Merge pull request #890 from jean-philippe-martin/jp_gff3reader_overload

josemduarte · web-flow · commit 129a0a1dd0fe · 2020-09-25T08:21:05.000-07:00
Add GFF3Reader overload that accepts Path
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
@@ -20,11 +20,13 @@
  */
 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;
 
 import java.io.BufferedReader;
-import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
@@ -65,13 +67,23 @@ public class GFF3Reader {
 	 * @return A FeatureList.
 	 * @throws IOException Something went wrong -- check exception detail message.
 	 */
-
 	public static FeatureList read(String filename, List<String> indexes) throws IOException {
-		logger.info("Reading: {}", filename);
+		return read(Paths.get(filename), indexes);
+	}
+
+	/**
+	 * Read a file into a FeatureList. Each line of the file becomes one Feature object.
+	 *
+	 * @param path The path to the GFF file.
+	 * @return A FeatureList.
+	 * @throws IOException Something went wrong -- check exception detail message.
+	 */
+	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 +115,10 @@ 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
