2.3.8

Changelog.md

@@ -1,4 +1,14 @@
 
+2.3.8
+
+* Write out crosslinker stub information to mzIdentML
+* updated to XLMOD java library 1.1 to reduce "unknown modifications"
+* BugFix: mzIdentML 1.3 empty protein descriptions no longer written out
+* BugFix: mzIdentML 1.3 export still had some mzIdentML 1.2 namespace attributes
+   * currently using a modified version of jmzIdentML (pull request pending)
+   * allow matching to crosslinker without mass definition (e.g. DSSO)
+* BugFix: mzIdentML export for non-covalent peptide pairs
+
 2.3.7
 
 * BugFix: xiview csv file can miss data

pom.xml

@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.rappsilberlab</groupId>
     <artifactId>xiFDR</artifactId>
-    <version>2.3.7</version>
+    <version>2.3.8</version>
     <packaging>jar</packaging>
     <dependencies>
         <dependency>
@@ -25,11 +25,6 @@
             <scope>runtime</scope>
             <type>jar</type>
         </dependency-->
-        <dependency>
-            <groupId>org.rappsilber</groupId>
-            <artifactId>XLMOD</artifactId>
-            <version>1.0</version>
-        </dependency>
         <dependency>
           <groupId>uk.ac.liv</groupId>
           <artifactId>mzidlib</artifactId>
@@ -104,16 +99,21 @@
             <artifactId>json-simple</artifactId>
             <version>1.1.1</version>
 	</dependency>
-        <dependency>
-          <groupId>uk.ac.ebi.jmzidml</groupId>
-          <artifactId>jmzidentml</artifactId>
-          <version>1.2.13</version>
-        </dependency>
         <dependency>
             <groupId>rappsilber</groupId>
             <artifactId>xiSEARCH</artifactId>
             <version>1.8.7</version>
         </dependency>
+        <dependency>
+            <groupId>uk.ac.ebi.jmzidml</groupId>
+            <artifactId>jmzidentml</artifactId>
+            <version>1.2.13-lf</version>
+        </dependency>
+        <dependency>
+            <groupId>org.rappsilber</groupId>
+            <artifactId>XLMOD</artifactId>
+            <version>1.1</version>
+        </dependency>
     </dependencies>
     <build>
 	<plugins>
@@ -170,5 +170,5 @@
         <maven.compiler.target>1.7</maven.compiler.target>
     </properties>
     <description>Application for FDR estimation cross-linking massspectrometry data </description>
-    <name>xiFDR-2.3.7</name>
+    <name>xiFDR-2.3.8</name>
 </project>

src/main/java/org/rappsilber/config/LocalProperties.java

@@ -132,7 +132,7 @@ public static Object setFolder(String key, String path) {
      */
     public static synchronized Object setProperty(String key, String value)  {
         String old = localProperties.getProperty(key);
-        if ((old == null && value != null) || old.contentEquals(value)) {
+        if ((old == null && value != null) || (old != null && old.contentEquals(value))) {
             Object ret = localProperties.setProperty(key, value);
             try {
                 localProperties.store(new FileOutputStream(userPropertiesFile), "XLink local properties file");

src/main/java/org/rappsilber/fdr/MZIdentXLFDR.java

@@ -16,24 +16,23 @@
 package org.rappsilber.fdr;
 
 import org.rappsilber.fdr.result.FDRResult;
-import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.OutputStreamWriter;
 import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-import org.rappsilber.fdr.OfflineFDR;
 import org.rappsilber.fdr.entities.PSM;
 import org.rappsilber.fdr.entities.PeptidePair;
 import org.rappsilber.fdr.utils.StreamReplaceWriter;
 import uk.ac.ebi.jmzidml.MzIdentMLElement;
-import uk.ac.ebi.jmzidml.model.mzidml.AbstractParam;
 import uk.ac.ebi.jmzidml.model.mzidml.AnalysisCollection;
 import uk.ac.ebi.jmzidml.model.mzidml.AnalysisProtocolCollection;
 import uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware;
@@ -49,19 +48,17 @@
 import uk.ac.ebi.jmzidml.model.mzidml.Param;
 import uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidence;
 import uk.ac.ebi.jmzidml.model.mzidml.PeptideEvidenceRef;
-import uk.ac.ebi.jmzidml.model.mzidml.PeptideHypothesis;
-import uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup;
 import uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis;
 import uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionList;
 import uk.ac.ebi.jmzidml.model.mzidml.Provider;
 import uk.ac.ebi.jmzidml.model.mzidml.SequenceCollection;
 import uk.ac.ebi.jmzidml.model.mzidml.SpectraData;
 import uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem;
-import uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItemRef;
 import uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationList;
 import uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationResult;
 import uk.ac.ebi.jmzidml.model.mzidml.SubstitutionModification;
 import uk.ac.ebi.jmzidml.model.mzidml.UserParam;
+import uk.ac.ebi.jmzidml.model.utils.MzIdentMLVersion;
 import uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller;
 import uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller;
 
@@ -704,11 +701,11 @@ public void writeMZIdentML(String  mzidFileName, FDRResult result) {
             if (!outFile.endsWith(".mzid")) {
                 outFile = outFile + ".mzid";
             }
-            FileWriter fwriter = new FileWriter(outFile);
-            StreamReplaceWriter writer = new StreamReplaceWriter(fwriter, "xmlns=\"http://psidev.info/psi/pi/mzIdentML/1.1\"", "");
+            FileOutputStream fwriter = new FileOutputStream(outFile);
+            OutputStreamWriter writer = new OutputStreamWriter(fwriter, "UTF-8");
 
             MzIdentMLMarshaller marshaller;
-            marshaller = new MzIdentMLMarshaller();
+            marshaller = new MzIdentMLMarshaller(MzIdentMLVersion.Version_1_3);
 
             writer.write(marshaller.createXmlHeader() + "\n");
 

src/main/java/org/rappsilber/fdr/calculation/Boost.java

@@ -81,7 +81,7 @@ public MaximisingStatus maximiseInner(FDRSettings fdrSettings, OfflineFDR.FDRLev
 
         try {
             int steps = settings.getBoostingSteps();
-            StringBuffer sb = new StringBuffer();
+            StringBuilder sb = new StringBuilder();
             double maxDelta = 1;
             double maxPeptideCoverage = 1;
 

src/main/java/org/rappsilber/fdr/dataimport/Xi2Xi1Config.java

@@ -17,11 +17,8 @@
 
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileInputStream;
 import java.io.FileReader;
 import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -30,7 +27,6 @@
 import java.util.logging.Logger;
 import org.json.simple.parser.ParseException;
 import org.json.simple.parser.JSONParser;
-import org.rappsilber.utils.RArrayUtils;
 import org.rappsilber.utils.ms.Composition;
 import rappsilber.config.AbstractRunConfig;
 import rappsilber.config.ConfigurationParserException;
@@ -42,7 +38,6 @@
 import rappsilber.ms.sequence.AminoAcid;
 import rappsilber.ms.sequence.AminoModification;
 import rappsilber.ms.sequence.digest.AAConstrainedDigestion;
-import rappsilber.ms.sequence.ions.AIon;
 
 
 /**
@@ -51,8 +46,6 @@
  */
 public class Xi2Xi1Config extends AbstractRunConfig{
     HashMap<String, Double> default_xl_masses = new HashMap<>();
-    {
-    }
     HashMap<String, CrossLinker> default_xl_xi1 = new HashMap<>();
     HashMap<String, Xi2Crosslinker> default_xl_xi2 = new HashMap<>();
     public boolean isModX = true;
@@ -97,12 +90,19 @@ public class Xi2Xi1Config extends AbstractRunConfig{
     }
 
 
+    /**
+     * Java representation of the xiSEARCH2 crosslinker definition. 
+     * Only the here needed information are retained
+     */
     public class Xi2Crosslinker {
         public String name;
         public Double mass ;
         String[][] specificity = new String[2][];
 
-
+        /**
+         * initialise just with name and get the rest from default definitions.
+         * @param name Name of the crosslinker
+         */
         public Xi2Crosslinker(String name) {
             this.name = name;
             if (default_xl_masses.containsKey(name.toUpperCase())) {
@@ -112,17 +112,32 @@ public Xi2Crosslinker(String name) {
             }
         }
 
+        /**
+         * Initialise by name and mass.
+         * @param name Name of the crosslinker
+         * @param mass mass of the reacted crosslinker
+         */
         public Xi2Crosslinker(String name, double mass) {
             this.name = name;
             this.mass = mass;
         }
 
+        /**
+         * Initialise by name, mass, and specificity.
+         * @param name Name of the crosslinker
+         * @param mass mass of the reacted crosslinker
+         * @param specificity where can the crosslinker react
+         */
         public Xi2Crosslinker(String name, double mass, String[][] specificity) {
             this.name = name;
             this.mass = mass;
             this.specificity = specificity;
         }
 
+        /**
+         * initialise based on a json crosslinker defintion derived map
+         * @param m 
+         */
         public Xi2Crosslinker(Map m) {
             this.name = m.get("name").toString();
             this.mass = (Double) m.get("mass");
@@ -154,6 +169,12 @@ public Xi2Crosslinker(Map m) {
             }
         }
 
+        /**
+         * Convert to a xiSEARCH1 crosslinker definition.
+         * @return
+         * @throws java.text.ParseException
+         * @throws ConfigurationParserException 
+         */
         public String toXi1Crosslinker() throws java.text.ParseException, ConfigurationParserException {
             StringBuilder sb = new StringBuilder("crosslinker:AsymetricSingleAminoAcidRestrictedCrossLinker:NAME:");
             sb.append(this.name);

src/main/java/org/rappsilber/fdr/entities/Protein.java

@@ -16,12 +16,14 @@
 package org.rappsilber.fdr.entities;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import org.rappsilber.fdr.utils.FDRGroupNames;
 import org.rappsilber.utils.DoubleArrayList;
+import java.util.regex.*;
 
 /**
  * Represents a single protein. 
@@ -53,8 +55,7 @@ public class Protein extends AbstractFDRElement<Protein> {//implements Comparabl
     public static String DECOY_PREFIX = null;
     String zero = ""+(char)0;
     private Pattern zerosplit = Pattern.compile(zero);
-    private Pattern spacesplit = Pattern.compile(" ");
-
+    private Pattern spacesplit = Pattern.compile("^\\s*(\"[^\"]*\"|'[^']*'|\\([^)]*\\)|[^\\s]+)");
 
 
     private String fdrgroup = null;
@@ -132,7 +133,13 @@ public Protein(long id, String accession, String description, boolean isDecoy, b
                 this.name = zerosplit.split(description)[1];
                 this.description = zerosplit.split(description)[0];
             } else {
-                this.name = spacesplit.split(description)[0];
+                // try parsing a name from description
+                Matcher m = spacesplit.matcher(description);
+                if (m.find()) {
+                    this.name = m.group(1);
+                } else {
+                    this.name = this.description;
+                }
             }
         }