formatting/ self review

otter606 · otter606 · commit 8aec708321a9 · 2021-11-16T08:16:49.000Z
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java
@@ -514,26 +514,5 @@ public static long uncompress(InputStream in, OutputStream out)
 
 	private static final boolean debugTiming = false;
 
-	/**
-	 * Reads a file, uncompresses it, and sends the result to stdout.
-	 * Also writes trivial statistics to stderr.
-	 * @param args An array with one String element, the name of the file to read.
-	 * @throws IOException for any failure
-	 */
-	public static void main(String[] args) throws Exception {
-		if (args.length != 1) {
-			logger.info("Usage: UncompressInputStream <file>");
-			System.exit(1);
-		}
-		long beg = System.currentTimeMillis();
-
-		long tot;
-		try (InputStream in = new FileInputStream(args[0])) {
-			tot = uncompress(in, System.out);
-		}
-
-		long end = System.currentTimeMillis();
-		logger.info("Decompressed {} bytes", tot);
-		logger.info("Time: {} seconds", (end - beg) / 1000);
-	}
+	
 }
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/ProteinSequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/ProteinSequenceTest.java
@@ -9,16 +9,17 @@
 import org.junit.jupiter.api.Test;
 
 public class ProteinSequenceTest {
-  
+
     @Test
-	 void basicTest() throws Exception {
-		ProteinSequence proteinSequence = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX");
-		assertNotNull( proteinSequence.toString());
+    void basicTest() throws Exception {
+        ProteinSequence proteinSequence = new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX");
+        assertNotNull(proteinSequence.toString());
         assertEquals(24, proteinSequence.getLength());
 
-		StringProxySequenceReader<AminoAcidCompound> sequenceStringProxyLoader = new StringProxySequenceReader<AminoAcidCompound>("XRNDCEQGHILKMFPSTWYVBZJA", AminoAcidCompoundSet.getAminoAcidCompoundSet());
-		ProteinSequence proteinSequenceFromProxy = new ProteinSequence(sequenceStringProxyLoader);
-		assertNotNull( proteinSequenceFromProxy.toString());
+        StringProxySequenceReader<AminoAcidCompound> sequenceStringProxyLoader = new StringProxySequenceReader<AminoAcidCompound>(
+                "XRNDCEQGHILKMFPSTWYVBZJA", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+        ProteinSequence proteinSequenceFromProxy = new ProteinSequence(sequenceStringProxyLoader);
+        assertNotNull(proteinSequenceFromProxy.toString());
         assertEquals(24, proteinSequence.getLength());
-	}  
+    }
 }
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreatorTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreatorTest.java
@@ -71,7 +71,6 @@ void booleanConversion() throws CompoundNotFoundException {
 		for (int i = 0; i < seq.getLength(); i++) {
 			assertEquals(expected[i], userCollection.next());
 		}
-
 	}
 
 }
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/InsdcParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/InsdcParserTest.java
@@ -43,11 +43,6 @@ public class InsdcParserTest {
 
 	private Logger log = LoggerFactory.getLogger(getClass());
 
-	static Collection<String[]> data() {
-		return Arrays.asList(new String[][] {
-
-		});
-	}
 
 	/**
 	 * Test for issue #254

Original file line number	Diff line number	Diff line change
`@@ -71,7 +71,6 @@ void booleanConversion() throws CompoundNotFoundException {`
`71`	`71`	`for (int i = 0; i < seq.getLength(); i++) {`
`72`	`72`	`assertEquals(expected[i], userCollection.next());`
`73`	`73`	`}`
`74`		`-`
`75`	`74`	`}`
`76`	`75`
`77`	`76`	`}`