Added release-jar to repository: "target/MPA.jar"

compomics · Feb 20, 2020 · aeb1afb · aeb1afb
1 parent 4a44153
commit aeb1afb
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Showing 7 changed files with 34 additions and 41 deletions.
diff --git a/config_LINUX.properties b/config_LINUX.properties
@@ -1,10 +1,10 @@
 #Mon Jun 19 16:24:59 CEST 2017
 
-default_qvalue_accepted=0.2
+default_qvalue_accepted=0.05
 
 app.qvality=qvality
 
-default_fdr=0.2
+default_fdr=0.05
 
 srvAddress=localhost
 blast.makeblastdb=software/blast_linux/bin/makeblastdb
@@ -18,13 +18,13 @@ path.xtandem=/software/xtandem_linux/bin/
 app.xtandem=tandem.exe
 path.xtandem.output=/data/output/xtandem/
 path.omssa.output=/data/output/omssa/
-dbUsername=kschallert
-app.port=9003
+dbUsername=mysql
+app.port=9000
 path.transfer=/data/transfer/
 path.blastdb=UP_SwissProt_Nov2016.fasta
 dbName=metaprot_MPAv2Paper
 xampp_path=
-dbPass=kschallert123
+dbPass=mysql
 apptitle=MetaProteomeAnalyzer
 fasta.formater.path=fastaformat.sh
 path.omssa=/software/omssa

diff --git a/src/de/mpa/client/ui/resultspanel/ComparePanel.java b/src/de/mpa/client/ui/resultspanel/ComparePanel.java
@@ -456,14 +456,9 @@ private void export2Csv() {
 								bw.append(SEP);
 							}
 							String someHeaderString = model.getColumnName(col);
-							System.out.println(someHeaderString);
 							if (someHeaderString.trim().equals("Description")) {
-								System.out.println("Detected");
-								System.out.println(ComparePanel.this.levelCompared);
-								System.out.println(ComparePanel.this.levelCounted);
 								if (ComparePanel.this.levelCompared == HierarchyLevel.META_PROTEIN_LEVEL 
 										&& ComparePanel.this.levelCounted == HierarchyLevel.SPECTRUM_LEVEL) {
-									System.out.println("Detect MP+Spec");
 									someHeaderString = "Metaprotein Number" 
 											+ "\t" + "Description"
 											+ "\t" + "Keywords"

diff --git a/src/de/mpa/client/ui/resultspanel/DbSearchResultPanel.java b/src/de/mpa/client/ui/resultspanel/DbSearchResultPanel.java
@@ -2132,7 +2132,6 @@ private void refreshProteinTables() {
 									if (nsaf < 0.0) {
 										// Calculate NSAF
 										nsaf = ProteinAnalysis.calculateLabelFree(new NormalizedSpectralAbundanceFactor(), Client.getInstance().getDatabaseSearchResult().getAllProteinHits(),	proteinHit);
-										System.out.println(nsaf);
 										proteinHit.setNSAF(nsaf);
 									}
 								} else {

diff --git a/src/de/mpa/io/ResultExporter.java b/src/de/mpa/io/ResultExporter.java
@@ -452,7 +452,7 @@ public static void exportMetaProteins(String filePath, DbSearchResult result, Li
 		// Filling the format with data
 		int metaProtCount = 0;
 		for (MetaProteinHit metaProtein : result.getAllMetaProteins()) {
-			System.out.println("Metaprotein : " + metaProtein.getAccession() + " Is Visible? " + metaProtein.isVisible() + " Is Selected? " + metaProtein.isSelected());
+			//System.out.println("Metaprotein : " + metaProtein.getAccession() + " Is Visible? " + metaProtein.isVisible() + " Is Selected? " + metaProtein.isSelected());
 			if (metaProtein.isVisible() && metaProtein.isSelected()) {
 				if (hasFeature[0])
 					writer.append(++metaProtCount + Constants.TSV_FILE_SEPARATOR);

diff --git a/src/de/mpa/model/analysis/UnipeptAnalyzer.java b/src/de/mpa/model/analysis/UnipeptAnalyzer.java
@@ -8,8 +8,9 @@
 import java.util.List;
 
 import de.mpa.model.dbsearch.PeptideHit;
-public class UnipeptAnalyzer {
 
+public class UnipeptAnalyzer {
+
     private List<String> peptideSequences = new ArrayList<String>();
 
     private URI unipeptURI;

diff --git a/src/de/mpa/model/dbsearch/DbSearchResult.java b/src/de/mpa/model/dbsearch/DbSearchResult.java
@@ -127,7 +127,7 @@ public void getSearchResultByView() throws SQLException {
 		// doing it in this order is important!!
 		taxonomyNodeMap.put(1L, TaxonomyUtils.createTaxonomyNode(1L, taxonomyMap, taxonomyNodeMap));
 		// TODO: test if this works properly
-//		taxonomyNodeMap.put(0L, TaxonomyUtils.createTaxonomyNode(0L, taxonomyMap, taxonomyNodeMap));
+		/// taxonomyNodeMap.put(0L, TaxonomyUtils.createTaxonomyNode(0L, taxonomyMap, taxonomyNodeMap));
 		// this is the "Uncategorized" Node, NCBI-ID=0, just use "root"
 		taxonomyNodeMap.put(0L, taxonomyNodeMap.get(1L));
 		// this is the "cellular organism" Node, NCBI-ID=131567, just use "root"
@@ -222,7 +222,7 @@ public void getSearchResultByView() throws SQLException {
 							pephit.addProteinHit(prot);
 							// TODO: DEBUG
 							prot.setSequence(prot_seq);
-//							prot.setSequence("");
+							// prot.setSequence("");
 							// DEBUG END
 							prot.setDescription(prot_description);
 							prot.addExperimentID(expID);
@@ -257,38 +257,36 @@ public void getSearchResultByView() throws SQLException {
 		// determine total spectral count
 		this.setTotalSpectrumCount(this.countTotalSpectraFromExperimentList(conn));
 		this.setFDR(Constants.getDefaultFDR());
-
 		//		// XXX: DEBUG OUTPUT POPULATING TABLES
-//				System.out.println("MP: " + this.metaProteins.size());
+		//				System.out.println("MP: " + this.metaProteins.size());
 		//		System.out.println("VMP: " + this.visMetaProteins.size());
-//				System.out.println("P: " + this.proteins.size());
+		//				System.out.println("P: " + this.proteins.size());
 		//		System.out.println("VP: " + this.visProteins.size());
-//				System.out.println("p: " + this.peptides.size());
+		//				System.out.println("p: " + this.peptides.size());
 		//		System.out.println("Vp: " + this.visPeptides.size());
-//				System.out.println("psm: " + this.searchHits.size());
+		//				System.out.println("psm: " + this.searchHits.size());
 		//		System.out.println("Vpsm: " + this.visSearchHits.size());
 		//		
-//				for (MetaProteinHit mp : this.getAllMetaProteins()) {
-//					
-//					System.out.println("MP : " + mp.getAccession());
-//					System.out.println("MP : " + mp.getDescription());
-//					System.out.println("MP : " + mp.getProteinHitList().size());
-//					for (ProteinHit ph : mp.getProteinHitList()) {
-//						System.out.println("P : " + ph.getAccession());
-//						System.out.println("P : " + ph.getDescription());
-//						for (PeptideHit pep : ph.getPeptideHitList()) {
-//							System.out.println("PEP : "+pep.getSequence());
-//							System.out.println("PEP : "+pep.getPeptideSpectrumMatches().size());
-//							System.out.println("TaxNode : "+pep.getTaxonomyNode().getName());
-//							for (PeptideSpectrumMatch psm : pep.getPeptideSpectrumMatches()) {
-//								System.out.println("PSM : " + psm.getSpectrumID());
-//								System.out.println("PSM : " + psm.getTitle());
-//								System.out.println("PSM : " + psm.getSearchHits());
-//							}
-//						}
-//					}
-//				}
-
+		//				for (MetaProteinHit mp : this.getAllMetaProteins()) {
+		//					
+		//					System.out.println("MP : " + mp.getAccession());
+		//					System.out.println("MP : " + mp.getDescription());
+		//					System.out.println("MP : " + mp.getProteinHitList().size());
+		//					for (ProteinHit ph : mp.getProteinHitList()) {
+		//						System.out.println("P : " + ph.getAccession());
+		//						System.out.println("P : " + ph.getDescription());
+		//						for (PeptideHit pep : ph.getPeptideHitList()) {
+		//							System.out.println("PEP : "+pep.getSequence());
+		//							System.out.println("PEP : "+pep.getPeptideSpectrumMatches().size());
+		//							System.out.println("TaxNode : "+pep.getTaxonomyNode().getName());
+		//							for (PeptideSpectrumMatch psm : pep.getPeptideSpectrumMatches()) {
+		//								System.out.println("PSM : " + psm.getSpectrumID());
+		//								System.out.println("PSM : " + psm.getTitle());
+		//								System.out.println("PSM : " + psm.getSearchHits());
+		//							}
+		//						}
+		//					}
+		//				}
 	}
 
 	/**

diff --git a/target/MPA.jar b/target/MPA.jar