Fix Sonar S1130 throws declarations should not be superfluous

biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java

@@ -132,7 +132,7 @@ public void computeMolecularWeight(ElementTable eTable){
 	 * @throws NullPointerException
 	 * 	thrown if AminoAcidCompositionTable.computeMolecularWeight(ElementTable) is not called before this method
 	 */
-	public double getMolecularWeight(Character aaSymbol) throws NullPointerException{
+	public double getMolecularWeight(Character aaSymbol) {
 		if(this.aaSymbol2MolecularWeight == null){
 			throw new NullPointerException("Please call AminoAcidCompositionTable.computeMolecularWeight(ElementTable) before this method");
 		}

biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileParser.java

@@ -283,7 +283,7 @@ public class StockholmFileParser {
 	 * @throws ParserException
 	 *             if unexpected format is encountered
 	 */
-	public StockholmStructure parse(String filename) throws IOException, ParserException {
+	public StockholmStructure parse(String filename) throws IOException {
 		InputStream inStream = new InputStreamProvider().getInputStream(filename);
 		StockholmStructure structure = parse(inStream);
 		inStream.close();
@@ -307,7 +307,7 @@ public StockholmStructure parse(String filename) throws IOException, ParserExcep
 	 * @throws ParserException
 	 *             if unexpected format is encountered
 	 */
-	public List<StockholmStructure> parse(String filename, int max) throws IOException, ParserException {
+	public List<StockholmStructure> parse(String filename, int max) throws IOException {
 		InputStreamProvider isp = new InputStreamProvider();
 		InputStream inStream = isp.getInputStream(filename);
 		return parse(inStream, max);
@@ -325,7 +325,7 @@ public List<StockholmStructure> parse(String filename, int max) throws IOExcepti
 	 * @throws IOException
 	 * @throws ParserException
 	 */
-	public StockholmStructure parse(InputStream inStream) throws ParserException, IOException {
+	public StockholmStructure parse(InputStream inStream) throws IOException {
 		return parse(inStream, 1).get(0);
 	}
 
@@ -391,7 +391,7 @@ public List<StockholmStructure> parseNext(int max) throws IOException {
 	 * @throws IOException
 	 * @throws Exception
 	 */
-	StockholmStructure parse(Scanner scanner) throws ParserException, IOException {
+	StockholmStructure parse(Scanner scanner) throws IOException {
 		if (scanner == null) {
 			if (internalScanner != null) {
 				scanner = internalScanner;
@@ -528,7 +528,7 @@ StockholmStructure parse(Scanner scanner) throws ParserException, IOException {
 	 *            the line to be parsed
 	 * @throws Exception
 	 */
-	private void handleSequenceLine(String line) throws ParserException {
+	private void handleSequenceLine(String line) {
 		String[] lineContent = line.split("\\s+");
 		if (lineContent.length != 2) {
 			throw new ParserException("Could not split sequence line into sequence name and sequence:\n" + line);

biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java

@@ -165,7 +165,7 @@ private void reset() {
 	 * {@inheritDoc}
 	 * The last accession passed to this routine will always be the one used.
 	 */
-	public void setVersion(int version) throws ParserException {
+	public void setVersion(int version) {
 		if (this.versionSeen) throw new ParserException("Current BioEntry already has a version");
 		else {
 			try {
@@ -182,23 +182,23 @@ public void setVersion(int version) throws ParserException {
 	 * {@inheritDoc}
 	 * The last accession passed to this routine will always be the one used.
 	 */
-	public void setAccession(String accession) throws ParserException {
+	public void setAccession(String accession) {
 		if (accession==null) throw new ParserException("Accession cannot be null");
 		this.accession = accession;
 	}
 
 	/**
 	 * {@inheritDoc}
 	 */
-	public void setDescription(String description) throws ParserException {
+	public void setDescription(String description) {
 		if (this.description!=null) throw new ParserException("Current BioEntry already has a description");
 		this.description = description;
 	}
 
 	/**
 	 * {@inheritDoc}
 	 */
-	public void setIdentifier(String identifier) throws ParserException {
+	public void setIdentifier(String identifier) {
 		if (identifier==null) throw new ParserException("Identifier cannot be null");
 		if (this.identifier!=null) throw new ParserException("Current BioEntry already has a identifier");
 		this.identifier = identifier;
@@ -207,7 +207,7 @@ public void setIdentifier(String identifier) throws ParserException {
 	/**
 	 * {@inheritDoc}
 	 */
-	public void setName(String name) throws ParserException {
+	public void setName(String name) {
 		if (name==null) throw new ParserException("Name cannot be null");
 		if (this.name!=null) throw new ParserException("Current BioEntry already has a name");
 		this.name = name;
@@ -216,7 +216,7 @@ public void setName(String name) throws ParserException {
 	/**
 	 * {@inheritDoc}
 	 */
-	public void setComment(String comment) throws ParserException {
+	public void setComment(String comment) {
 		if (comment==null) throw new ParserException("Comment cannot be null");
 		this.comments.add(comment);
 	}

biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java

@@ -242,7 +242,7 @@ public String getName() {
 		 * {@link #getCodons(CompoundSet, CompoundSet)} was not called first.
 		 */
 				@Override
-		public boolean isStart(AminoAcidCompound compound) throws IllegalStateException {
+		public boolean isStart(AminoAcidCompound compound) {
 			if(this.codons.isEmpty()) {
 				throw new IllegalStateException("Codons are empty; please request getCodons() fist before asking this");
 			}

biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java

@@ -87,7 +87,7 @@ public static void copy(InputStream input, OutputStream output)
 	 * @param processor The processor to invoke on all lines
 	 * @throws ParserException Can throw this if we cannot parse the given reader
 	 */
-	public static void processReader(BufferedReader br, ReaderProcessor processor) throws ParserException {
+	public static void processReader(BufferedReader br, ReaderProcessor processor) {
 		String line;
 		try {
 			while( (line = br.readLine()) != null ) {
@@ -109,7 +109,7 @@ public static void processReader(BufferedReader br, ReaderProcessor processor) t
 	 * @return List of Strings
 	 * @throws ParserException Can throw this if we cannot parse the given reader
 	 */
-	public static List<String> getList(BufferedReader br) throws ParserException {
+	public static List<String> getList(BufferedReader br) {
 		final List<String> list = new ArrayList<String>();
 		processReader(br, new ReaderProcessor() {
 			@Override
@@ -130,7 +130,7 @@ public void process(String line) {
 	 * @throws ParserException Can throw this if the file is not a file or we
 	 * cannot parse it
 	 */
-	public static List<String> getList(InputStream is) throws ParserException {
+	public static List<String> getList(InputStream is) {
 		return getList(new BufferedReader(new InputStreamReader(is)));
 	}
 

biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java

@@ -638,7 +638,7 @@ private StringBuilder fetchUniprotXML(String uniprotURL)
 	 * @throws IOException
 	 */
 	private StringBuilder fetchFromCache(String key)
-			throws FileNotFoundException, IOException {
+			throws IOException {
 		int index;
 		File f = new File(uniprotDirectoryCache + File.separatorChar + key + ".xml");
 		StringBuilder sb = new StringBuilder();

biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java

@@ -131,7 +131,7 @@ public void setSequenceLength(long sequenceLength) {
 	 * @return The parsed location
 	 * @throws ParserException thrown in the event of any error during parsing
 	 */
-	public Location parse(String locationString) throws ParserException {
+	public Location parse(String locationString) {
 		featureGlobalStart = Integer.MAX_VALUE;
 		featureGlobalEnd = 1;
 
@@ -151,7 +151,7 @@ public Location parse(String locationString) throws ParserException {
 		return l;
 	}
 
-	private List<Location> parseLocationString(String string, int versus) throws ParserException {
+	private List<Location> parseLocationString(String string, int versus) {
 		Matcher m;
 		List<Location> boundedLocationsCollection = new ArrayList<Location>();
 

biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java

@@ -368,7 +368,7 @@ public C getCompoundAt(int position) {
 		 * @return Byte representation of the compound
 		 * @throws IllegalStateException Done whenever this method is invoked
 		 */
-		protected byte processUnknownCompound(C compound, int position) throws IllegalStateException {
+		protected byte processUnknownCompound(C compound, int position) {
 			throw new IllegalStateException("Do not know how to translate the compound " + compound + " to a " + bitsPerCompound() + "bit representation");
 		}
 

biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java

@@ -263,7 +263,7 @@ public C next() {
 
 
 			@Override
-			public void remove() throws UnsupportedOperationException {
+			public void remove() {
 				throw new UnsupportedOperationException("Cannot remove from this Sequence");
 			}
 		};
@@ -289,7 +289,7 @@ public int countCompounds(C... compounds) {
 
 
 	@Override
-	public AccessionID getAccession() throws UnsupportedOperationException {
+	public AccessionID getAccession() {
 		throw new UnsupportedOperationException();
 	}
 

biojava-ontology/src/main/java/org/biojava/nbio/ontology/IntegerOntology.java

@@ -96,7 +96,7 @@ public void remove() {
 	}
 
 	@Override
-	public Term getTerm(String s) throws NoSuchElementException {
+	public Term getTerm(String s) {
 		int val = Integer.parseInt(s);
 		return resolveInt(val);
 	}
@@ -117,37 +117,37 @@ public Set getRemoteTerms() {
 	}
 
 	@Override
-	public Term createTerm(String name) throws AlreadyExistsException,  IllegalArgumentException {
+	public Term createTerm(String name) throws AlreadyExistsException  {
 		throw new IllegalArgumentException(getName() + " is immutable");
 	}
 
 	@Override
 	public Term createTerm(String name, String description)
 			throws
-			AlreadyExistsException,
+			AlreadyExistsException
 
-			IllegalArgumentException
-			{
+
+		{
 		throw new IllegalArgumentException(getName() + " is immutable");
 			}
 
 	@Override
 	public Term createTerm(String name, String description, Object[] synonyms)
 			throws
-			AlreadyExistsException,
+			AlreadyExistsException
 
-			IllegalArgumentException
-			{
+
+		{
 		throw new IllegalArgumentException(getName() + " is immutable");
 			}
 
 	@Override
 	public Variable createVariable(String name, String description)
 			throws
-			AlreadyExistsException,
+			AlreadyExistsException
 
-			IllegalArgumentException
-			{
+
+		{
 		throw new IllegalArgumentException(getName() + " is immutable");
 			}