* Made export to Unipept fully functional

* Added commons codecs v1.12 mvn dependency to pom.xml
* Updated to MPA version 1.9.1

pom.xml

@@ -349,5 +349,10 @@
             <artifactId>org-openide-util-lookup</artifactId>
             <version>RELEASE110</version>
         </dependency>
+        <dependency>
+            <groupId>commons-codec</groupId>
+            <artifactId>commons-codec</artifactId>
+            <version>1.12</version>
+        </dependency>
     </dependencies>
 </project>

src/de/mpa/analysis/UnipeptAnalyzer.java

@@ -19,7 +19,6 @@ public class UnipeptAnalyzer {
     public UnipeptAnalyzer(List<PeptideHit> peptideHits) {
         for (PeptideHit peptideHit : peptideHits) {
             peptideSequences.add(peptideHit.getSequence());
-            System.out.println(peptideHit.getSequence());
         }
         analyzeInUnipept(peptideSequences);
     }

src/de/mpa/client/Constants.java

@@ -51,12 +51,12 @@ public class Constants {
 	/**
 	 * The application version number.
 	 */
-	public final static String VER_NUMBER = "1.9.0";
+	public final static String VER_NUMBER = "1.9.1";
 
 	/**
 	 * The application version date.
 	 */
-	public final static String VER_DATE = "06/2019";
+	public final static String VER_DATE = "07/2019";
 
 	/**
 	 * The client frame minimum width in pixels.

src/de/mpa/client/model/FileExperiment.java

@@ -287,20 +287,22 @@ public DbSearchResult getSearchResult() {
 					File file = new File(filePath);
 					String pathname = file.getAbsolutePath();
 					// Check if reader already has the current experiment selected.
-					if (GenericContainer.MGFReaders.get(pathname) == null || !file.getName().equals(GenericContainer.MGFReaders.get(pathname).getFilename())) {
-						client.firePropertyChange("new message", null, "INDEXING SPECTRA");
-						try {
-							client.firePropertyChange("resetcur", -1L, file.length());
-							MascotGenericFileReader mgfReader = new MascotGenericFileReader(new File(pathname));
-
-							GenericContainer.SpectrumPosMap.put(pathname, mgfReader.getSpectrumPositions(false));
-							client.firePropertyChange("indeterminate", true, false);
-							client.firePropertyChange("new message", null, "INDEXING SPECTRA FINISHED");
-							mgfReader.setSpectrumPositions(GenericContainer.SpectrumPosMap.get(pathname));
-							GenericContainer.MGFReaders.put(pathname, mgfReader);
-						} catch (IOException e) {
-							e.printStackTrace();
-							Client.getInstance().firePropertyChange("new message", null, "INDEXING SPECTRA FAILED");
+					if (false) {
+						if (GenericContainer.MGFReaders.get(pathname) == null || !file.getName().equals(GenericContainer.MGFReaders.get(pathname).getFilename())) {
+							client.firePropertyChange("new message", null, "INDEXING SPECTRA");
+							try {
+								client.firePropertyChange("resetcur", -1L, file.length());
+								MascotGenericFileReader mgfReader = new MascotGenericFileReader(new File(pathname));
+
+								GenericContainer.SpectrumPosMap.put(pathname, mgfReader.getSpectrumPositions(false));
+								client.firePropertyChange("indeterminate", true, false);
+								client.firePropertyChange("new message", null, "INDEXING SPECTRA FINISHED");
+								mgfReader.setSpectrumPositions(GenericContainer.SpectrumPosMap.get(pathname));
+								GenericContainer.MGFReaders.put(pathname, mgfReader);
+							} catch (IOException e) {
+								e.printStackTrace();
+								Client.getInstance().firePropertyChange("new message", null, "INDEXING SPECTRA FAILED");
+							}
 						}
 					}
 				}

src/de/mpa/client/model/dbsearch/DbSearchResult.java

@@ -227,6 +227,18 @@ public PeptideHit getPeptideHit(String sequence) {
 		}
 		return null;
 	}
+
+    /**
+     * Returns a list of all peptides found in the results (including duplicate entries).
+     * @return list of all peptides found in the results
+     */
+	public List<PeptideHit> getAllPeptideHits() {
+		List<PeptideHit> peptideList = new ArrayList<PeptideHit>();
+		for (ProteinHit proteinHit : this.getProteinHits().values()) {
+			peptideList.addAll(proteinHit.getPeptideHitList());
+		}
+		return peptideList;
+	}
 
 	/**
 	 * Returns the spectrum match for a particular search spectrum ID.
@@ -316,15 +328,6 @@ public int getDistinctPeptideCount() {
 		return this.getMetaProteins().getPeptideSet().size();
 	}
 
-	/**
-	 * @return peptidelist
-	 */
-	public List<PeptideHit> getPeptideList() {
-		return new ArrayList<PeptideHit>(this.getMetaProteins().getPeptideSet());
-		//System.out.println(this.getMetaProteins().getPeptideList().toString());
-		//return this.visMetaProteins.getPeptideList();
-	}
-
 	/**
 	 * Returns the number of peptides with PTMs.
 	 * @return the number of modified peptides

src/de/mpa/client/model/dbsearch/ProteinHitList.java

@@ -35,11 +35,6 @@ public class ProteinHitList extends ArrayList<ProteinHit> implements Serializabl
 	 * The set of spectrum matches with distinct search spectrum IDs.
 	 */
 	private Set<SpectrumMatch> matchSet;
-
-    /**
-     * The global list of peptides found within the search result.
-     */
-	private List<PeptideHit> peptideList;
 
 	/**
 	 * Flag to indicate whether the cached sets need to be regenerated.
@@ -143,19 +138,6 @@ public Set<PeptideHit> getPeptideSet() {
 		return peptideSet;
 	}
 
-	/**
-	 * Utility method to return a list of peptide hits with all sequence
-	 * strings - including duplicated peptides
-	 * @return the peptide hit list
-	 */
-	public List<PeptideHit> getPeptideList() {
-		if (this.hasChanged) {
-			regenerateSets();
-		}
-
-		return peptideList;
-	}
-
 	/**
 	 * Utility method to return a set of spectrum matches with distinct search
 	 * spectrum IDs.
@@ -174,7 +156,6 @@ public Set<SpectrumMatch> getMatchSet() {
 	private void regenerateSets() {
 		proteinSet = new TreeSet<ProteinHit>();
 		peptideSet = new TreeSet<PeptideHit>();
-		peptideList = new ArrayList<PeptideHit>();
 		matchSet = new TreeSet<SpectrumMatch>();
 		if (!this.isEmpty()) {
 			// check whether this list contains meta-proteins or proteins
@@ -184,27 +165,17 @@ private void regenerateSets() {
 					MetaProteinHit metaProteinHit = (MetaProteinHit) proteinHit;
 					proteinSet.addAll(metaProteinHit.getProteinSet());
 					peptideSet.addAll(metaProteinHit.getPeptideSet());
-					peptideList.addAll(metaProteinHit.getPeptideHitList());
 					matchSet.addAll(metaProteinHit.getMatchSet());
-					// TODO: please also check whether we need this for unipept at all?
-                    // Case check what happens once the user hits the "Process results" button for the meta-protein generation: is the peptide list still the same or do need to have an update here?
-
 				}
 			} else {
 				// this list contains protein hits
 				for (ProteinHit proteinHit : this) {
 					List<PeptideHit> peptideHitList = proteinHit.getPeptideHitList();
 					for (PeptideHit peptideHit : peptideHitList) {
 						matchSet.addAll(peptideHit.getSpectrumMatches());
-						//peptideList.add(peptideHit);
 					}
 					peptideSet.addAll(peptideHitList);
-					System.out.println(peptideSet.size());
-
-					peptideList.addAll(peptideHitList);
-					System.out.println(peptideList.size());
 					proteinSet.add(proteinHit);
-
 				}
 			}
 		}

src/de/mpa/client/ui/ClientFrameMenuBar.java

@@ -488,7 +488,7 @@ private void exportCSV() {
     private void exportUnipept() {
     	Client client = Client.getInstance();
 
-    	UnipeptAnalyzer unipeptAnalyzer = new UnipeptAnalyzer(client.getDatabaseSearchResult().getPeptideList());
+    	UnipeptAnalyzer unipeptAnalyzer = new UnipeptAnalyzer(client.getDatabaseSearchResult().getAllPeptideHits());
     	URI unipeptURI = unipeptAnalyzer.getUnipeptURI();
 
 		try {