Enable parsing of Comet TSV files

julianu · Dec 15, 2023 · e041584 · e041584
1 parent 523db8e
commit e041584
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Showing 6 changed files with 5,699 additions and 2 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
 	<groupId>de.mpc.pia</groupId>
 	<artifactId>pia</artifactId>
-	<version>1.4.11</version>
+	<version>1.5.0</version>
 	<name>PIA - Protein Inference Algorithms</name>
 	<url>https://github.com/mpc-bioinformatics/pia</url>
 

diff --git a/src/main/java/de/mpc/pia/intermediate/compiler/parser/InputFileParserFactory.java b/src/main/java/de/mpc/pia/intermediate/compiler/parser/InputFileParserFactory.java
@@ -9,6 +9,7 @@
 import org.apache.logging.log4j.Logger;
 
 import de.mpc.pia.intermediate.compiler.PIACompiler;
+import de.mpc.pia.intermediate.compiler.parser.searchengines.CometTSVFileParser;
 import de.mpc.pia.intermediate.compiler.parser.searchengines.MascotDatFileParser;
 import de.mpc.pia.intermediate.compiler.parser.searchengines.TandemFileParser;
 import de.mpc.pia.intermediate.compiler.parser.searchengines.ThermoMSFFileParser;
@@ -20,6 +21,38 @@ public class InputFileParserFactory {
 	private static final Logger LOGGER = LogManager.getLogger();
 
     public enum InputFileTypes {
+
+        /**
+         * the input file is a Comet TSV file
+         */
+        COMET_TSV_INPUT {
+            @Override
+            public String getFileSuffix() {
+                return "txt";
+            }
+
+            @Override
+            public String getFileTypeName() {
+                return "Comet TSV";
+            }
+
+            @Override
+            public String getFileTypeShort() {
+                return "comet";
+            }
+
+            @Override
+            public boolean checkFileType(String fileName) {
+                return CometTSVFileParser.checkFileType(fileName);
+            }
+
+            @Override
+            public boolean parseFile(String name, String fileName,
+                    PIACompiler compiler, String additionalInfoFileName) {
+                return CometTSVFileParser.getDataFromCometTSVFile(name, fileName, compiler);
+            }
+        },
+
         /**
          * the input file is a FASTA database file
          */