Try-with from sonar

josemduarte · josemduarte · commit d0fa3136e8a8 · 2023-06-30T13:53:32.000-07:00
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java
@@ -62,27 +62,27 @@ public static FeatureList read(String filename) throws IOException {
 		logger.info("Reading: {}", filename);
 
 		FeatureList features = new FeatureList();
-		BufferedReader br = new BufferedReader(new FileReader(filename));
+		try (BufferedReader br = new BufferedReader(new FileReader(filename))) {
 
-		String s;
-		for (s = br.readLine(); null != s; s = br.readLine()) {
-			s = s.trim();
+			String s;
+			for (s = br.readLine(); null != s; s = br.readLine()) {
+				s = s.trim();
 
-			if (s.length() > 0) {
-				if (s.charAt(0) == '#') {
-					//ignore comment lines
-				} else {
+				if (s.length() > 0) {
+					if (s.charAt(0) == '#') {
+						//ignore comment lines
+					} else {
 
-					FeatureI f = parseLine(s);
-					if (f != null) {
-						features.add(f);
+						FeatureI f = parseLine(s);
+						if (f != null) {
+							features.add(f);
+						}
 					}
 				}
+
 			}
 
 		}
-
-		br.close();
 		return features;
 	}
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java
@@ -63,27 +63,27 @@ public static FeatureList read(String filename) throws IOException {
 		logger.info("Reading: {}", filename);
 
 		FeatureList features = new FeatureList();
-		BufferedReader br = new BufferedReader(new FileReader(filename));
+		try (BufferedReader br = new BufferedReader(new FileReader(filename))) {
 
-		String s;
-		for (s = br.readLine(); null != s; s = br.readLine()) {
-			s = s.trim();
+			String s;
+			for (s = br.readLine(); null != s; s = br.readLine()) {
+				s = s.trim();
 
-			if (s.length() > 0) {
-				if (s.charAt(0) == '#') {
-					//ignore comment lines
-				} else {
+				if (s.length() > 0) {
+					if (s.charAt(0) == '#') {
+						//ignore comment lines
+					} else {
 
-					FeatureI f = parseLine(s);
-					if (f != null) {
-						features.add(f);
+						FeatureI f = parseLine(s);
+						if (f != null) {
+							features.add(f);
+						}
 					}
 				}
+
 			}
 
 		}
-
-		br.close();
 		return features;
 	}
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.java
@@ -371,32 +371,31 @@ public static void main(String[] args) throws Exception {
 			logger.info("Resulting fasta data will be written in stdout.");
 			return;
 		}
-		TwoBitParser p = new TwoBitParser(new File(args[0]));
-		if(args.length==1) {
-			String[] names = p.getSequenceNames();
-			for(int i=0;i<names.length;i++) {
-				p.setCurrentSequence(names[i]);
-				p.printFastaSequence();
+		try (TwoBitParser p = new TwoBitParser(new File(args[0]))) {
+			if (args.length == 1) {
+				String[] names = p.getSequenceNames();
+				for (int i = 0; i < names.length; i++) {
+					p.setCurrentSequence(names[i]);
+					p.printFastaSequence();
+					p.close();
+				}
+			} else {
+				String name = args[1];
+				p.setCurrentSequence(name);
+				if (args.length > 2) {
+					long start = Long.parseLong(args[2]);
+					p.skip(start);
+				}
+				if (args.length > 3) {
+					long len = Long.parseLong(args[3]);
+					p.printFastaSequence(len);
+				} else {
+					p.printFastaSequence();
+				}
 				p.close();
 			}
+			p.closeParser();
 		}
-		else {
-			String name = args[1];
-			p.setCurrentSequence(name);
-			if(args.length>2) {
-				long start = Long.parseLong(args[2]);
-				p.skip(start);
-			}
-			if(args.length>3) {
-				long len = Long.parseLong(args[3]);
-				p.printFastaSequence(len);
-			}
-			else {
-				p.printFastaSequence();
-			}
-			p.close();
-		}
-		p.closeParser();
 	}
 }
 
