Add GFF3Reader overload that accepts Path

jean-philippe-martin · jean-philippe-martin · commit 35594ef4d63c · 2020-09-16T17:35:23.000-07:00
The String-based functions are still here, and almost all the code is shared.
The Path overload allows us to read files via NIO providers, such as e.g.
the GCS NIO provider for reading files on Google Cloud Storage.
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Reader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Reader.java
@@ -20,6 +20,9 @@
  */
 package org.biojava.nbio.genome.parsers.gff;
 
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -67,11 +70,15 @@ public class GFF3Reader {
 	 */
 
 	public static FeatureList read(String filename, List<String> indexes) throws IOException {
-		logger.info("Reading: {}", filename);
+		return read(Paths.get(filename), indexes);
+	}
+
+	public static FeatureList read(Path path, List<String> indexes) throws IOException {
+		logger.info("Reading: {}", path.toString());
 
 		FeatureList features = new FeatureList();
 		features.addIndexes(indexes);
-		BufferedReader br = new BufferedReader(new FileReader(filename));
+		BufferedReader br = Files.newBufferedReader(path);
 
 		String s;
 		for (s = br.readLine(); null != s; s = br.readLine()) {
@@ -103,6 +110,10 @@ public static FeatureList read(String filename) throws IOException {
 	   return read(filename,new ArrayList<String>(0));
 	}
 
+	public static FeatureList read(Path path) throws IOException {
+		return read(path,new ArrayList<String>(0));
+	}
+
 
 	/**
 	 * create Feature from line of GFF file
