-        <dependency>
-            <groupId>uk.ac.ebi.pride.tools</groupId>
-            <artifactId>mgf-parser</artifactId>
-            <version>1.3.8</version>
-            <type>jar</type>
-        </dependency>
-        <dependency>
-            <groupId>uk.ac.ebi.pride.tools</groupId>
-            <artifactId>mzdata-parser</artifactId>
-            <version>1.2.5</version>
-            <type>jar</type>
-        </dependency>
-        <dependency>
-            <groupId>uk.ac.ebi.pride.tools</groupId>
-            <artifactId>mzml-wrapper</artifactId>
-            <version>1.3.2</version>
-            <type>jar</type>
+            <groupId>uk.ac.ebi.jmzidml</groupId>
+            <artifactId>jmzidentml</artifactId>
+            <version>1.2.7</version>
         </dependency>
         <dependency>
             <groupId>uk.ac.ebi.pride.tools</groupId>
-            <artifactId>pride-wrapper</artifactId>
-            <version>1.2.5</version>
+            <artifactId>jmzreader</artifactId>
+            <version>2.0.1</version>
             <type>jar</type>
         </dependency>
-        <dependency>
-            <groupId>uk.ac.ebi.pride.tools</groupId>
-            <artifactId>mzxml-parser</artifactId>
-            <version>1.3.8</version>
-        </dependency>
-        <dependency>
-            <groupId>uk.ac.ebi.jmzidml</groupId>
-            <artifactId>jmzidentml</artifactId>
-            <version>1.2.4</version>
-        </dependency>
         <dependency>
             <groupId>org.systemsbiology.jrap</groupId>
             <artifactId>stax</artifactId>

src/main/java/edu/ucsd/msjava/mzml/MzMLAdapter.java

@@ -1,18 +1,17 @@
 package edu.ucsd.msjava.mzml;
 
+import org.slf4j.LoggerFactory;
+import ch.qos.logback.classic.Logger;
+import ch.qos.logback.classic.LoggerContext;
+
 import edu.ucsd.msjava.mzid.Constants;
-import org.apache.log4j.Level;
-import org.apache.log4j.LogManager;
-import org.apache.log4j.Logger;
 import uk.ac.ebi.jmzidml.model.mzidml.CvParam;
 import uk.ac.ebi.jmzml.model.mzml.CVParam;
 import uk.ac.ebi.jmzml.model.mzml.SourceFile;
 import uk.ac.ebi.jmzml.xml.io.MzMLObjectIterator;
 import uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller;
 
 import java.io.File;
-import java.util.Collections;
-import java.util.List;
 
 public class MzMLAdapter {
 
@@ -86,11 +85,10 @@ public CvParam getSpectrumIDFormatCvParam() {
     public static void turnOffLogs() {
         if (!logOff) {
             @SuppressWarnings("unchecked")
-            List<Logger> loggers = Collections.<Logger>list(LogManager.getCurrentLoggers());
-            loggers.add(LogManager.getRootLogger());
-            for (Logger logger : loggers) {
-                logger.setLevel(Level.OFF);
-            }
+            LoggerContext context = (LoggerContext) LoggerFactory.getILoggerFactory();
+            context.reset();
+            Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME);
+            rootLogger.detachAndStopAllAppenders();
         }
     }
 

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

@@ -21,8 +21,8 @@
 
 
 public class MSGFPlus {
-    public static final String VERSION = "Release (v2017.05.18)";
-    public static final String RELEASE_DATE = "18 May 2017";
+    public static final String VERSION = "Release (v2017.07.21)";
+    public static final String RELEASE_DATE = "21 July 2017";
 
     public static final String DECOY_DB_EXTENSION = ".revCat.fasta";
     public static final String DECOY_PROTEIN_PREFIX = "XXX";