Added a new JVM/system property: paxtools.pattern.blacklist

README.md

@@ -43,6 +43,7 @@ Paxtools can be build and run with JDK-17 or newer, e.g. Temurin-21. Add these J
  - `-Dpaxtools.CollectionProvider=org.biopax.paxtools.trove.TProvider` to use a high-performance collections provider for BioPAX elements Map or Set (recommended).
  - `-Dpaxtools.normalizer.use-latest-registry=true` (if using Normalizer/Resolver) to use the latest registry.json from bioregistry.io.
  - `-Dpaxtools.core.use-latest-genenames=true` for the HGNC utility class use id mapping data from genenames.org instead of built-in older file.
+ - `-Dpaxtools.pattern.blacklist=<path>` path to "ubique molecules blacklist" file to use with SIF searcher.
 
 If you have [homebrew](http://brew.sh/) installed on your system (Mac OS X), you can install the latest release of Paxtools via the following brew command (could be old version):
 

pattern/src/main/java/org/biopax/paxtools/pattern/util/Blacklist.java

@@ -380,7 +380,7 @@ private String getSMRID(PhysicalEntity pe)
 	 */
 	public Collection<SmallMolecule> getUbiques(Set<PhysicalEntity> entities, RelType context)
 	{
-		Map<String, SmallMolecule> ubiques = new HashMap<String, SmallMolecule>();
+		Map<String, SmallMolecule> ubiques = new HashMap<>();
 		boolean allUbiques = true;
 
 		for (PhysicalEntity pe : entities)

paxtools-console/src/main/java/org/biopax/paxtools/Commands.java

@@ -347,7 +347,8 @@ static void toSifnx(String[] argv) throws IOException {
 		SIFSearcher searcher = new SIFSearcher(idFetcher, sifTypes.toArray(new SIFEnum[]{}));
 		log.info("toSIF: using SIFTypes: " + sifTypes);
 		//load and set blacklist.txt file if exists
-		File blacklistFile = new File("blacklist.txt");
+		String blacklistPath = System.getProperty("paxtools.pattern.blacklist", "blacklist.txt");
+		File blacklistFile = new File(blacklistPath);
 		if(blacklistFile.exists()) {
 			log.info("toSIF: using blacklist.txt from current directory");
 			searcher.setBlacklist(new Blacklist(new FileInputStream(blacklistFile)));